Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/ChangeLog @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 =============================================================================== |
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2 2009-07-29: RELEASE 1.12.2 |
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3 |
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4 ------------------------------------------------------------------------ |
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5 r1952 | jkbonfield | 2010-01-14 17:28:02 +0000 (Thu, 14 Jan 2010) | 2 lines |
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6 Changed paths: |
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7 M /io_lib/trunk/CHANGES |
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8 M /io_lib/trunk/README |
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9 M /io_lib/trunk/configure.in |
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10 |
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11 Updates to produce 1.12.2 |
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12 |
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13 ------------------------------------------------------------------------ |
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14 r1951 | jkbonfield | 2010-01-14 17:21:14 +0000 (Thu, 14 Jan 2010) | 3 lines |
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15 Changed paths: |
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16 M /io_lib/trunk/io_lib/os.h |
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17 |
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18 Guarded HAVE_* definitions behind #ifndef checks to avoid warnings in |
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19 certain cases. |
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20 |
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21 ------------------------------------------------------------------------ |
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22 r1950 | jkbonfield | 2010-01-14 16:44:42 +0000 (Thu, 14 Jan 2010) | 5 lines |
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23 Changed paths: |
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24 M /io_lib/trunk/man/man1/srf2fastq.1 |
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25 M /io_lib/trunk/progs/srf2fastq.c |
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26 |
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27 Added -r option as requested in source forge Patch ID: 2926627, as |
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28 suggested by jmendler. |
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29 |
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30 The exact implementation differs in minor ways. |
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31 ------------------------------------------------------------------------ |
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32 r1939 | jkbonfield | 2010-01-07 09:36:18 +0000 (Thu, 07 Jan 2010) | 3 lines |
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33 Changed paths: |
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34 M /io_lib/trunk/progs/srf2fasta.c |
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35 M /io_lib/trunk/progs/srf2fastq.c |
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36 M /io_lib/trunk/progs/srf_extract_hash.c |
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37 |
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38 Fixed the usage() function to exit 1 instead of 0. |
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39 (Patch from Jordan Mendler) |
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40 |
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41 ------------------------------------------------------------------------ |
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42 r1930 | jkbonfield | 2009-12-03 14:04:01 +0000 (Thu, 03 Dec 2009) | 7 lines |
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43 Changed paths: |
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44 M /io_lib/trunk/io_lib/sff.c |
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45 |
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46 Fixed a bug in read_sff_read_data (with thanks to Tim Massingham). |
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47 After reading the data the function did not pad out to the next 8-byte |
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48 boundary. |
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49 |
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50 This only surfaces when using the library from your own tools as the |
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51 programs supplied with io_lib never read more than a single sff read. |
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52 |
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53 ------------------------------------------------------------------------ |
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54 r1924 | jkbonfield | 2009-11-23 12:20:18 +0000 (Mon, 23 Nov 2009) | 6 lines |
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55 Changed paths: |
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56 M /io_lib/trunk/progs/srf2fastq.c |
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57 |
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58 Applied patch from Jordan Mendler: |
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59 https://sourceforge.net/tracker/index.php?func=detail&aid=2900087&group_id=100316&atid=627060 |
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60 |
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61 This adds a -S (sequential) option to srf2fastq to interleave forward |
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62 and reverse fragments in the same output file as desired by BFast. |
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63 |
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64 ------------------------------------------------------------------------ |
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65 r1851 | daviesrob | 2009-10-02 10:29:05 +0100 (Fri, 02 Oct 2009) | 1 line |
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66 Changed paths: |
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67 M /io_lib/trunk/progs/srf2fastq.c |
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68 |
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69 Fixed buffer overrun in parse_regn |
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70 ------------------------------------------------------------------------ |
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71 r1850 | daviesrob | 2009-10-02 10:02:30 +0100 (Fri, 02 Oct 2009) | 1 line |
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72 Changed paths: |
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73 M /io_lib/trunk/progs/srf_info.c |
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74 |
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75 Fixed buffer overrun in parse_regn |
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76 ------------------------------------------------------------------------ |
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77 r1834 | daviesrob | 2009-09-11 17:48:32 +0100 (Fri, 11 Sep 2009) | 1 line |
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78 Changed paths: |
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79 M /io_lib/trunk/Makefile.am |
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80 M /io_lib/trunk/io_lib/ztr.c |
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81 |
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82 Added pooled_alloc.h to list of include files to install. Fixed |
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83 ztr_add_text so |
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84 that it leaves two NUL bytes on the end of the TEXT chunk, as |
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85 documented in the |
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86 ZTR specification. |
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87 ------------------------------------------------------------------------ |
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88 r1813 | daviesrob | 2009-09-01 12:37:37 +0100 (Tue, 01 Sep 2009) | 1 line |
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89 Changed paths: |
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90 M /io_lib/trunk/io_lib/Makefile.am |
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91 M /io_lib/trunk/io_lib/hash_table.c |
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92 M /io_lib/trunk/io_lib/hash_table.h |
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93 A /io_lib/trunk/io_lib/pooled_alloc.c |
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94 A /io_lib/trunk/io_lib/pooled_alloc.h |
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95 M /io_lib/trunk/io_lib/srf.c |
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96 M /io_lib/trunk/io_lib/srf.h |
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97 |
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98 Added HASH_POOL_ITEMS option to hash table code to allocate HashItems |
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99 in pools, |
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100 which reduces malloc overhead in big hash tables. Also made |
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101 srf_index_add_trace |
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102 _body use pooled storage for trace names. |
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103 |
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104 |
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105 =============================================================================== |
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106 2009-07-29: RELEASE 1.12.1 |
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107 |
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108 ------------------------------------------------------------------------ |
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109 r1806 | jkbonfield | 2009-08-07 16:46:20 +0100 (Fri, 07 Aug 2009) | 1 line |
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110 Changed paths: |
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111 M /io_lib/trunk/README |
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112 M /io_lib/trunk/configure.in |
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113 |
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114 Updated version to 1.12.1 |
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115 ------------------------------------------------------------------------ |
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116 r1805 | jkbonfield | 2009-08-07 16:18:28 +0100 (Fri, 07 Aug 2009) | 1 line |
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117 Changed paths: |
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118 M /io_lib/trunk/Makefile.am |
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119 M /io_lib/trunk/README |
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120 |
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121 Minor edit |
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122 ------------------------------------------------------------------------ |
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123 r1792 | jkbonfield | 2009-08-03 11:58:49 +0100 (Mon, 03 Aug 2009) | 4 lines |
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124 Changed paths: |
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125 M /io_lib/trunk/io_lib/os.h |
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126 |
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127 Moved the autoconf detection of endianness to the start of os.h. This |
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128 means that machine/compiler testing #ifdefs take precedence, allowing |
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129 for cross-compilation and "fat" binaries on MacOS X. |
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130 |
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131 ------------------------------------------------------------------------ |
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132 r1791 | jkbonfield | 2009-08-03 11:56:50 +0100 (Mon, 03 Aug 2009) | 2 lines |
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133 Changed paths: |
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134 M /io_lib/trunk/tests/Makefile.am |
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135 M /io_lib/trunk/tests/srf_index.test |
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136 |
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137 Minor tweaks to checks/dist. |
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138 |
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139 ------------------------------------------------------------------------ |
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140 r1789 | jkbonfield | 2009-07-31 12:17:27 +0100 (Fri, 31 Jul 2009) | 2 lines |
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141 Changed paths: |
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142 M /io_lib/trunk/io_lib-config.in |
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143 |
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144 Fixed -lread to be -lstaden-read |
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145 |
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146 ------------------------------------------------------------------------ |
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147 r1780 | jkbonfield | 2009-07-29 10:07:56 +0100 (Wed, 29 Jul 2009) | 2 lines |
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148 Changed paths: |
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149 M /io_lib/trunk/CHANGES |
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150 M /io_lib/trunk/ChangeLog |
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151 M /io_lib/trunk/README |
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152 |
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153 Minor updates to state version 1.12.0 |
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154 |
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155 |
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156 =============================================================================== |
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157 2009-07-29: RELEASE 1.12.0 |
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158 |
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159 ------------------------------------------------------------------------ |
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160 r1779 | jkbonfield | 2009-07-29 09:53:33 +0100 (Wed, 29 Jul 2009) | 2 lines |
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161 Changed paths: |
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162 M /io_lib/trunk/Makefile.am |
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163 |
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164 The man1 pages are now installed too. |
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165 |
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166 ------------------------------------------------------------------------ |
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167 r1778 | jkbonfield | 2009-07-28 17:42:26 +0100 (Tue, 28 Jul 2009) | 2 lines |
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168 Changed paths: |
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169 M /io_lib/trunk/tests/Makefile.am |
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170 D /io_lib/trunk/tests/data/.params |
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171 A /io_lib/trunk/tests/data/both.info (from /io_lib/trunk/tests/data/slx_out/both.info:1776) |
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172 A /io_lib/trunk/tests/data/both.run (from /io_lib/trunk/tests/data/slx_out/both.run:1776) |
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173 A /io_lib/trunk/tests/data/both.srf (from /io_lib/trunk/tests/data/slx_out/both.srf:1776) |
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174 A /io_lib/trunk/tests/data/proc.info (from /io_lib/trunk/tests/data/slx_out/proc.info:1776) |
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175 A /io_lib/trunk/tests/data/proc.srf (from /io_lib/trunk/tests/data/slx_out/proc.srf:1776) |
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176 A /io_lib/trunk/tests/data/proc.srf.indexed (from /io_lib/trunk/tests/data/slx_out/proc.srf.indexed:1776) |
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177 A /io_lib/trunk/tests/data/raw.info (from /io_lib/trunk/tests/data/slx_out/raw.info:1776) |
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178 A /io_lib/trunk/tests/data/raw.srf (from /io_lib/trunk/tests/data/slx_out/raw.srf:1776) |
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179 A /io_lib/trunk/tests/data/slx-C.fasta (from /io_lib/trunk/tests/data/slx_out/slx-C.fasta:1776) |
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180 A /io_lib/trunk/tests/data/slx-C.fastq (from /io_lib/trunk/tests/data/slx_out/slx-C.fastq:1776) |
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181 A /io_lib/trunk/tests/data/slx.fasta (from /io_lib/trunk/tests/data/slx_out/slx.fasta:1776) |
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182 A /io_lib/trunk/tests/data/slx.fastq (from /io_lib/trunk/tests/data/slx_out/slx.fastq:1776) |
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183 D /io_lib/trunk/tests/data/slx_in |
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184 D /io_lib/trunk/tests/data/slx_out |
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185 A /io_lib/trunk/tests/data/test_run_4_134_369_182.srf (from /io_lib/trunk/tests/data/slx_out/test_run_4_134_369_182.srf:1776) |
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186 A /io_lib/trunk/tests/data/traces.srf (from /io_lib/trunk/tests/data/slx_out/traces.srf:1776) |
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187 D /io_lib/trunk/tests/illumina2srf.test |
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188 M /io_lib/trunk/tests/srf2fasta.test |
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189 M /io_lib/trunk/tests/srf2fastq.test |
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190 D /io_lib/trunk/tests/srf2illumina.test |
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191 M /io_lib/trunk/tests/srf_filter.test |
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192 M /io_lib/trunk/tests/srf_index.test |
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193 M /io_lib/trunk/tests/srf_info.test |
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194 |
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195 Updated tests now that srf2illumina and illumina2srf have been removed. |
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196 |
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197 ------------------------------------------------------------------------ |
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198 r1777 | jkbonfield | 2009-07-28 16:44:43 +0100 (Tue, 28 Jul 2009) | 3 lines |
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199 Changed paths: |
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200 D /io_lib/trunk/Makefile |
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201 M /io_lib/trunk/bootstrap |
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202 D /io_lib/trunk/io_lib/Makefile |
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203 D /io_lib/trunk/progs/Makefile |
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204 |
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205 Removed remnant Makefiles from the old staden package build |
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206 system. All we have left now is the autoconf build files. |
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207 |
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208 ------------------------------------------------------------------------ |
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209 r1775 | jkbonfield | 2009-07-28 16:37:18 +0100 (Tue, 28 Jul 2009) | 8 lines |
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210 Changed paths: |
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211 A /io_lib/branches |
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212 A /io_lib/tags |
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213 A /io_lib/trunk |
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214 A /io_lib/trunk/CHANGES (from /staden/trunk/src/io_lib/CHANGES:1774) |
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215 A /io_lib/trunk/COPYRIGHT (from /staden/trunk/src/io_lib/COPYRIGHT:1774) |
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216 A /io_lib/trunk/ChangeLog (from /staden/trunk/src/io_lib/ChangeLog:1774) |
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217 A /io_lib/trunk/Makefile (from /staden/trunk/src/io_lib/Makefile:1774) |
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218 A /io_lib/trunk/Makefile.am (from /staden/trunk/src/io_lib/Makefile.am:1774) |
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219 A /io_lib/trunk/README (from /staden/trunk/src/io_lib/README:1774) |
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220 A /io_lib/trunk/acinclude.m4 (from /staden/trunk/src/io_lib/acinclude.m4:1774) |
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221 A /io_lib/trunk/bootstrap (from /staden/trunk/src/io_lib/bootstrap:1774) |
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222 A /io_lib/trunk/configure.in (from /staden/trunk/src/io_lib/configure.in:1774) |
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223 A /io_lib/trunk/dependencies (from /staden/trunk/src/io_lib/dependencies:1774) |
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224 A /io_lib/trunk/docs (from /staden/trunk/src/io_lib/docs:1774) |
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225 A /io_lib/trunk/include (from /staden/trunk/src/io_lib/include:1774) |
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226 A /io_lib/trunk/io_lib (from /staden/trunk/src/io_lib/io_lib:1774) |
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227 A /io_lib/trunk/io_lib-config.in (from /staden/trunk/src/io_lib/io_lib-config.in:1774) |
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228 A /io_lib/trunk/io_lib.m4 (from /staden/trunk/src/io_lib/io_lib.m4:1774) |
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229 A /io_lib/trunk/man (from /staden/trunk/src/io_lib/man:1774) |
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230 A /io_lib/trunk/options.mk (from /staden/trunk/src/io_lib/options.mk:1774) |
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231 A /io_lib/trunk/progs (from /staden/trunk/src/io_lib/progs:1774) |
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232 A /io_lib/trunk/tests (from /staden/trunk/src/io_lib/tests:1774) |
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233 D /staden/trunk/src/io_lib/CHANGES |
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234 D /staden/trunk/src/io_lib/COPYRIGHT |
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235 D /staden/trunk/src/io_lib/ChangeLog |
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236 D /staden/trunk/src/io_lib/Makefile |
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237 D /staden/trunk/src/io_lib/Makefile.am |
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238 D /staden/trunk/src/io_lib/README |
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239 D /staden/trunk/src/io_lib/acinclude.m4 |
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240 D /staden/trunk/src/io_lib/bootstrap |
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241 D /staden/trunk/src/io_lib/configure.in |
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242 D /staden/trunk/src/io_lib/dependencies |
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243 D /staden/trunk/src/io_lib/docs |
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244 D /staden/trunk/src/io_lib/include |
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245 D /staden/trunk/src/io_lib/io_lib |
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246 D /staden/trunk/src/io_lib/io_lib-config.in |
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247 D /staden/trunk/src/io_lib/io_lib.m4 |
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248 D /staden/trunk/src/io_lib/man |
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249 D /staden/trunk/src/io_lib/options.mk |
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250 D /staden/trunk/src/io_lib/progs |
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251 D /staden/trunk/src/io_lib/tests |
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252 |
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253 Moved io_lib from staden source tree into it's own top-level |
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254 subversion directory, complete with tags, branches, and trunk. |
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255 |
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256 For now the old tagged copies of io_lib are still in the staden/tags/ |
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257 directory with tag names io_lib-<version>, but that is perhaps right |
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258 and proper (as it's where the code actually resided at that release |
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259 number). |
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260 |
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261 ------------------------------------------------------------------------ |
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262 r1772 | jkbonfield | 2009-07-28 15:32:58 +0100 (Tue, 28 Jul 2009) | 4 lines |
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263 Changed paths: |
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264 M /staden/trunk/src/io_lib/progs/Makefile.am |
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265 D /staden/trunk/src/io_lib/progs/solexa2srf.c |
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266 D /staden/trunk/src/io_lib/progs/srf2solexa.c |
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267 |
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268 Removed Illumina/Solexa specific programs. These are now out of date |
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269 with respect to Illumina's own fork, plus I don't think they belong in |
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270 the largely platform agnostic library. |
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271 |
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272 ------------------------------------------------------------------------ |
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273 r1771 | jkbonfield | 2009-07-28 12:44:07 +0100 (Tue, 28 Jul 2009) | 7 |
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274 lines |
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275 Changed paths: |
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276 M /staden/trunk/src/io_lib/CHANGES |
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277 M /staden/trunk/src/io_lib/ChangeLog |
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278 M /staden/trunk/src/io_lib/README |
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279 M /staden/trunk/src/io_lib/configure.in |
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280 M /staden/trunk/src/io_lib/io_lib/Makefile.am |
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281 |
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282 Preparations for 1.12.0 release. |
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283 |
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284 There is now proper versioning support for the library too. The soname |
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285 used here is libstaden-read.so.1, to distinguish from any earlier |
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286 dynamic libraries. (The ABI definitely has changed over the years in |
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287 incompatible manners.) |
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288 |
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289 ------------------------------------------------------------------------ |
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290 r1770 | jkbonfield | 2009-07-28 09:17:29 +0100 (Tue, 28 Jul 2009) | 1 line |
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291 Changed paths: |
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292 M /staden/trunk/src/io_lib/tests/data/slx_out/both.info |
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293 M /staden/trunk/src/io_lib/tests/data/slx_out/raw.info |
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294 |
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295 Updated for new format srf_info output |
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296 ------------------------------------------------------------------------ |
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297 r1769 | jkbonfield | 2009-07-28 09:16:11 +0100 (Tue, 28 Jul 2009) | 2 lines |
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298 Changed paths: |
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299 M /staden/trunk/src/io_lib/tests/data/slx_out/proc.info |
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300 |
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301 Updated with new format output. |
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302 |
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303 ------------------------------------------------------------------------ |
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304 r1768 | jkbonfield | 2009-07-27 17:49:44 +0100 (Mon, 27 Jul 2009) | 2 lines |
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305 Changed paths: |
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306 M /staden/trunk/src/io_lib/io_lib/vlen.c |
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307 |
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308 Include os.h so we can pick up NEED_VA_COPY definition. |
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309 |
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310 ------------------------------------------------------------------------ |
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311 r1767 | jkbonfield | 2009-07-27 17:48:37 +0100 (Mon, 27 Jul 2009) | 5 lines |
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312 Changed paths: |
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313 M /staden/trunk/src/io_lib/progs/srf_filter.c |
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314 |
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315 Reorganisation to allow chunks to be added as well as removed. At |
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316 present this only supports adding REGN chunks. |
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317 |
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318 (Patch supplied by Steven Leonard.) |
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319 |
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320 ------------------------------------------------------------------------ |
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321 r1766 | jkbonfield | 2009-07-27 17:46:07 +0100 (Mon, 27 Jul 2009) | 3 lines |
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322 Changed paths: |
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323 M /staden/trunk/src/io_lib/progs/index_tar.c |
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324 |
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325 Handle GNU tar extensions: LongLink notation. |
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326 (Patch supplied by Steven Leonard). |
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327 |
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328 ------------------------------------------------------------------------ |
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329 r1765 | jkbonfield | 2009-07-27 17:45:16 +0100 (Mon, 27 Jul 2009) | 4 lines |
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330 Changed paths: |
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331 M /staden/trunk/src/io_lib/progs/srf2fasta.c |
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332 M /staden/trunk/src/io_lib/progs/srf2fastq.c |
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333 M /staden/trunk/src/io_lib/progs/srf_extract_hash.c |
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334 |
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335 Changed the maximum read length from 1024 to 10000. This allows for |
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336 capillary traces to be stored in SRF. |
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337 (Patch supplied by Steven Leonard) |
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338 |
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339 ------------------------------------------------------------------------ |
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340 r1764 | jkbonfield | 2009-07-27 17:43:36 +0100 (Mon, 27 Jul 2009) | 3 lines |
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341 Changed paths: |
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342 M /staden/trunk/src/io_lib/progs/srf_info.c |
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343 |
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344 Use int64_t instead of long for base counts and chunk sizes. |
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345 (Supplied by Steven Leonard.) |
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346 |
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347 ------------------------------------------------------------------------ |
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348 r1763 | jkbonfield | 2009-07-27 16:49:10 +0100 (Mon, 27 Jul 2009) | 3 lines |
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349 Changed paths: |
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350 M /staden/trunk/src/io_lib/man/man1/srf_info.1 |
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351 M /staden/trunk/src/io_lib/progs/srf_info.c |
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352 |
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353 Added compressed chunk size to the per-chunk type output. This allows |
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354 us to see what takes up the most storage in an SRF. |
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355 |
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356 ------------------------------------------------------------------------ |
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357 r1762 | jkbonfield | 2009-07-27 16:47:20 +0100 (Mon, 27 Jul 2009) | 1 line |
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358 Changed paths: |
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359 M /staden/trunk/src/io_lib/io_lib/ztr.c |
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360 |
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361 removed C9Xism |
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362 |
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363 ------------------------------------------------------------------------ |
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364 r1761 | jkbonfield | 2009-07-27 15:01:16 +0100 (Mon, 27 Jul 2009) | 5 lines |
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365 Changed paths: |
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366 M /staden/trunk/src/io_lib/configure.in |
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367 M /staden/trunk/src/io_lib/io_lib/Makefile.am |
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368 M /staden/trunk/src/io_lib/progs/Makefile.am |
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369 |
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370 Re-enabled libtool, with a workaround to remove the infuriating rpath |
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371 nonsense. (It's now 2x slower to configure, 3x slower to compile and |
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372 10x more anguish to debug, but at least I can sleep at night knowing |
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373 rpath hasn't had it's wicked way with the code.) |
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374 |
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375 ------------------------------------------------------------------------ |
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376 r1756 | jkbonfield | 2009-07-24 10:27:29 +0100 (Fri, 24 Jul 2009) | 5 lines |
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377 Changed paths: |
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378 M /staden/trunk/src/Makefile.in |
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379 A /staden/trunk/src/io_lib/io_lib/Makefile |
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380 |
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381 Added a Makefile for io_lib/io_lib; so the library itself. This isn't |
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382 expected to be used normally, but it allows me to test local copies of |
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383 io_lib (under a different library name) in conjunction with the staden |
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384 source tree before releasing either. |
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385 |
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386 ------------------------------------------------------------------------ |
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387 r1723 | jkbonfield | 2009-06-22 12:38:26 +0100 (Mon, 22 Jun 2009) | 2 lines |
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388 Changed paths: |
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389 M /staden/trunk/src/io_lib/io_lib/ztr_translate.c |
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390 |
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391 Gracefully handle the case of a trace with no BPOS chunk in ztr2read(). |
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392 |
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393 ------------------------------------------------------------------------ |
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394 r1722 | jkbonfield | 2009-06-22 12:37:32 +0100 (Mon, 22 Jun 2009) | 2 lines |
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395 Changed paths: |
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396 M /staden/trunk/src/io_lib/io_lib/hash_table.c |
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397 M /staden/trunk/src/io_lib/io_lib/hash_table.h |
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398 |
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399 Added the hash table iterator functions (copied from Gap5's hache tables). |
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400 |
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401 ------------------------------------------------------------------------ |
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402 r1721 | jkbonfield | 2009-06-22 12:36:52 +0100 (Mon, 22 Jun 2009) | 2 lines |
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403 Changed paths: |
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404 M /staden/trunk/src/io_lib/io_lib/deflate_interlaced.c |
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405 |
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406 Fixed a memory allocation issue of codes2codeset(). |
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407 |
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408 ------------------------------------------------------------------------ |
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409 r1720 | jkbonfield | 2009-06-22 12:35:21 +0100 (Mon, 22 Jun 2009) | 4 lines |
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410 Changed paths: |
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411 M /staden/trunk/src/io_lib/Makefile |
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412 |
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413 Remove use of curl-config --libs. While useful for linking against |
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414 static libraries, it just adds unwanted dependencies in a dynamic |
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415 build environment. |
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416 |
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417 ------------------------------------------------------------------------ |
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418 r1596 | jkbonfield | 2009-04-20 12:34:23 +0100 (Mon, 20 Apr 2009) | 6 lines |
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419 Changed paths: |
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420 M /staden/trunk/src/io_lib/io_lib/compress.c |
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421 M /staden/trunk/src/io_lib/io_lib/compress.h |
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422 |
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423 Made pipe2() internal as it's not used anywhere else yet. |
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424 |
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425 Also renamed from pipe2 to pipe_into. This resolves SF bug #2629155; |
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426 pipe2 has been added as a system function to glibc 2.9 as an interface |
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427 to the new (2.6.27+) kernel system call of the same name. |
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428 |
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429 ------------------------------------------------------------------------ |
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430 r1526 | jkbonfield | 2009-03-04 14:38:16 +0000 (Wed, 04 Mar 2009) | 5 lines |
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431 Changed paths: |
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432 M /staden/trunk/src/io_lib/progs/srf_info.c |
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433 |
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434 Fixed the same bug with mf_end and ztr_partial_decode from srf.c. |
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435 |
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436 Specifically a ZTR file with no chunks in the srf data block header |
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437 failed. |
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438 |
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439 ------------------------------------------------------------------------ |
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440 r1525 | jkbonfield | 2009-03-04 14:23:58 +0000 (Wed, 04 Mar 2009) | 4 lines |
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441 Changed paths: |
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442 M /staden/trunk/src/io_lib/io_lib/srf.c |
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443 |
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444 Bug fix to srf_next_ztr_flags. When faced with a ZTR header with no |
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445 ZTR chunks in the srf data block header it erroneously set mf_end to |
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446 zero instead of the actual length. |
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447 |
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448 ------------------------------------------------------------------------ |
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449 r1455 | jkbonfield | 2009-01-22 17:19:25 +0000 (Thu, 22 Jan 2009) | 3 lines |
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450 Changed paths: |
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451 M /staden/trunk/src/io_lib/io_lib/array.c |
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452 M /staden/trunk/src/io_lib/io_lib/array.h |
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453 |
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454 Updated the Array struct to use size_t, matching the copy in Misc (yes |
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455 I know, multiple variants is asking for trouble). |
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456 |
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457 ------------------------------------------------------------------------ |
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458 r1428 | jkbonfield | 2008-12-11 10:22:25 +0000 (Thu, 11 Dec 2008) | 3 lines |
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459 Changed paths: |
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460 M /staden/trunk/src/io_lib/progs/srf2solexa.c |
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461 |
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462 Changed dump_qcal so it handles negative log-odds scores. In practice |
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463 I've never seen these occur with the 1.0 solexa pipeline release though. |
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464 |
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465 |
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466 =============================================================================== |
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467 2008-12-10 James Bonfield <jkb@sanger.ac.uk> |
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468 |
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469 * 1.11.6.1 released. |
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470 |
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471 * progs/solexa2srf.c: |
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472 Removal of debugging output. |
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473 |
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474 2008-12-10 James Bonfield <jkb@sanger.ac.uk> |
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475 |
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476 * 1.11.6 released. |
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477 |
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478 2008-12-10 jkbonfield <jkb@sanger.ac.uk> |
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479 |
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480 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
481 Fixed the add_qcal_chunk code so it doesn't assume that it can strlen |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
482 the binary quality string. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
483 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
484 * man/man1/srf2fastq.1, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
485 * man/man1/srf_info.1: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
486 (10:17:27) Updated to reflect newly added options. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
487 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
488 * progs/srf2fastq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
489 (10:19:25) Merged in changes from Steven Leonard. - Extra options |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
490 were added to provide explicit control over the read names |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
491 (whether to add /1, /2, ...) and filenames. - Renamed -p (primer) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
492 as -e (explicit). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
493 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
494 * progs/srf_info.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
495 (10:20:18) Merged in changes from Steven Leonard - Call srf_destroy |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
496 before exiting in various failure cases. This has no real impact |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
497 except to make it easier to look for real memory leaks. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
498 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
499 2008-12-09 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
500 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
501 * progs/srf2fastq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
502 (10:20:00) Fixed an error with split file mode - it read past the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
503 end of an array. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
504 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
505 We now check the SCALE option on CNF4 and CNF1 chunks and convert |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
506 the data accordingly to phred. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
507 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
508 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
509 (10:23:31) Merged in some of the changes made by Chris Saunders |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
510 from Illumina. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
511 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
512 Most significantly this now stores CNF1 data in log-odds format and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
513 sets SCALE meta-data accordingly. This makes srf2illumina work |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
514 better as it doesn't go from log-odds to phred back to log-odds, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
515 destroying data in rounding. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
516 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
517 * tests/data/slx_out/both.info, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
518 * tests/data/slx_out/both.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
519 * tests/data/slx_out/proc.info, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
520 * tests/data/slx_out/proc.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
521 * tests/data/slx_out/proc.srf.indexed, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
522 * tests/data/slx_out/raw.info, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
523 * tests/data/slx_out/raw.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
524 * tests/data/slx_out/test_run_4_134_369_182.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
525 * tests/data/slx_out/both.run/4_PROGRAM_ID.txt: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
526 (12:26:13) Updated to accommodate illumina2srf version string |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
527 change. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
528 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
529 * progs/srf_filter.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
530 (12:28:30) Bad case of missing braces! |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
531 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
532 2008-12-08 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
533 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
534 * io_lib/compression.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
535 (12:32:38) Better error handling in tshift method |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
536 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
537 * io_lib/compress.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
538 * io_lib/compress.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
539 (12:33:40) Added remove_extension() function. (Not yet used by |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
540 io_lib, but potentially handy and used by some external tools.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
541 (Steven Leonard) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
542 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
543 * progs/srf2solexa.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
544 (12:34:38) Bug fixed the qcal conversion - now use the correct |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
545 lookup table and added .499 to match the rounding used in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
546 solexa2srf.c. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
547 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
548 * progs/srf2fastq.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
549 * progs/srf_filter.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
550 * progs/srf_info.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
551 (12:35:40) Merged in Steven Leonard's changes. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
552 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
553 These mainly involve better support for multiple index blocks in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
554 SRF files (eg concatenated files), support for splitting output |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
555 files in srf2fastq, and extra reporting options in srf_info. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
556 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
557 * io_lib/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
558 * io_lib/ztr.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
559 (17:15:58) Added const to string params in ztr_add_text. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
560 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
561 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
562 * io_lib/srf.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
563 (17:23:53) New function srf_next_ztr_flags. This is the same as the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
564 old srf_next_ztr function except with the addition of an extra |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
565 argument into which the SRF Data Block 'flags' value is copied when |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
566 returning the next trace. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
567 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
568 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
569 2008-12-04 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
570 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
571 * 1.11.5 released. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
572 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
573 2008-12-03 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
574 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
575 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
576 (17:29:10) Fixed qcal format so it now correctly drops quality by |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
577 the 64 offset added in the fastq-a-like strings. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
578 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
579 Fixed a bug with the 2-file calibration mode (-qf and -qr). A |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
580 single combined -qf alone works fine, but when pasting the split |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
581 file mode (fwd + rev) a newline crept halfway into the quality |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
582 string causing the reverse qualities to be shifted by one. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
583 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
584 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
585 (17:29:56) Bumped version to 1.11 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
586 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
587 2008-12-02 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
588 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
589 * progs/srf_filter.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
590 (14:38:58) Removed some major memory leaks. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
591 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
592 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
593 * progs/srf_filter.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
594 (15:01:04) More memory leak fixed (although tiny). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
595 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
596 2008-10-23 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
597 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
598 * progs/hash_sff.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
599 (14:08:19) Added support for outputting only the table of contents |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
600 to a new file without copying the existing sff files. This is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
601 useful if we have the original sff files in an archive that we |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
602 cannot modify. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
603 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
604 2008-10-07 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
605 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
606 * progs/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
607 (16:02:51) Added extract_fastq to the list of programs to build. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
608 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
609 2008-09-29 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
610 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
611 * man/man1/illumina2srf.1, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
612 * man/man1/srf2fasta.1, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
613 * man/man1/srf2fastq.1, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
614 * man/man1/srf_info.1, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
615 * man/man1/srf_list.1: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
616 (13:40:01) Added the first draft of several manual pages. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
617 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
618 * man/man1/illumina2srf.1: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
619 (13:44:09) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
620 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
621 * progs/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
622 * progs/srf_list.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
623 (14:00:22) Added new program: srf_list. This lists or counts the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
624 sequence names within an SRF file. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
625 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
626 * io_lib/srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
627 (14:01:38) The srf_next_block_details now uses the trace_body |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
628 struct held within the srf struct. This means it can be queried |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
629 after a successful call and is utilised by srf_list to obtain the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
630 trace body size. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
631 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
632 * man/man1/srf_index_hash.1: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
633 (14:08:36) First draft of man page. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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changeset
|
634 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
635 2008-09-18 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
636 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
637 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
638 (12:59:37) Fixed a bug with parsing the directory name. If it fails |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
639 it left the run number in an inconsistent state. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
640 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
641 This shouldn't cause issues in production pipelines, but does if |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
642 you copy the files out of the run folders. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
643 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
644 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
645 * io_lib/srf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
646 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
647 (16:33:45) Overhauled the SRF indexing code. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
648 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
649 Much of the indexing code in srf_index_hash.c has been moved over |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
650 to srf.c so it can be used by other programs. An API has been |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
651 created too so it is now far easier to create, add to and save an |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
652 index. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
653 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
654 Added support for writing indexes in illumina2srf. Note that now if |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
655 no index is written we also write out 8 bytes of zero, indicating |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
656 the length of the index is zero. (This is required by more recent |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
657 versions of the SRF specification.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
658 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
659 Still to do: tools such as srf_filter should be updating the index |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
660 (or at least removing the old ones). This will now be easier to do |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
661 with these code updates. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
662 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
663 Updated the tests to check the new illumina2srf -i option too. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
664 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
665 * progs/srf_index_hash.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
666 * tests/illumina2srf.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
667 * tests/srf_index.test, |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
668 * tests/data/slx_out/both.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
669 * tests/data/slx_out/proc.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
670 * tests/data/slx_out/raw.srf: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
671 (16:33:46) Overhauled the SRF indexing code. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
672 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
673 Much of the indexing code in srf_index_hash.c has been moved over |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
674 to srf.c so it can be used by other programs. An API has been |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
675 created too so it is now far easier to create, add to and save an |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
676 index. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
677 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
678 Added support for writing indexes in illumina2srf. Note that now if |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
679 no index is written we also write out 8 bytes of zero, indicating |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
680 the length of the index is zero. (This is required by more recent |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
681 versions of the SRF specification.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
682 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
683 Still to do: tools such as srf_filter should be updating the index |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
684 (or at least removing the old ones). This will now be easier to do |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
685 with these code updates. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
686 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
687 Updated the tests to check the new illumina2srf -i option too. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
688 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
689 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
690 2008-09-11 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
691 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
692 * 1.11.4 released. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
693 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
694 2008-09-11 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
695 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
696 * Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
697 * bootstrap, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
698 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
699 (08:43:42) Updated for version number and inclusion of tests dir. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
700 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
701 * io_lib/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
702 (08:43:55) Removed due to being auto-generated from Makefile.am |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
703 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
704 * io_lib/os.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
705 (08:44:56) Tidy up of endianness detection. I split apart the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
706 endian step from the os-components (no strdup, etc). Also changed |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
707 the order so that when using autoconf the automatically detected |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
708 settings override any existing assumptions from os.h. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
709 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
710 * io_lib/hash_table.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
711 (08:46:10) Included sys/types.h for off_t type. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
712 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
713 * CHANGES, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
714 * ChangeLog, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
715 * README: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
716 (10:25:27) Final tweaks for preparing 1.11.4 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
717 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
718 * io_lib/srf.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
719 (10:52:37) Changed block_type from char to int. This cures a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
720 problem on PowerMac (PPC) running Debian where char is by default |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
721 an unsigned type, meaning it cannot be compared to EOF (-1). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
722 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
723 * tests/srf_index.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
724 * tests/data/slx_out/Attic/test_run:4:134:369:182.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
725 * tests/data/slx_out/test_run_4_134_369_182.srf: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
726 (11:09:11) Renamed test_run:4:134:369:182.srf to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
727 test_run_4_134_369_182.srf as Windows cannot cope with colons in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
728 filenames, causing the tar file to fail to unpack. Grrr. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
729 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
730 * Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
731 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
732 * progs/solexa2srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
733 * progs/srf2fasta.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
734 * progs/srf2fastq.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
735 * progs/srf2solexa.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
736 * progs/srf_dump_all.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
737 * progs/srf_extract_linear.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
738 * tests/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
739 * tests/srf_index.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
740 * tests/srf_info.test: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
741 (15:25:29) A variety of changes to make the code work correctly |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
742 using msys/mingw on Windows. These mainly revolve around binary |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
743 mode and nl/cr issues. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
744 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
745 2008-09-10 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
746 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
747 * tests/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
748 * tests/illumina2srf.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
749 * tests/srf2fasta.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
750 * tests/srf2fastq.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
751 * tests/srf2illumina.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
752 * tests/srf_filter.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
753 * tests/srf_index.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
754 * tests/srf_info.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
755 * tests/data/.params, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
756 * tests/data/slx_in/.params, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
757 * tests/data/slx_in/s_4_0133_int.txt.gz, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
758 * tests/data/slx_in/s_4_0133_nse.txt.gz, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
759 * tests/data/slx_in/s_4_0134_int.txt.gz, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
760 * tests/data/slx_in/s_4_0134_nse.txt.gz, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
761 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_prb.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
762 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_qhg.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
763 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_seq.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
764 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0133_sig2.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
765 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_prb.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
766 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_qhg.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
767 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_seq.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
768 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/s_4_0134_sig2.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
769 * tests/data/slx_in/Bustard1.9.5_28-08-2008_auto/Phasing/s_4_01_phasing.xml, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
770 * tests/data/slx_in/Matrix/s_4_02_matrix.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
771 * tests/data/slx_out/both.info, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
772 * tests/data/slx_out/both.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
773 * tests/data/slx_out/proc.info, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
774 * tests/data/slx_out/proc.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
775 * tests/data/slx_out/proc.srf.indexed, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
776 * tests/data/slx_out/raw.info, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
777 * tests/data/slx_out/raw.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
778 * tests/data/slx_out/slx-C.fasta, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
779 * tests/data/slx_out/slx-C.fastq, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
780 * tests/data/slx_out/slx.fasta, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
781 * tests/data/slx_out/slx.fastq, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
782 * tests/data/slx_out/test_run:4:134:369:182.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
783 * tests/data/slx_out/traces.srf, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
784 * tests/data/slx_out/both.run/4_ILLUMINA_GA_BUSTARD_PARAMS.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
785 * tests/data/slx_out/both.run/4_ILLUMINA_GA_CHASTITY.txt: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
786 (15:53:41) First pass at a "make check" target. Currently this is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
787 centred around the newer code, specifically SRF support. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
788 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
789 * tests/data/slx_out/both.run/4_ILLUMINA_GA_FIRECREST_PARAMS.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
790 * tests/data/slx_out/both.run/4_ILLUMINA_GA_MATRIX_FWD.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
791 * tests/data/slx_out/both.run/4_ILLUMINA_GA_PHASING_FWD.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
792 * tests/data/slx_out/both.run/4_PROGRAM_ID.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
793 * tests/data/slx_out/both.run/s_4_0133_int.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
794 * tests/data/slx_out/both.run/s_4_0133_nse.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
795 * tests/data/slx_out/both.run/s_4_0133_prb.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
796 * tests/data/slx_out/both.run/s_4_0133_seq.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
797 * tests/data/slx_out/both.run/s_4_0133_sig2.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
798 * tests/data/slx_out/both.run/s_4_0134_int.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
799 * tests/data/slx_out/both.run/s_4_0134_nse.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
800 * tests/data/slx_out/both.run/s_4_0134_prb.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
801 * tests/data/slx_out/both.run/s_4_0134_seq.txt, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
802 * tests/data/slx_out/both.run/s_4_0134_sig2.txt: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
803 (15:53:42) First pass at a "make check" target. Currently this is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
804 centred around the newer code, specifically SRF support. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
805 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
806 * tests/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
807 * tests/illumina2srf.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
808 * tests/srf2fasta.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
809 * tests/srf2fastq.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
810 * tests/srf2illumina.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
811 * tests/srf_filter.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
812 * tests/srf_index.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
813 * tests/srf_info.test: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
814 (16:13:19) Fixed tests to use $outdir for output directory so we |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
815 can neatly tidy it up for make distclean. Without this make |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
816 distcheck fails. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
817 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
818 * tests/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
819 * tests/illumina2srf.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
820 * tests/srf2fasta.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
821 * tests/srf2fastq.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
822 * tests/srf2illumina.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
823 * tests/srf_filter.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
824 * tests/srf_index.test, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
825 * tests/srf_info.test: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
826 (16:43:33) Fixed some bashisms and switched to make use of srcdir |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
827 instead of top_srcdir/tests. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
828 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
829 2008-09-09 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
830 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
831 * acinclude.m4: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
832 (13:27:35) Fixed the LIBCURL_CHECK_CONFIG code to not believe the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
833 output from "curl-config --libs". We try -lcurl first off to see if |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
834 that also works. The reason is simply that curl-config --libs |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
835 typically loves to explicitly specify all the implicit |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
836 dependencies, such as -lssl -lcrypto -ldl, etc. This in turn locks |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
837 compiled io_lib libraries and binaries into requiring very specific |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
838 version of system libraries. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
839 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
840 * io_lib/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
841 (13:27:57) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
842 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
843 * io_lib/compression.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
844 (13:30:24) Minor speed tweaks to qshift and unqshift |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
845 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
846 * io_lib/mFILE.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
847 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
848 (13:31:41) Added include of io_lib_config.h for autoconf builds so |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
849 that the ftello and similar functions get the correct prototypes. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
850 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
851 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
852 * io_lib/srf.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
853 (13:32:44) Made partial_decode_ztr non-static and added it, along |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
854 with ztr_dup and construct_trace_name to the external header file |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
855 for use in other parts of io_lib. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
856 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
857 * progs/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
858 * progs/srf_filter.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
859 * progs/srf_info.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
860 (13:36:40) Added two new programs from Steven Leonard. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
861 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
862 srf_info: dumps out basic information on the contents of an SRF |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
863 file, including the read name prefixes used, how many |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
864 DBs per DBH and frequencies of ZTR chunk and meta-data |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
865 strings. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
866 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
867 srf_filter: a tool to produce new srf files by filtering in or out |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
868 data from an existing srf file. This can be performed |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
869 either at the entire trace level (eg tagged as good or |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
870 bad) or also at individual ZTR chunk levels (eg processed |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
871 data only). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
872 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
873 * progs/srf2fasta.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
874 * progs/srf2fastq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
875 (13:37:37) Include string.h for additional prototypes (for -Wall |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
876 -Wno-paranthesis compilations). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
877 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
878 * progs/srf_extract_hash.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
879 (13:38:47) Major overhaul from Steven Leonard. It now supports a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
880 -fastq option to output fastq instead of ZTR files and optionally |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
881 can use calibrated or non-calibrated confidence values too. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
882 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
883 * progs/srf_extract_linear.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
884 (13:39:44) Added support for SRFB_NULL_INDEX so that srf files with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
885 a blank index do not causes crashes. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
886 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
887 * progs/srf_index_hash.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
888 (13:40:44) Added extra error checking from Steven Leonard to spot |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
889 duplicate read names. The new -c option also allows checking of an |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
890 existing srf file without attempting to write a new index. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
891 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
892 2008-09-08 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
893 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
894 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
895 (08:40:20) Fixed bug reported by Robert Sanders. The fwd matrix was |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
896 being written twice on paired-end runs instead of fwd+reverse. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
897 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
898 * COPYRIGHT, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
899 * io_lib/open_trace_file.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
900 * io_lib/sff.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
901 (10:56:46) Updated 454's copyright notice (following correspondence |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
902 from Jim Knight at 454) to explicitly include permission to modify |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
903 and redistribute the code. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
904 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
905 Also updated the GRL licence to be explicit rather than just an |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
906 implied BSD style. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
907 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
908 2008-08-29 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
909 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
910 * io_lib/deflate_interlaced.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
911 (09:00:39) Added external codes2codeset() function to turn |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
912 bit-length arrays into codesets. Useful for tools that wish to use |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
913 this code to use their own precomputed huffman trees. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
914 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
915 * io_lib/deflate_interlaced.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
916 (09:00:53) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
917 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
918 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
919 (09:01:21) Renamed ILLUMINA_GA_PARAMS and ILLUMINA_GA_PARAMS2 to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
920 ILLUMINA_GA_BUSTARD_PARAMS and ILLUMINA_GA_FIRECREST_PARAMS. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
921 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
922 2008-08-26 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
923 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
924 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
925 (11:07:09) Added the second .params file (Data directory). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
926 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
927 Major reduction in memory usage when adding the .params files; we |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
928 only hold this in memory for the first ZTR file per DBH as it ends |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
929 up in the header anyway. (This also speeds things up too.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
930 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
931 2008-08-08 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
932 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
933 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
934 (10:21:28) Fixed a bug in parse_4_float when handling strings with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
935 leading zeroes after the point, eg "17.04". Fortunately this is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
936 never triggered in the solexa data as it's always one single value |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
937 after the decimal point. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
938 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
939 * configure.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
940 * io_lib/os.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
941 (10:33:29) Applied Chris Saunders' patch to use autoconf for |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
942 checking machine endianness. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
943 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
944 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
945 (16:52:10) Added a MAX_READS_PER_DBH #define to solexa2srf |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
946 (defaults at 10000) to reduce the maximum number of traces per tile |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
947 we process between SRF data block headers. This helps reduce the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
948 maximum memory usage which is especially important on dense GA2 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
949 runs where 200,000 clusters in a tile can be achieved. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
950 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
951 Also fixed a bug with using -qf/-qr when not supplying a list of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
952 tiles consecutively starting with tile 1. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
953 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
954 2008-08-05 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
955 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
956 * io_lib/srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
957 (08:18:14) Fixed memory leak in srf_next_ztr reported by Rob Egan. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
958 Triggered by srf2fastq -C. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
959 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
960 2008-07-24 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
961 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
962 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
963 (15:47:32) Updated version to v1.10 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
964 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
965 Added -pf/-pr parameters to allow the phasing files to be stored. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
966 By default it attempts to derive these filenames from the fwd/rev |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
967 cycle numbers. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
968 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
969 Auto-compute the basecaller name and version string from the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
970 directory name. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
971 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
972 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
973 (15:58:15) Bug fix to get_base_caller() so that it can identify the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
974 directory when given a full pathname to elsewhere other than the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
975 cwd. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
976 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
977 2008-07-18 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
978 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
979 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
980 (15:54:51) No longer iterate through tiles printing up . or ! |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
981 depending on whether we encounter an error. Now it just aborts at |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
982 the point of failure. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
983 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
984 Also made the parsing code more robust as in a couple specific |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
985 cases it only wrote to stderr without actually generating a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
986 non-zero exit code. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
987 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
988 These mean the tool is more amenable to running in a production |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
989 pipeline. If it gets any error at all it'll be more obvious and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
990 forces attention. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
991 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
992 2008-07-11 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
993 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
994 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
995 (11:35:28) Updated the rounding of int/nse/sig2 to all use the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
996 rint() function to round to closest integer value. Previously |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
997 int/nse rounded down and sig2 rounded closest. (Although the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
998 rounding on sig2 was via +/- 0.5 and so the half-way cases |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
999 sometimes give different answers to the new code using rint()). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1000 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1001 It has a very minor impact overall, but it is now consistent. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1002 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1003 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1004 2008-07-09 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1005 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1006 * 1.11.3 released. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1007 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1008 2008-07-09 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1009 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1010 * io_lib/mFILE.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1011 * io_lib/Read.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1012 * io_lib/mFILE.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1013 (13:54:59) Fixed a bug visible with "extract_seq -fasta_out -fofn f |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1014 -output f.fasta" whereby only the last file was visible. This is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1015 due to the mFILE mechanism and an explicit fseek upon writing each |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1016 file. Fixed this by using an extended freopen option ("wbx" instead |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1017 of "wb") to override this feature. It's not ideal, but gets the job |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1018 done - I hope. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1019 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1020 2008-07-08 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1021 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1022 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1023 * io_lib/srf.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1024 (13:22:57) Added SRFB_NULL_INDEX as an SRF block type. It's |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1025 essentially type 0 and is defined to be 8 long (with 7 more zeros). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1026 The purpose is to transparently gloss over the 8-zeros that may be |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1027 on the end of some files indicating a missing index block. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1028 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1029 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1030 (13:34:40) MAJOR BUG FIX! |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1031 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1032 Fixed a bug in reorder_ztr() whereby the sorted order of multiple |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1033 chunks of the same chunk type were not "stable". The result of this |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1034 is that 3 SMP4 chunks (say A, B, C) may end up sorted A, B, C with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1035 nchunks==9 and C, A, B with nchunks==15. Given that an optimisation |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1036 means that we change the number of chunks depending on whether |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1037 we've encoded HUFF chunks this causes a "corruption" in as far as |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1038 the correct data is stored but with potentially an incorrect |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1039 meta-data block for the first SMP4 chunk. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1040 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1041 See srf_fix.c to reverse this problem. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1042 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1043 Also added a warning regarding the -C option and -qf option. These |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1044 are inherently incompatible (right now) as purity filtered data is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1045 not calibrated. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1046 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1047 Updated version to v1.8 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1048 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1049 2008-06-12 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1050 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1051 * progs/srf2fasta.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1052 * progs/srf2fastq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1053 (10:44:23) Removed memory leaks from using ztr_find_chunks and not |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1054 freeing the result. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1055 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1056 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1057 2008-06-04 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1058 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1059 * 1.11.2 released. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1060 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1061 2008-06-04 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1062 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1063 * docs/ZTR_format: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1064 (13:06:36) Added some text regarding *ideas* for version 2. These |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1065 are not officially part of any stanard yet. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1066 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1067 * io_lib/compression.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1068 (13:06:54) Comment change only. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1069 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1070 2008-06-03 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1071 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1072 * io_lib/srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1073 (16:23:50) Applied bug fix from John Emhoff: srf_read_xml was |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1074 incorrectly interpreting the XML length as the length of the XML |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1075 string rather than the entire SRF block itself including header. It |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1076 now agrees with srf_write_xml, which interpreted this correctly. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1077 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1078 2008-05-23 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1079 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1080 * docs/ZTR_format: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1081 (08:38:05) Documented TYPE meta-data for SMP4 and removed the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1082 comment about being mutually exclusive with SAMP. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1083 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1084 Added explanation of log-odds vs phred scales. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1085 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1086 Added CNF1 chunk type (how did I miss this before?). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1087 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1088 2008-05-21 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1089 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1090 * io_lib/srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1091 (09:12:23) Fixed memory leak in construct_trace_name. (Patch from |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1092 John Emhoff at Heliocos.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1093 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1094 2008-05-14 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1095 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1096 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1097 (13:08:34) Fixed floating point to integer rounding of trace data |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1098 to round to closest instead of floor(value). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1099 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1100 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1101 * io_lib/srf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1102 * progs/solexa2srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1103 * progs/srf2fasta.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1104 * progs/srf2fastq.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1105 * progs/srf2solexa.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1106 * progs/srf_dump_all.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1107 (14:13:15) Added changes from Camil Toma (albeit modified here and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1108 there) to incorporate the -C option to various tools. This allows |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1109 for chastity filtered data to be stored in SRF, but tagged as being |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1110 bad data. We then get the option to filter it on extraction |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1111 instead. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1112 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1113 2008-05-13 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1114 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1115 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1116 (14:25:53) Reverted the footer position change in encode_ztr() back |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1117 (to the 20th February 2008) to taking out the meta-data into the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1118 header block too. Although this contains variable data (OFFS=value) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1119 it's the same for all members of a tile. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1120 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1121 2008-05-08 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1122 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1123 * io_lib/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1124 (11:06:53) Sped up searching in SRF files by stripping off the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1125 directory name when calling srf_find_trace(). (It got to this |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1126 before eventually, but only after searching various false |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1127 combinations.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1128 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1129 * io_lib/os.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1130 (11:07:31) Minor change to prevent errors when compiling within the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1131 Staden Package. No impact for autoconf version. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1132 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1133 * io_lib/srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1134 (11:08:18) Fixed bug in srf_find_trace that caused it to rarely |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1135 fail to find a trace when querying the hash table. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1136 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1137 2008-05-06 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1138 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1139 * docs/ZTR_format: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1140 (11:44:51) Fixed error in the pictoral diagram describing the magic |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1141 number. (It is correct everywhere else.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1142 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1143 * io_lib/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1144 (14:27:24) Added SRF interfaces to open_trace_file meaning we can |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1145 now try specifying traces file fubar.srf/tname or |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1146 TRACE_PATH=SRF=fubar.srf and tname. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1147 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1148 * configure.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1149 * io_lib/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1150 * progs/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1151 * progs/solexa2srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1152 * progs/srf2solexa.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1153 (15:35:36) Implemented Come Raczy's (Illumina) changes. These |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1154 involved renaming the solexa2srf and srf2solexa tools to be |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1155 illumina2srf and srf2illumina and the addition of qcal support in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1156 preparation for the GA v1.0 release. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1157 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1158 Note that currently the filenames are the same as before, in order |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1159 to preserve change history. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1160 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1161 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1162 (15:43:33) Added srf.o to the Staden Package Makefile (NB: not part |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1163 of the autoconf system.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1164 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1165 2008-04-15 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1166 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1167 * io_lib/hash_table.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1168 (15:09:41) Initialises pb and pc in hash() function when using |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1169 HASH_FUNC_JENKINS3. Bug reported by Cristian Goina. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1170 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1171 2008-04-08 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1172 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1173 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1174 (11:22:33) Fixed a code inefficiency when using -qf and -qr. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1175 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1176 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1177 * io_lib/srf.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1178 (16:16:55) Fixed bugs regarding binary format read_id suffixes, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1179 reported and mostly patched by Cristian Goina. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1180 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1181 The srf_trace_body_t struct now has a read_id_length field. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1182 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1183 The srf_construct_trace_body() function has an extra argument to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1184 pass in the length, or -1 if unknown (it'll use strlen then). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1185 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1186 New function srf_write_pstringb to write binary pstrings, avoiding |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1187 the requirement for strlen(). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1188 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1189 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1190 (16:21:57) Added extra arg to srf_construct_trace_body call (see |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1191 srf.c change log). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1192 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1193 Fixed a bug introduced in the recent efficiency improvements for |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1194 -qf/-qr. These meant that many sequences were incorrectly skipped. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1195 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1196 2008-04-07 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1197 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1198 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1199 (08:54:06) Increased the estimation of number of bytes per cycle in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1200 the allocation in get_sig(). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1201 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1202 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1203 (15:11:06) Fixed error that crept in when error checking was added |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1204 to compress_chunk calls. Missing curly braces meant that some |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1205 chunks were not compressed while other chunks got needless |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1206 additional layers of compression. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1207 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1208 2008-04-03 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1209 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1210 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1211 (15:57:06) The defaults for -N and -n are now using the same naming |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1212 conventions used in Gerald during the fastq generation steps. To do |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1213 this is looks at the run folder root directory name to get the run |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1214 date, machine name and run number. (These are available for use as |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1215 %d, %m and %r in the format strings.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1216 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1217 Calibrated confidence values are now automatically included if the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1218 -qf or -qr parameters are used (specifying the fastq filename). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1219 Note this only works currently if the number of bases after |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1220 calibration is the same as the number before. The calibrated |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1221 confidence values are written in a CNF1 ztr chunk (in addition to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1222 the existing CNF4 chunk for uncalibrated values) and are rescaled |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1223 to adhere to the phred scale (-10 * log10(1-P)). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1224 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1225 Added meta-data to the confidence chunks (CNF1 and CNF4) with a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1226 SCALE key. The value is either LO (log-odds) or PH (phred). This |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1227 increases file size somewhat as it's written once per trace, but |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1228 the long-term goal is to upgrade ZTR to support the ability to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1229 specific default meta-data keys/values. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1230 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1231 * progs/srf2fastq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1232 (15:57:58) Added a -c option to output calibrated confidence values |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1233 instead of uncalibrated ones. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1234 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1235 Plus additionally it should be able to handle multiple archives on |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1236 the command line instead of a single one. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1237 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1238 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1239 (17:00:28) Added support for using popen() to gzip -cd instead of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1240 using gzopen. The reason is that it's between 3 and 5 times faster |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1241 doing that. I'm unsure why, but overall it sped up solexa2srf -r 3 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1242 fold when the Firecrest data is gzipped. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1243 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1244 2008-04-02 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1245 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1246 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1247 (09:14:45) Fixed the footer(aka body) position calculation so it |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1248 works still on trace files containing no trace data at all. Ie |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1249 solexa2srf -P. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1250 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1251 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1252 (09:28:02) Added Camil Toma's (Broad) changes to support -mf and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1253 -mr paremeters. These provide finer grained control over the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1254 filenames of the forward and reverse matrices. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1255 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1256 * progs/srf2solexa.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1257 (09:29:04) Added Camil Toma's (Broad) changes to extract text files |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1258 embedded in ZTR TEXT chunks. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1259 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1260 * progs/srf_dump_all.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1261 (10:54:29) Added Camil Toma's (Broad) changes to srf_dump_all. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1262 These add multiple new features, increasing the source length 7 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1263 fold. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1264 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1265 * progs/srf2solexa.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1266 * progs/srf_dump_all.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1267 (10:56:06) Fixed bug reported by Cristian Goina (JCVI): we now use |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1268 srf_open with mode "rb" instead of "r". This resolves an issue on |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1269 Windows/DOS when dealing with binary data including ^Z characters |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1270 being interpreted as EOF. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1271 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1272 * progs/srf_dump_all.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1273 (11:05:25) Fixed missing newlines in the standard "dump" format. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1274 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1275 2008-03-20 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1276 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1277 * io_lib/hash_table.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1278 * progs/hash_list.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1279 (09:45:07) Added more includes of io_lib_config.h to ensure 64-bit |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1280 file support works correctly. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1281 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1282 2008-03-13 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1283 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1284 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1285 (09:32:15) Fixed an error when passing in fully qualified |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1286 pathnames. We now chdir() to the directory containing the seq.txt |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1287 file and work from there. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1288 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1289 Also some functions involved in supporting fastq files with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1290 callibrated confidence values. This is unfinished and needs more |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1291 work, specifically it doesn't do anything with the sequence/qual |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1292 yet (just parses it) and the entire operation should probably work |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1293 from the GERALD directory instead of the Bustard directory. Hence |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1294 for now the -qf and -qr options are undocumented. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1295 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1296 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1297 (11:53:32) Incorporated Come Razy's changes to solexa2srf, with a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1298 few modifications to adhere to C89 instead of C9X C standards. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1299 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1300 These add support for the new Illumina IPAR file format via the -I |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1301 command line option. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1302 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1303 2008-02-29 jkbonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1304 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1305 * acinclude.m4, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1306 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1307 (14:10:53) Fixed autoconf build environment for Fedora. We no |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1308 longer assume /usr/lib is a valid default for zlib, instead relying |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1309 on either the compiler to find it or an explicit --with-zlib |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1310 option. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1311 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1312 See SF bug 1898427 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1313 https://sourceforge.net/tracker/index.php?func=detail&aid=1898427&g |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1314 roup_id=100316&atid=627058 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1315 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1316 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1317 2008-02-20 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1318 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1319 * 1.11.0 released. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1320 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1321 2008-02-20 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1322 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1323 * progs/srf2fastq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1324 (12:49:09) Removed the ztr2read conversion and operate |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1325 directly on |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1326 the ztr struct. This is now 25% faster. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1327 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1328 * progs/srf2fasta.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1329 (12:49:30) New program - trivially modelled on srf2fastq.c |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1330 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1331 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1332 (10:33:36) Altered the header/footer split for ZTR to stop just |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1333 before the metadata part of a SMP4 chunk. Previously it was after |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1334 this and just before the data, but now we can have multiple SMP4 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1335 chunks in a single ZTR file this was breaking things. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1336 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1337 2008-02-18 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1338 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1339 * io_lib/ztr.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1340 (16:53:52) Added ZTR_TYPE_REGN definition. We have no explicit code |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1341 to implement this yet in ztr.c, but for now it's in solexa2srf. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1342 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1343 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1344 (16:55:38) Added support for specifying the start coord for the 2nd |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1345 read in a paired-read run (solexa2srf -2 <cycle.no.>). This also |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1346 adds a REGN chunk to the ZTR file and stores the second matrix file |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1347 too. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1348 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1349 * progs/srf2solexa.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1350 (16:56:39) Major overhaul to support raw data as well as processed |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1351 data. Still to-do: write out .params and the two matrix files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1352 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1353 2008-02-15 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1354 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1355 * io_lib/srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1356 (10:05:54) Fixed memory leak in srf_read_trace_body usage. This was |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1357 primarily visible from within srf_index_hash. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1358 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1359 * progs/srf2solexa.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1360 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1361 * progs/srf_index_hash.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1362 * progs/srf_extract_hash.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1363 (12:35:19) Added include of io_lib-config.h to ensure picking up |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1364 the correct compiler definitions for 64-bit file size support. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1365 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1366 * progs/srf_extract_linear.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1367 (12:40:55) Fixed memory leaks. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1368 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1369 2008-02-14 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1370 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1371 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1372 (17:02:42) Don't bother performing ZTR_FORM_TSHIFT transformation |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1373 on the solexa noise data as it doesn't help it at all. Also hard |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1374 coded the interlaced huffman to operate in batches of 2 instead of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1375 8 for noise data for the same reason. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1376 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1377 * io_lib/ztr_translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1378 (17:07:15) ztr2read() now correctly handles translation of ZTR |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1379 files with multiple samples in. Specifically it only sets the Read |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1380 struct baseline and trace[ACGT] arrays when the TYPE meta-data |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1381 field is blank, PROC or A,C,G T. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1382 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1383 This fixes trace_dump etc on solexa srf files, (note that the srf |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1384 files themselves were perfect valid anyway). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1385 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1386 2008-02-06 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1387 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1388 * progs/extract_seq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1389 (11:04:38) Use set_compression_method to explicitly disable gzipped |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1390 output from extract_seq (which is by default on if the input is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1391 gzipped). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1392 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1393 * io_lib/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1394 * progs/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1395 * progs/extract_qual.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1396 (11:04:59) Added Steven Leonard's extract_qual program (derived |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1397 from extract_seq). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1398 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1399 2008-01-28 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1400 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1401 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1402 (09:47:42) Sped up parse_4_int and parse_4_float substantially. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1403 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1404 2008-01-25 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1405 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1406 * Tagged iolib-1-11-0b8 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1407 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1408 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1409 (11:38:34) Fixed small memory leak in zfopen/zfclose. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1410 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1411 Fixed a bug where reorder_ztr could put CNF4 before BASE, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1412 breaking |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1413 the decoding. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1414 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1415 Added support for loading solexa matrix and params files into |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1416 appropriately named TEXT key/value pairs. It also adds the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1417 PROGRAM_ID there now too. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1418 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1419 Sped up chastity filtering. We now only read the line of text |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1420 rather than decode it for data that is filtered. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1421 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1422 Minor tweaks to program usage output. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1423 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1424 * progs/trace_dump.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1425 (11:39:09) Updated output to be more inline with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1426 srf_dump_all. Also |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1427 now supports baseline properly. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1428 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1429 * progs/ztr_dump.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1430 (11:39:34) Added ZTR_FORM_XRLE2, ZTR_FORM_QSHIFT and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1431 ZTR_FORM_TSHIFT. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1432 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1433 2008-01-24 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1434 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1435 * io_lib/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1436 * io_lib/ztr.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1437 (17:17:52) Two new utility functions that are *long* overdue. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1438 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1439 ztr_new_chunk() - creates and initialises a new chunk in a ztr |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1440 struct. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1441 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1442 ztr_add_text() - adds arbitrary key/value pairs to the TEXT |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1443 chunk, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1444 creating it if required. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1445 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1446 2008-01-22 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1447 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1448 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1449 * io_lib/srf.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1450 (11:07:40) Allow for srf_read_index_hdr() to be used to read |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1451 an index internal to the file rather than at the end of the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1452 file. To accommodate this an extra "no_seek" argument has been |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1453 added. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1454 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1455 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1456 (11:10:56) Support multiple trace channels (raw "int" & noise, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1457 in addition to or instead of the processed data). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1458 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1459 Input data may now optionally be compressed. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1460 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1461 Added a -c option to do chastity filtering via the .qhg files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1462 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1463 Improved the dynamic range filtering. We no longer trim all |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1464 negative values in preference for high positive values. Instead we |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1465 set the clip points to trim the least number of total values. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1466 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1467 * progs/srf2solexa.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1468 (11:11:35) Fixed the baseline subtraction. It now uses the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1469 correct value instead of a hardcoded 32768. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1470 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1471 * progs/srf_extract_linear.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1472 (11:12:15) Changed to use the new srf_read_index_hdr arguments. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1473 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1474 * progs/srf_index_hash.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1475 (11:13:12) Improved index support when the input is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1476 concatenated SRF files already containing indices. It now |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1477 overwrites the last index. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1478 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1479 * progs/ztr_dump.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1480 (11:13:47) Added display of meta-data TYPE field for trace |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1481 sample chunks. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1482 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1483 2008-01-14 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1484 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1485 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1486 * io_lib/srf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1487 * progs/srf_index_hash.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1488 (16:57:36) Bug fixes to do with reading and writing the index |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1489 format. We incorrectly handled having null dbhFile and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1490 containerFile elements, plus also computed the index size wrong |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1491 for these fields too. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1492 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1493 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1494 2008-01-11 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1495 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1496 * 1.11.0b7 released. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1497 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1498 * io_lib/srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1499 (11:35:09) IMPORTANT BUG FIX: The SRF Data Block Header |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1500 had the blockSize field 4 bytes too large, so SRF files produced |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1501 did not conform to the standard. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1502 Also fixed SRF reading support for when headerBlob is zero length. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1503 We then delay ztr decoding until we've read the actual data blob. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1504 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1505 * io_lib/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1506 * io_lib/deflate_interlaced.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1507 * io_lib/deflate_interlaced.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1508 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1509 * io_lib/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1510 * io_lib/ztr_translate.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1511 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1512 (12:26:11) Added missing prototypes and fixed various signed vs |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1513 unsigned assignments, as spotted by the Intel C Compiler. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1514 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1515 2008-01-02 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1516 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1517 * Tagged iolib-1-11-0b6 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1518 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1519 2008-01-02 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1520 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1521 * io_lib/srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1522 (11:41:00) Removed some debugging output |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1523 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1524 2007-12-12 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1525 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1526 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1527 * io_lib/srf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1528 * progs/srf_index_hash.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1529 (18:50:46) Updates to SRF 1.3. This includes removal of the readID |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1530 counter and added support for printf style formatting. It also has |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1531 some tweaks to the format for the index (32-bit vs 64-bit and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1532 dbh/container file strings). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1533 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1534 Both versions have therefore been bumped (SRF 1.3 and index 1.01). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1535 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1536 TODO: support for extracting data from an SRF file that's split |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1537 with container headers, trace headers and trace bodies all in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1538 separate files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1539 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1540 2007-11-12 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1541 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1542 * Tagged iolib-1-11-0b5 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1543 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1544 2007-11-08 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1545 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1546 * io_lib/Read.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1547 * io_lib/Read.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1548 * io_lib/abi.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1549 * io_lib/alf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1550 * io_lib/array.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1551 * io_lib/array.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1552 * io_lib/compress.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1553 * io_lib/compress.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1554 * io_lib/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1555 * io_lib/compression.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1556 * io_lib/ctfCompress.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1557 * io_lib/deflate_interlaced.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1558 * io_lib/deflate_interlaced.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1559 * io_lib/error.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1560 * io_lib/error.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1561 * io_lib/expFileIO.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1562 * io_lib/expFileIO.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1563 * io_lib/files.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1564 * io_lib/find.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1565 * io_lib/fpoint.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1566 * io_lib/fpoint.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1567 * io_lib/hash_table.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1568 * io_lib/hash_table.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1569 * io_lib/jenkins_lookup3.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1570 * io_lib/jenkins_lookup3.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1571 * io_lib/mFILE.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1572 * io_lib/mFILE.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1573 * io_lib/mach-io.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1574 * io_lib/mach-io.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1575 * io_lib/misc.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1576 * io_lib/misc_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1577 * io_lib/open_trace_file.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1578 * io_lib/open_trace_file.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1579 * io_lib/os.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1580 * io_lib/plain.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1581 * io_lib/read_alloc.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1582 * io_lib/read_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1583 * io_lib/scf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1584 * io_lib/scf_extras.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1585 * io_lib/scf_extras.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1586 * io_lib/seqIOABI.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1587 * io_lib/seqIOABI.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1588 * io_lib/seqIOALF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1589 * io_lib/seqIOCTF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1590 * io_lib/seqIOCTF.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1591 * io_lib/seqIOPlain.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1592 * io_lib/sff.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1593 * io_lib/sff.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1594 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1595 * io_lib/srf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1596 * io_lib/stdio_hack.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1597 * io_lib/strings.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1598 * io_lib/tar_format.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1599 * io_lib/traceType.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1600 * io_lib/traceType.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1601 * io_lib/translate.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1602 * io_lib/translate.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1603 * io_lib/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1604 * io_lib/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1605 * io_lib/vlen.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1606 * io_lib/vlen.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1607 * io_lib/write_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1608 * io_lib/xalloc.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1609 * io_lib/xalloc.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1610 * io_lib/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1611 * io_lib/ztr.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1612 * io_lib/ztr_translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1613 (14:58:14) Renamed files from |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1614 {abi,alf,ctf,exp_file,plain,read,scf,sff,srf,utils,ztr} subdirs to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1615 a single io_lib subdir. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1616 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1617 The purpose of this is so that code can #include <io_lib/foo.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1618 from both within this source tree and externally when compiling |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1619 against io_lib, resolving problems when including files that then |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1620 include other io_lib files. Plus it's simply tidier this way. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1621 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1622 * io_lib/Read.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1623 * io_lib/Read.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1624 * io_lib/abi.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1625 * io_lib/alf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1626 * io_lib/array.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1627 * io_lib/compress.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1628 * io_lib/compress.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1629 * io_lib/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1630 * io_lib/compression.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1631 * io_lib/ctfCompress.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1632 * io_lib/deflate_interlaced.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1633 * io_lib/expFileIO.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1634 * io_lib/expFileIO.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1635 * io_lib/files.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1636 * io_lib/find.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1637 * io_lib/fpoint.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1638 * io_lib/hash_table.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1639 * io_lib/jenkins_lookup3.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1640 * io_lib/mFILE.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1641 * io_lib/mach-io.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1642 * io_lib/mach-io.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1643 * io_lib/misc.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1644 * io_lib/misc_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1645 * io_lib/open_trace_file.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1646 * io_lib/open_trace_file.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1647 * io_lib/plain.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1648 * io_lib/read_alloc.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1649 * io_lib/read_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1650 * io_lib/scf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1651 * io_lib/scf_extras.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1652 * io_lib/scf_extras.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1653 * io_lib/seqIOABI.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1654 * io_lib/seqIOABI.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1655 * io_lib/seqIOALF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1656 * io_lib/seqIOCTF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1657 * io_lib/seqIOCTF.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1658 * io_lib/seqIOPlain.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1659 * io_lib/sff.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1660 * io_lib/sff.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1661 * io_lib/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1662 * io_lib/srf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1663 * io_lib/stdio_hack.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1664 * io_lib/strings.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1665 * io_lib/traceType.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1666 * io_lib/traceType.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1667 * io_lib/translate.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1668 * io_lib/translate.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1669 * io_lib/vlen.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1670 * io_lib/write_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1671 * io_lib/xalloc.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1672 * io_lib/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1673 * io_lib/ztr.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1674 * io_lib/ztr_translate.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1675 * progs/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1676 * progs/append_sff.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1677 * progs/convert_trace.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1678 * progs/extract_fastq.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1679 * progs/extract_seq.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1680 * progs/get_comment.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1681 * progs/hash_exp.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1682 * progs/hash_extract.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1683 * progs/hash_list.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1684 * progs/hash_sff.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1685 * progs/hash_tar.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1686 * progs/index_tar.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1687 * progs/makeSCF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1688 * progs/scf_dump.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1689 * progs/scf_info.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1690 * progs/scf_update.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1691 * progs/solexa2srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1692 * progs/srf2fastq.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1693 * progs/srf2solexa.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1694 * progs/srf_dump_all.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1695 * progs/srf_extract_hash.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1696 * progs/srf_extract_linear.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1697 * progs/srf_index_hash.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1698 * progs/trace_dump.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1699 * progs/ztr_dump.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1700 (17:24:16) Modify the include paths to use "io_lib/foo.h" instead |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1701 of "foo.h" or <foo.h>. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1702 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1703 The advantage of this is that the source for external programs |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1704 compiled and linked against io_lib can use exactly the same |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1705 #include statements as the progs/* files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1706 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1707 * Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1708 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1709 (17:37:00) Updated to handle the filename movements. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1710 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1711 * docs/Hash_File_Format, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1712 * docs/ZTR_format: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1713 (17:42:14) Moved from elsewhere |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1714 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1715 2007-11-06 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1716 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1717 * README, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1718 * CHANGES |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1719 Updated |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1720 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1721 * progs/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1722 (10:09:33) Added srf_extract_hash; demonstration of using |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1723 srf_find_trace to query a hash table index. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1724 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1725 * progs/srf_extract_hash.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1726 (10:09:34) Added srf_extract_hash; demonstration of using |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1727 srf_find_trace to query a hash table index. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1728 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1729 * srf/srf.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1730 (10:10:15) Bug fix: updated version string to 1.2. (We were already |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1731 writing using the 1.2 standard but claiming 1.1) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1732 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1733 * srf/srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1734 (10:12:04) Bug fix when using glibc: added explicit include of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1735 io_lib_config.h prior to stdio.h so the AC_SYS_LARGEFILE autoconf |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1736 magic does its tricks. This is only required for glibc, which |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1737 appears broken by default as it doesn't contain a prototype for |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1738 fseeko despite exporting the system, unless explicit macros are |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1739 defined. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1740 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1741 2007-11-02 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1742 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1743 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1744 (13:57:30) Improved handling of out-of-range data. Specifically |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1745 what happens when the minimum value in a trace is -40000 and the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1746 maximum value is +50000. We now clip -ve values if the range |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1747 doesn't fit. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1748 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1749 * ztr/ztr_translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1750 (13:59:41) Added SMP4 'OFFS' metadata and Read->baseline support |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1751 when converting from read2ztr. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1752 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1753 2007-11-01 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1754 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1755 * srf/srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1756 (14:24:30) More error checking paranoia in SRF support; given that |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1757 fwrite() can sometimes claim success even when it failed we now |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1758 explicitly call ferror and check fclose() return. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1759 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1760 * ztr/FORMAT, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1761 * ztr/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1762 * ztr/ztr.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1763 * ztr/ztr_translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1764 (14:26:02) Better support for ZTR v1.2. We now correctly handle |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1765 SAMP/SMP4 metadata fields and make use of OFFS when converting to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1766 Read. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1767 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1768 * progs/solexa2srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1769 * progs/srf_dump_all.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1770 (14:26:35) Improved support for ztr OFFS metadata and removed the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1771 old crufty SHIFT_BY #define. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1772 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1773 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1774 (17:35:58) Bug fix: we were missing the trailing nul of the trace |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1775 OFFS metadata value. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1776 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1777 Also the setting of min_val when the range is too high was invalid. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1778 Note further work is needed here as we've already truncated to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1779 16-bit making it impossible to tell where the wraparound occurs. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1780 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1781 * ztr/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1782 * ztr/ztr_translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1783 (18:00:55) Fixed memory leaks. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1784 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1785 2007-10-26 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1786 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1787 * progs/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1788 * progs/srf2fastq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1789 (10:35:56) Added srf2fastq conversion to demonstrate usage of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1790 read_sections() and as a benchmark for pure sequence+quality |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1791 extraction. (It appears to cope at about 100,000 sequences/second.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1792 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1793 * ztr/deflate_interlaced.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1794 * ztr/deflate_interlaced.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1795 (10:38:04) Changed generate_code_set and huffman_codeset_destroy to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1796 keep the same huffman_codeset_t structure for all uses of one of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1797 the predetermined CODE_* codesets. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1798 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1799 * ztr/ztr_translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1800 (10:40:37) ztr2read() now honours the read_sections() setting. To |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1801 do this it also means it uncompresses data on the fly, but only for |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1802 chunk types that it needs to. Hence this code no longer needs |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1803 uncompress_ztr() calling first either. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1804 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1805 * srf/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1806 * srf/srf.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1807 (10:46:07) Moved some static local variables out of srf_next_ztr |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1808 into the srf_t object. This means the code should be |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1809 multi-threaded. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1810 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1811 * ztr/FORMAT: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1812 (10:47:07) Current v1.3 draft |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1813 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1814 * ztr/Attic/deflate_simple.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1815 * ztr/Attic/deflate_simple.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1816 (10:50:32) Replaced by deflate_interlaced.[ch] some time ago. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1817 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1818 * progs/srf2solexa.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1819 (11:35:59) Switched to using srf_next_ztr() in order to avoid |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1820 repeated huffman codeset decoding. Now much faster. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1821 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1822 * CHANGES: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1823 (14:28:27) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1824 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1825 * README, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1826 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1827 (14:31:48) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1828 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1829 2007-10-25 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1830 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1831 * progs/srf_dump_all.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1832 * progs/srf_extract_linear.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1833 * srf/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1834 * srf/srf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1835 * ztr/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1836 * ztr/deflate_interlaced.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1837 * ztr/deflate_interlaced.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1838 * ztr/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1839 * ztr/ztr.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1840 (14:21:16) Upgraded SRF to support v1.2 specification. NOTE: No |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1841 support is kept for v1.1! |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1842 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1843 Dramatically improved the speed of sequential decoding (eg in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1844 srf_dump_all) by use of caching huffman_codeset_t structs. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1845 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1846 * progs/srf_dump_all.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1847 (16:55:24) Added unused (#if-ed out) printf variant. It's for |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1848 possible efficiency gains, but ignoring for now. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1849 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1850 * ztr/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1851 * ztr/deflate_interlaced.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1852 (16:56:06) Fixed unsthuff uncompression for the predfined CODE_* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1853 huffman trees. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1854 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1855 2007-10-17 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1856 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1857 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1858 (16:56:11) Dropped ZLIB compression of BPOS as A) it's tiny anyway |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1859 and B) we don't want to waste time compressing it over and over |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1860 again. (TODO: actually we don't need to encode it over and over |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1861 again either.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1862 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1863 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1864 2007-10-16 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1865 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1866 * progs/solexa2srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1867 * srf/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1868 * ztr/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1869 * ztr/deflate_interlaced.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1870 * ztr/deflate_interlaced.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1871 * ztr/ztr.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1872 * ztr/ztr.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1873 (08:36:06) Improvements to speed following code profiling. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1874 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1875 * progs/solexa2srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1876 (16:49:38) Major overhaul of parsing code. We now roll our own |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1877 specialist parser instead of using strtok and sscanf. This has |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1878 approximately doubled the speed (so maybe 4-5x faster in the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1879 parsing component). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1880 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1881 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1882 (16:52:06) Boost version to 1.11.0b3 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1883 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1884 2007-10-11 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1885 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1886 * ztr/deflate_interlaced.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1887 (13:34:48) Fixed a buffer overrun. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1888 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1889 * ztr/compression.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1890 (13:35:59) Removed a small memory leak and improved initialisation |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1891 in tshift to avoid (harmless) valgrind error. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1892 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1893 * progs/srf2solexa.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1894 * progs/srf_dump_all.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1895 * srf/srf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1896 (13:37:29) Removed memory leaks. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1897 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1898 2007-10-02 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1899 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1900 * README, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1901 * ztr/FORMAT: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1902 (08:55:47) Minor doc updates |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1903 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1904 * read/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1905 (08:57:02) Fixed src vs srf typo. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1906 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1907 * README: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1908 (08:58:09) Version change |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1909 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1910 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1911 (08:59:11) Version change |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1912 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1913 2007-09-28 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1914 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1915 * Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1916 * configure.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1917 * progs/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1918 * progs/solexa2srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1919 * progs/srf2solexa.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1920 * progs/srf_dump_all.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1921 (11:07:15) File Edit Options Buffers Tools Help Version 1.11.0b1 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1922 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1923 Added preliminary SRF support. This consists of a new subdirectory |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1924 'srf' (yes these all really need merging into a single directory, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1925 but that's a later task), a substantial update to ZTR and a variety |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1926 of SRF tools in progs. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1927 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1928 The old huffman_static.[ch] files were renamed and substantially |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1929 worked upon to create deflate_interlaced.[ch]. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1930 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1931 Added new compression types. xrle2, tshift and qshift. The latter |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1932 two of these are very specific to trace and quality packings. May |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1933 need to rename to be more generic. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1934 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1935 * progs/srf_extract_linear.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1936 * progs/srf_index_hash.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1937 * progs/ztr_dump.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1938 * read/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1939 * srf/srf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1940 * srf/srf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1941 * ztr/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1942 * ztr/compression.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1943 * ztr/deflate_interlaced.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1944 * ztr/deflate_interlaced.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1945 * ztr/Attic/huffman_static.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1946 * ztr/Attic/huffman_static.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1947 * ztr/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1948 * ztr/ztr.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1949 (11:07:16) File Edit Options Buffers Tools Help Version 1.11.0b1 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1950 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1951 Added preliminary SRF support. This consists of a new subdirectory |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1952 'srf' (yes these all really need merging into a single directory, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1953 but that's a later task), a substantial update to ZTR and a variety |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1954 of SRF tools in progs. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1955 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1956 The old huffman_static.[ch] files were renamed and substantially |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1957 worked upon to create deflate_interlaced.[ch]. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1958 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1959 Added new compression types. xrle2, tshift and qshift. The latter |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1960 two of these are very specific to trace and quality packings. May |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1961 need to rename to be more generic. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1962 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1963 * ztr/compression.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1964 (15:28:12) Fixed a bug in run length encoding XRLE2 format when |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1965 dealing with very long repeat runs. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1966 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1967 * ztr/FORMAT-1.2: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1968 (15:34:26) Fixed error in XRLE description. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1969 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1970 * ztr/FORMAT: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1971 (15:34:41) Further updates documenting version 1.3 changes |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1972 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1973 2007-09-03 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1974 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1975 * ztr/Attic/deflate_simple.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1976 * ztr/Attic/deflate_simple.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1977 (11:11:12) Mostly a rename from huffman_static to deflate_simple, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1978 but also a large overhaul and redesign. This code implements the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1979 huffman component of the Deflate algorithm. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1980 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1981 * ztr/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1982 * ztr/compression.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1983 * ztr/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1984 * ztr/ztr.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1985 (11:12:16) Updates to deal with the change from huffman_static to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1986 deflate_simple. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1987 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1988 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1989 * Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1990 * read/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1991 * progs/ztr_dump.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1992 (11:35:50) Update for rename of huffman_static.h to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1993 deflate_simple.h |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1994 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1995 2007-08-15 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1996 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1997 * ztr/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1998 * ztr/Attic/huffman_static.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1999 * ztr/Attic/huffman_static.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2000 (15:30:04) Major overhaul of huffman_static.c. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2001 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2002 It's been substantially tuned for speed and also has several bug |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2003 fixes to ensure we have a consistent sort function before applying |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2004 the canonical_codes function (which previously meant differing |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2005 qsort implementations would give different codes). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2006 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2007 * ztr/FORMAT-1.2: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2008 (15:31:58) Created a snapshot of FORMAT for ZTR v1.2 only |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2009 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2010 2007-07-16 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2011 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2012 * acinclude.m4, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2013 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2014 (08:03:42) Updated configure.in to support --with-lib=DIR. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2015 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2016 * utils/files.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2017 (08:05:23) Switched from using tempnam() to tmpfile(). This meant |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2018 recreating tmpfile() wrapper on MS Windows to avoid bugs with it |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2019 always attempting to write to the root directory, regardless of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2020 user privs. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2021 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2022 * utils/open_trace_file.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2023 * utils/os.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2024 (08:05:24) Switched from using tempnam() to tmpfile(). This meant |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2025 recreating tmpfile() wrapper on MS Windows to avoid bugs with it |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2026 always attempting to write to the root directory, regardless of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2027 user privs. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2028 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2029 * progs/hash_extract.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2030 (09:01:39) Fixed bug on windows: we now set stdout to be binary |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2031 mode first. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2032 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2033 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2034 (09:02:51) INCOMPATIBLE CHANGE: On windows we now use semi-colon as |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2035 the path separator. The reason is that with the MinGW getenv() |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2036 seems to do "clever things" with PATH variables and consequently |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2037 ends up corrupting our clumsy attempt of escaping colons in paths. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2038 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2039 2007-07-11 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2040 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2041 * Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2042 * Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2043 * read/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2044 * utils/hash_table.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2045 * utils/hash_table.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2046 * utils/jenkins_lookup3.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2047 * utils/jenkins_lookup3.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2048 (13:57:26) Added Bob Jenkins' lookup3.c code to the hash_table |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2049 support. It also now uses this for 64-bit hashing. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2050 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2051 2007-07-06 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2052 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2053 * ztr/Attic/huffman_static.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2054 (09:06:46) Bug fix to last commit - finish adding the CODE_ENGLISH |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2055 and removal of other code sets. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2056 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2057 2007-07-05 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2058 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2059 * plain/seqIOPlain.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2060 (08:27:43) For FASTA format files we now, eventually, read the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2061 first sequence. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2062 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2063 * ztr/FORMAT, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2064 * ztr/Attic/huffman_static.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2065 * ztr/Attic/huffman_static.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2066 * ztr/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2067 * ztr/ztr.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2068 (08:28:30) Work-in-progress update to support HUFF chunks and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2069 STHUFF (static huffman) compression methods. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2070 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2071 * progs/ztr_dump.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2072 (08:29:15) Updated to support the new static-huffman compression |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2073 method. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2074 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2075 * ztr/Attic/huffman_static.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2076 * ztr/Attic/huffman_static.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2077 (10:45:48) Removed potentially variable huffman trees (solexa |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2078 trace, confidence values) and added an english text tree. This was |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2079 based on War of the Worlds, The Gold Bug, 200000 Leagues Under the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2080 Sea and the "man ascii" unix manual page for a bit of variety. It |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2081 also includes the SYM_ANY escape code for handling out-of-band |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2082 data. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2083 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2084 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2085 2007-05-30 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2086 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2087 * progs/extract_seq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2088 (11:10:59) Fixed usage string (added -ztr). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2089 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2090 * io_lib-config.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2091 (11:11:26) Added explicit @LIBZ@ to --libs. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2092 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2093 * progs/hash_sff.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2094 (11:12:07) Fixed FILE handling bug. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2095 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2096 * ztr/ztr.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2097 (11:13:07) Maded entropy() static to avoid clash with ztr_dump.c |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2098 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2099 * CHANGES, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2100 * README, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2101 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2102 (11:34:53) Updated to version 1.10.2 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2103 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2104 2007-04-19 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2105 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2106 * utils/hash_table.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2107 (16:18:19) Fixed a memory leak and also changed to use off_t |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2108 instead of long for file offsets. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2109 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2110 * ztr/Attic/huffman_static.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2111 * ztr/Attic/huffman_static.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2112 * ztr/ztr.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2113 * ztr/ztr.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2114 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2115 * Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2116 * read/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2117 (16:21:59) Added HUFFMAN_STATIC ZTR compression method. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2118 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2119 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2120 * abi/fpoint.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2121 * abi/seqIOABI.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2122 * ctf/seqIOCTF.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2123 * exp_file/expFileIO.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2124 * progs/convert_trace.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2125 * progs/extract_fastq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2126 * progs/extract_seq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2127 * progs/hash_sff.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2128 * progs/makeSCF.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2129 * progs/ztr_dump.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2130 * read/Read.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2131 * read/scf_extras.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2132 * read/translate.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2133 * scf/scf.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2134 * sff/sff.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2135 * utils/array.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2136 * utils/compress.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2137 * utils/error.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2138 * utils/hash_table.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2139 * utils/mFILE.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2140 * utils/mach-io.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2141 * utils/misc.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2142 * utils/open_trace_file.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2143 * utils/os.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2144 * utils/stdio_hack.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2145 * utils/tar_format.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2146 * utils/traceType.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2147 * utils/vlen.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2148 * utils/xalloc.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2149 * ztr/compression.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2150 (16:30:14) Added extern "C" {...} guards around all header files to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2151 ease use from within C++ source. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2152 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2153 2006-08-07 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2154 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2155 * progs/convert_trace.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2156 (14:12:39) Added -signed and -noneg options to perform shifting of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2157 trace data to avoid the unsigned issues for TRACE. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2158 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2159 2006-07-18 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2160 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2161 * utils/traceType.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2162 (13:44:13) Added support for anytr in str2int and int2str |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2163 conversions. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2164 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2165 2006-07-06 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2166 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2167 * progs/hash_exp.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2168 (08:45:18) Use binary mode, for windows. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2169 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2170 * progs/hash_exp.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2171 (09:20:20) Remove control-M from end of line when indexing ID |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2172 lines. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2173 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2174 * progs/hash_exp.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2175 (09:22:52) Oops; removal of debugging info |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2176 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2177 2006-07-05 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2178 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2179 * Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2180 * dependencies: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2181 (15:45:01) Fixed dependency generation for io_lib |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2182 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2183 2006-07-04 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2184 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2185 * utils/mFILE.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2186 * utils/mFILE.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2187 (13:43:28) Added mfcreate_from(). It has a usage syntax identical |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2188 to mfreopen(), but unlike mfreopen() it doesn't do anything with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2189 the file pointer (neither closing ie or remembering it in the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2190 structure). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2191 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2192 * progs/extract_fastq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2193 (16:19:30) Pathname hacking and listed -ztr on command line. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2194 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2195 * progs/extract_seq.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2196 * progs/makeSCF.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2197 (16:20:17) Added -ztr as a command line option. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2198 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2199 * progs/hash_exp.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2200 (16:21:14) Hash_exp now outputs to the same file containing the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2201 experiment files (in appended hash-table mode). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2202 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2203 * progs/hash_extract.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2204 (16:21:53) Bug fix: now only needs at least 1 filename specified |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2205 when fofn mode is not in use. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2206 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2207 * progs/hash_list.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2208 (16:22:40) error detection and protection |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2209 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2210 2006-06-27 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2211 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2212 * utils/mFILE.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2213 (11:16:21) Bug fix to the previous change: mstdin(), mstdout() and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2214 mstderr() now correctly mark their streams and read and write |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2215 capable. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2216 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2217 * utils/mFILE.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2218 * utils/mFILE.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2219 (15:48:15) Added mfdetach() to allow the file pointer to be closed |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2220 without deallocating the mFILE structure. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2221 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2222 Also removed the mFILE->fname component and replaced uses with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2223 checks to mode & MF_WRITE. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2224 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2225 * utils/mFILE.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2226 * utils/mFILE.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2227 (15:58:52) Corrected duff spelling! |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2228 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2229 2006-06-26 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2230 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2231 * utils/mFILE.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2232 * utils/mFILE.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2233 (16:47:30) Fixed a bug in mfflush whereby it could attempt to write |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2234 HUGE amounts of data (-ve size) when files are truncated before |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2235 flushing; it now fseeks before doing the write and checks if the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2236 size is +ve. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2237 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2238 Also fixed mfwrite to correctly reset the flush_pos record. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2239 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2240 Added a mode field to the mFILE structure so we can keep track of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2241 append and read-only flags. These are checked for in the mfwrite |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2242 function so mfwrite now writes to the correct location when append |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2243 mode is used (ie forced to the end of file) and it now returns 0 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2244 when attempting to write to a read-only mFILE. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2245 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2246 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2247 2006-06-20 awhitwham <awhitwham@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2248 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2249 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2250 (11:37:24) Changed to open trace files as read only |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2251 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2252 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2253 (13:42:57) Updated to version 1.10.1 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2254 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2255 2006-06-15 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2256 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2257 * io_lib.m4: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2258 (10:58:46) First working(?) version; testing on the Internal Trace |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2259 Server. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2260 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2261 * io_lib.m4: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2262 (11:18:39) bug fix IO_LIB_CPPFLAGS & IO_LIB_LDFLAGS initialisation" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2263 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2264 * Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2265 (11:25:57) Added io_lib-config to install scripts |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2266 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2267 * progs/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2268 (11:26:28) Added LIBCURL flags |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2269 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2270 * read/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2271 (11:26:54) Added LIBCURL_CPPFLAGS usage. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2272 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2273 * CHANGES: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2274 (15:40:12) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2275 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2276 * progs/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2277 (15:40:28) Added ztr_dump to the list of progs. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2278 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2279 * progs/ztr_dump.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2280 (15:41:05) Support for log2 format. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2281 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2282 * ztr/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2283 * ztr/compression.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2284 * ztr/ztr.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2285 (15:42:06) Added a ZTR_FORM_LOG2 compression technique. It's an |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2286 experimental lossy compression and is turned off right now; the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2287 space saving was only about 10% and if we go lossy I want big |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2288 changes not small ones. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2289 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2290 * ztr/ztr.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2291 (15:42:07) Added a ZTR_FORM_LOG2 compression technique. It's an |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2292 experimental lossy compression and is turned off right now; the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2293 space saving was only about 10% and if we go lossy I want big |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2294 changes not small ones. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2295 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2296 * README: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2297 (15:43:46) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2298 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2299 2006-06-14 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2300 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2301 * progs/convert_trace.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2302 (08:53:43) Added a -error option to request stderr goes to a file |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2303 instead of stderr. (from Saul Kravitz) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2304 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2305 * scf/misc_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2306 * scf/read_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2307 * scf/write_scf.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2308 (08:58:12) Renamed delta_samples[12] to be scf_delta_samples[12]. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2309 (patch supplied by Saul Kravitz) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2310 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2311 * scf/scf.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2312 (08:58:29) Renamed delta_samples[12] to be scf_delta_samples[12]. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2313 (patch supplied by Saul Kravitz) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2314 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2315 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2316 (08:58:55) Comment update |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2317 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2318 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2319 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2320 (16:28:29) Renamed USE_LIBCURL to be HAVE_LIBCURL to make it |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2321 compatible with autoconf. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2322 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2323 * bootstrap: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2324 (16:28:56) Added removal of io_lib-config |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2325 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2326 * acinclude.m4, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2327 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2328 (16:29:55) Added libcurl checking code (in acinclude.m4). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2329 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2330 * io_lib-config.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2331 (16:31:18) New io_lib-config program to query the compile and link |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2332 parameters needed when using io_lib. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2333 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2334 * io_lib.m4: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2335 (16:46:32) Initial draft (unchecked) of autoconf macros for use by |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2336 packages (in configure.in) that want to make use of io_lib. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2337 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2338 2006-06-13 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2339 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2340 * progs/Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2341 (11:50:47) Added ZLIB_INC include path. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2342 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2343 2006-06-09 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2344 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2345 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2346 (08:53:24) Somewhere along the line I managed to break the most |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2347 common of all search mechanisms; local filenames on disk! Fixed |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2348 find_file_dir(). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2349 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2350 2006-06-08 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2351 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2352 * Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2353 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2354 (13:21:59) Added libcurl support and made this the default instead |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2355 of using WGET for URL based accesses. Fixed a bug in the old wget |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2356 code also though involving handling of zero-sized replies. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2357 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2358 Removed the compressed file extension iteration code in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2359 find_file_dir as it's now included in the master open_trace_file |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2360 function instead (and so was yielding stats on fubar.scf.gz.bz2 and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2361 similar). It's also now possible to turn off the compressed file |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2362 extension iteration code by prefixing a search path element with a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2363 "|" symbol. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2364 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2365 Replaced RAWDATA environment with EXP_PATH and TRACE_PATH. These |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2366 default back to RAWDATA when not defined. Created new functions |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2367 named open_exp_file and open_exp_mfile which use EXP_PATH instead |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2368 of TRACE_PATH. These allow for experiment files and trace files to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2369 share the same names (as is the case in external "trace servers") |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2370 but use different accessor routes to return the data. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2371 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2372 * utils/open_trace_file.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2373 (13:22:40) New prototypes or the open_exp_{file,mfile} code and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2374 iolib_[sg]et_{trace,exp}_path calls. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2375 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2376 * progs/Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2377 * progs/hash_exp.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2378 (13:25:15) New program hash_exp. This allows for multiple |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2379 experiment files to be concatenated together instead a single |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2380 multi-sequence file and then be indexed (using hash_exp) to allow |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2381 for a HASH=... EXP_PATH element to extract the data back out again. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2382 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2383 * progs/convert_trace.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2384 * progs/extract_seq.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2385 * read/Read.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2386 * read/Read.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2387 * read/scf_extras.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2388 * read/translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2389 (13:28:29) Make use of open_exp_mfile instead of open_trace_mfile |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2390 when we know we've explicitly requested a file in EXP format. This |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2391 ensures we'll use the correct search path where appropriate. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2392 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2393 Also defined an ANYTR trace format which is identical to the old |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2394 ANY format except that it excludes EXP and PLN (ie "ANY TRace"). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2395 Again this is used internally to ensure we pick the correct search |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2396 path when dealing with fetching traces and/or experiment files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2397 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2398 * utils/mFILE.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2399 (13:29:23) Fixed a bug in mfseek and mrewind. Both now clear the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2400 EOF flag. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2401 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2402 * utils/traceType.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2403 (13:33:16) Bug fix to fdetermine_trace_type: now rewinds back. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2404 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2405 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2406 (15:21:02) Fixed the include/.links target (added sff) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2407 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2408 * progs/Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2409 * progs/extract_fastq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2410 (15:22:24) Added extract_fastq program. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2411 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2412 2006-05-30 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2413 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2414 * ztr/compression.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2415 (08:46:57) Fixed a bug in xrle(); it now correctly handles runs of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2416 256 or more. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2417 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2418 2006-04-12 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2419 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2420 * read/Read.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2421 (10:53:27) Changed various fwrite_* functions to not close the FILE |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2422 pointer given to them. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2423 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2424 2006-02-28 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2425 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2426 * ztr/compression.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2427 (17:10:36) Fixed bug reading past memory in xrle(). (Thanks to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2428 Kathryn Beal for identifying this.) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2429 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2430 2006-02-27 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2431 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2432 * ztr/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2433 * ztr/ztr.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2434 (14:40:06) Removed static from compress_chunk and uncompress_chunk. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2435 Added prototypes to ztr.h. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2436 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2437 2006-02-23 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2438 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2439 * utils/read_alloc.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2440 (15:08:36) Fixed a bug in read_dup and not initialising read->info. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2441 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2442 * utils/read_alloc.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2443 (16:00:44) Fixed typo. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2444 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2445 2006-02-20 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2446 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2447 * utils/hash_table.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2448 (12:16:50) Allow HashTableAdd to take a non-string for the key. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2449 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2450 2006-01-26 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2451 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2452 * utils/hash_table.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2453 * utils/hash_table.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2454 (09:37:02) Fixed HashTableAdd with non-string keys and without |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2455 HASH_NONVOLATILE_KEYS defined. It used strdup, but now allocates |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2456 and memcpys. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2457 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2458 Added HashTableDel and HashTableRemove functions. HashTableDel |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2459 removes and destroys a specified HashItem. HashTableRemove removes |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2460 and destroys all items attached to a given key. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2461 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2462 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2463 2005-12-14 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2464 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2465 * CHANGES, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2466 * README, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2467 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2468 (14:35:00) Update for 1.9.2 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2469 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2470 2005-12-09 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2471 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2472 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2473 (17:32:31) Added AC_CHECK_LIB calls for nsl and socket |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2474 (gethostbyname and socket). Needed for Solaris compilations. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2475 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2476 2005-11-16 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2477 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2478 * progs/extract_seq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2479 (14:14:16) Used open_trace_mfile instead of open_trace_file to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2480 avoid the need for temporary files and hence speeds this up. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2481 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2482 * read/Read.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2483 (14:23:23) fwrite_reading now frees the temporary mFILE it created. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2484 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2485 * read/Read.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2486 * read/translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2487 (14:45:41) Added private_data and private_size to the Read |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2488 structure & populate from SCF. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2489 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2490 * utils/compress.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2491 (14:48:51) mfreopen_compressed no longer closes the original FILE*. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2492 This makes it backwards compatible once more with the original |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2493 version and also cures a bug whereby the old file pointer was often |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2494 left open, leading to running out of file descriptors. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2495 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2496 * utils/mFILE.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2497 (15:05:51) Fixed uninitialised check when filename was specified |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2498 but not found in mfload. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2499 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2500 * utils/read_alloc.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2501 (15:17:01) Added private_data to read struct |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2502 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2503 2005-11-10 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2504 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2505 * progs/hash_extract.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2506 (11:32:06) Now returns an error code (to the calling process) if it |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2507 failed to extract a sequence. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2508 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2509 * utils/hash_table.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2510 (11:33:07) Fixed problem in hashquery when searching for something |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2511 that has a hash key not present (ie empty hash bucket). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2512 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2513 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2514 2005-10-27 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2515 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2516 * utils/mFILE.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2517 (15:46:45) Fixed hang in mfload when given zero length files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2518 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2519 2005-10-25 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2520 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2521 * read/translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2522 (08:20:26) NDEBUG checks |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2523 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2524 2005-10-21 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2525 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2526 * bootstrap: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2527 (09:15:23) Removed more auto-generated files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2528 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2529 * configure.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2530 * progs/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2531 (09:16:43) Further removal of libtool specific bits (AC_CHECK_LIB). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2532 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2533 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2534 (16:03:35) Fixed bug with IOLIB_ZTR vs IOLIB_SFF macro. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2535 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2536 * Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2537 * bootstrap, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2538 * configure.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2539 * read/Read.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2540 * utils/compress.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2541 (16:04:48) Replaced automake's generated config.h file |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2542 io_lib_config and allow for it to be installed with "make install". |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2543 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2544 * progs/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2545 (16:05:19) Added append_sff to the targets. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2546 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2547 * read/translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2548 (16:05:42) Disabled asserts |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2549 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2550 * utils/mFILE.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2551 (16:06:25) Fixed bug in mfgetc when dealing with 8-bit data. It |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2552 always now returns unsigned values except when EOF |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2553 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2554 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2555 (16:07:20) Updated TAR magic number to be just the 5 first bytes as |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2556 the 6th differs between systems (space vs nul). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2557 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2558 2005-10-20 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2559 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2560 * sff/sff.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2561 (13:31:22) Split the read functions into read & decode functions so |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2562 that we can unpack SFF structs from other sources. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2563 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2564 * progs/Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2565 * progs/append_sff.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2566 (13:31:58) Added an append_sff.c program, to combine multiple SFF |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2567 archives into a single archive. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2568 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2569 2005-10-18 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2570 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2571 * progs/convert_trace.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2572 (16:41:44) Modified to check RAWDATA search path when loading |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2573 traces. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2574 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2575 * progs/hash_sff.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2576 (16:42:58) Major overhaul to not load the entire SFF file into |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2577 memory. It also handles copying the SFF file to a new file and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2578 adding an index to an SFF archive that already has an index. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2579 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2580 * sff/sff.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2581 * sff/sff.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2582 (16:44:31) Restructured read functions to load & decode functions |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2583 so we can decode SFF data blocks obtained via other means (eg as |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2584 used in the indexing code). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2585 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2586 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2587 (16:45:42) Added SFF "sorted index" code, based on 454's getsff.c |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2588 implementation. Also restructured the SFF querying code a bit so |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2589 that it caches this data. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2590 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2591 2005-10-14 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2592 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2593 * CHANGES: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2594 (16:07:36) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2595 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2596 * exp_file/expFileIO.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2597 (16:08:32) Renamed _MSV_VER to _WIN32 so that the binary/ascii |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2598 conversions for experiment file IO works once more under Windows. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2599 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2600 * progs/Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2601 * progs/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2602 * progs/hash_sff.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2603 (16:09:08) Added hash_sff program. This adds a .hsh format index to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2604 the SFF container. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2605 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2606 * sff/sff.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2607 * sff/sff.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2608 (16:10:10) A total rewrite of the SFF code due to the recent |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2609 changes in file format. This code handles access of a *single* SFF |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2610 entry. The code to manipulate multi-file SFF (ie the container) is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2611 in open_trace_file.c. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2612 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2613 * utils/hash_table.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2614 * utils/hash_table.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2615 (16:11:33) HashFileSave now returns the length of the saved hash. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2616 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2617 HashFileFopen now sets afp by default to be the same as hfp. Extra |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2618 checking has been added when closing these file pointers to ensure |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2619 we don't close twice if they point to the same FILE*. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2620 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2621 * utils/mFILE.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2622 * utils/mFILE.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2623 (16:12:58) Added an mfascii() function. This allows for changing |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2624 from binary to ascii after a file has been opened. It should be |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2625 called in place of where the windows-specific _set_mode() function |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2626 would be used. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2627 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2628 There is currently no analagous ascii-to-binary conversion, but I |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2629 have not yet found a need for it either. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2630 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2631 * utils/mach-io.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2632 * utils/mach-io.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2633 (16:13:29) Added [bl]e_{read,write}_int_8 functions for use with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2634 8-byte data types found in SFF. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2635 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2636 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2637 (16:14:55) Added a SFF= format for the RAWDATA search path. This |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2638 handles the SFF container in much the same way that TAR= and HASH= |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2639 works. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2640 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2641 Also for all three of these types you can now do archive/entry |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2642 instead. Eg "extract_seq traces.tar/xyz.ztr" will work and it'll |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2643 even look for traces.tar in RAWDATA if required. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2644 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2645 * utils/os.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2646 (16:15:19) Added a uint1 typedef for completeness. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2647 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2648 * Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2649 * read/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2650 (16:16:06) Makefile support for new sff.c files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2651 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2652 * dependencies: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2653 (16:16:23) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2654 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2655 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2656 (16:16:43) Updated to version 1.9.1. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2657 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2658 2005-10-04 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2659 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2660 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2661 (08:54:30) Added sff to make distsrc |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2662 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2663 * utils/hash_table.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2664 (11:34:03) Cast ptrdiff_t value to int for %.*s argument. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2665 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2666 2005-09-29 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2667 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2668 * utils/hash_table.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2669 * utils/hash_table.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2670 (16:04:06) Fixed the hash file saving and loading so that it works |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2671 on all platforms instead of just x86 linux. There were bugs in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2672 assuming the size of structures. The assumptions are still there in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2673 that I assume they pad the same internally (for ease of coding - we |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2674 can change it when we finally see a system which operates |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2675 differently), but the final "boundary" padding has been resolved. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2676 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2677 2005-09-28 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2678 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2679 * progs/hash_list.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2680 (10:16:49) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2681 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2682 2005-09-19 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2683 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2684 * utils/compress.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2685 (13:58:02) Fixed a file descriptor (and some memory) leak in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2686 freopen_compressed. (Bug ID 1289095) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2687 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2688 2005-09-08 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2689 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2690 * ztr/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2691 * ztr/ztr_translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2692 (11:29:06) Don't try to compress SAMP chunks with meta-data PYRW as |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2693 the raw pyrosequencing data from 454 doesn't compress. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2694 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2695 * progs/Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2696 * progs/hash_tar.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2697 * utils/Hash_File_Format, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2698 * utils/hash_table.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2699 * utils/hash_table.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2700 (11:30:56) Changed the HashFile format slightly. It's now format |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2701 1.00. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2702 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2703 The key difference is that it has a file footer pointing back to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2704 the hashfile header (so the hashfile can be appended to an archive) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2705 and it also has an offset in the header to apply to all seeks |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2706 within the archive itself, so it can be prepending to an archive |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2707 that's already been indexed without breaking the offsets. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2708 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2709 Extended the hash_tar program to allow control over these header |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2710 options. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2711 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2712 2005-08-26 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2713 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2714 * dependencies: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2715 (08:24:32) Rebuilt |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2716 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2717 2005-08-25 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2718 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2719 * progs/makeSCF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2720 * ztr/ztr.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2721 (10:22:20) General code tidyup to prevent warnings. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2722 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2723 2005-08-15 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2724 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2725 * utils/hash_table.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2726 (15:25:18) Fixed HashTableLoad so it correctly stores the HashTable |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2727 in the HashFile structure. It also now checks for the correct size |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2728 of file to load. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2729 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2730 * sff/sff.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2731 * sff/sff.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2732 (15:25:44) Added SFF (454 flowgram) file reading support. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2733 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2734 2005-08-10 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2735 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2736 * Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2737 * README, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2738 * options.mk: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2739 (15:15:24) Added draft SFF format support. I need to verify if the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2740 example data files I tested this with are correct or if the SFF |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2741 draft spec is correct (as they differ marginally in places). Hence |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2742 this format may change soon. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2743 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2744 * read/Read.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2745 * read/Read.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2746 * utils/traceType.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2747 (15:15:25) Added draft SFF format support. I need to verify if the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2748 example data files I tested this with are correct or if the SFF |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2749 draft spec is correct (as they differ marginally in places). Hence |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2750 this format may change soon. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2751 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2752 * progs/ztr_dump.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2753 (15:16:31) Added (commented out) code for extra debugging. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2754 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2755 * progs/Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2756 (15:16:48) Added hash_extract to the Makefile. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2757 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2758 2005-07-22 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2759 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2760 * utils/compress.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2761 (15:52:07) Unset compression_used when opening uncompressed files |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2762 instead of leaving as the last value. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2763 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2764 2005-07-15 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2765 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2766 * read/Read.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2767 (15:16:58) Removed file descriptor 'leak' in write_reading(). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2768 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2769 2005-07-14 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2770 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2771 * exp_file/expFileIO.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2772 (13:53:45) Commenting only |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2773 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2774 * read/Read.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2775 * utils/mFILE.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2776 (13:54:54) mfopen now honours binary verses ascii differences (and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2777 so updated Read.c calls accordingly) so that Windows works better. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2778 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2779 Also improved append mode of opening. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2780 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2781 2005-07-13 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2782 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2783 * ztr/ztr.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2784 (08:41:16) Removed the warning for unknown chunk types. It now just |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2785 silently stores them in memory. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2786 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2787 2005-07-11 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2788 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2789 * utils/mFILE.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2790 (14:01:50) Fixed divide-by-zero buf when calling mfread for zero |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2791 bytes. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2792 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2793 * read/Read.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2794 (16:07:38) Fixed IO_LIB_* macros to be IOLIB_* macros. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2795 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2796 2005-07-07 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2797 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2798 * Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2799 * progs/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2800 (09:01:50) Removed libtool requirements. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2801 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2802 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2803 (09:02:07) Removed use of libtool. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2804 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2805 * Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2806 * abi/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2807 * alf/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2808 * ctf/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2809 * exp_file/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2810 * plain/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2811 * progs/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2812 * read/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2813 * scf/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2814 * utils/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2815 * ztr/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2816 * Attic/config.h.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2817 * Attic/configure: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2818 * Attic/depcomp, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2819 * Attic/install-sh, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2820 * Attic/ltmain.sh, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2821 * Attic/missing: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2822 * abi/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2823 * alf/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2824 * ctf/Attic/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2825 * exp_file/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2826 * plain/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2827 * scf/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2828 * utils/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2829 * ztr/Attic/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2830 (09:09:50) Removed as these have now been collapsed into the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2831 read/Makefile.am. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2832 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2833 * README: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2834 (09:10:19) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2835 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2836 * read/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2837 (09:12:18) Subsumed the other */Makefile.am files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2838 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2839 * progs/hash_tar.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2840 (09:12:48) On Windows, set stdout to be _O_BINARY. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2841 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2842 * read/Read.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2843 (09:13:22) Fixed the _O_BINARY setting code on windows to check for |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2844 fp being valid and to use the mf->fp instead of fp. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2845 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2846 * utils/compress.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2847 (09:15:30) Added checks for HAVE_SYS_WAIT_H for Windows handling. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2848 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2849 * utils/compress.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2850 (09:20:04) Moved HAVE_ZLIB_H from compress.c and put in os.h (when |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2851 autoconf is not in use). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2852 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2853 * utils/hash_table.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2854 (09:21:45) Changed bucket_pos from int64_t to int32_t (as was |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2855 intended) so it works on windows correctly. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2856 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2857 * utils/mFILE.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2858 (09:22:50) Added more _O_BINARY checks for windows. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2859 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2860 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2861 (09:23:28) Added error checking in open_trace_file(). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2862 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2863 * bootstrap: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2864 (10:28:38) Added to simplify initialisation of the autoconf system. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2865 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2866 * utils/os.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2867 (10:34:54) Moved os.h from include to utils. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2868 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2869 * Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2870 (10:49:17) Fixed missing backslash in pkginclude_HEADERS. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2871 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2872 * Attic/config.guess, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2873 * Attic/config.sub, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2874 * Attic/ltconfig, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2875 * Attic/mkinstalldirs, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2876 * Attic/stamp-h.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2877 (10:55:09) Removed more auto-generated files from CVS tree. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2878 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2879 * read/Read.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2880 (14:28:29) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2881 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2882 2005-07-04 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2883 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2884 * README: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2885 (09:24:49) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2886 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2887 * CHANGES: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2888 (09:24:50) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2889 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2890 * Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2891 * progs/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2892 * read/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2893 * scf/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2894 * utils/Attic/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2895 (09:25:34) Adjusted EXTRA_DIST definitions to only include files we |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2896 still appear to have! |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2897 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2898 * Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2899 * progs/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2900 * read/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2901 * scf/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2902 * utils/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2903 * Attic/config.h.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2904 * Attic/configure: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2905 * configure.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2906 (09:27:05) Updated to use newer AC_INIT syntax. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2907 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2908 * read/Read.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2909 (10:21:50) Made the default output format ZTR. Do not compress |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2910 output (via gzip for example) if ZTR2 or ZTR3 is used. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2911 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2912 * utils/compress.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2913 (10:25:19) If HAVE_ZLIB isn't defined then the memgzip/memgunzip |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2914 functions are now also not built (and hence removes compilation |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2915 errors). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2916 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2917 The pipe2 function now uses waitpid to avoid zombies. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2918 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2919 * utils/mFILE.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2920 * utils/mFILE.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2921 (10:29:41) Added mfrecreate() function to change an existing |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2922 mFILE to point to new data. Better handling of append mode in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2923 mfreopen. Fixed mf->fname such that it's now always a pointer to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2924 malloced data. Added mfdestroy to deallocate memory, but without |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2925 flushing or closing file descriptors. Changed mfflush to write data |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2926 regardless of whether it's stdin/stdout. This means that |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2927 mfflush+mfdestroy can be used to close an mFILE without closing |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2928 the underlying FILE pointer used. Added mftruncate. Rewrote mfread |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2929 to do a single memcpy instead of looped memcpys. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2930 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2931 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2932 2005-06-29 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2933 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2934 * CHANGES, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2935 * Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2936 * README, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2937 * dependencies: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2938 (13:33:14) Version 1.9.0-test |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2939 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2940 * Significant speed ups, particularly when dealing with reading |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2941 gzipped files or when extracting data from tar files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2942 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2943 * New external functions for faster access via mFILE (memory-file) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2944 structs. These mimic the fread/fwrite calls, but with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2945 mfread/mfwrite etc. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2946 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2947 * Some functions previously available in external scope, but not |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2948 defined in header files, have now been made internal only |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2949 ("static"). Please contact me if you were using these and have a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2950 burning need for them to remain external. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2951 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2952 * Numerous minor tweaks and updates to fix compiler warnings on |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2953 more stricter modes of the Intel C Compiler. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2954 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2955 * Preliminary support for storing pyrosequencing style traces. This |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2956 has been modeled on the flowgram data from 454, but should be |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2957 applicable to other platforms. ZTR has been updated to incorporate |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2958 this too. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2959 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2960 The Read structure also has flow, flow_order, nflows and flow_raw |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2961 elements too. Code to convert these into the more usual |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2962 traceA/C/G/T arrays exists currently as part of Trev (in tk_utils |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2963 in the Staden Package), but this may move into io_lib for the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2964 next official release. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2965 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2966 * New hash_tar and hash_extract programs. These replace the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2967 index_tar program for rast random access. For RAWDATA include |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2968 "HASH=hashfile" as an element to get io_lib to use the archive |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2969 hash. It's possible to create hash files of most archive formats |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2970 as the hash itself contains the offset and size of each item in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2971 the archive. This means that extracting an item does not need to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2972 know the format of the original archive. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2973 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2974 Some benchmarks show that on ext3 it's actually faster to extract |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2975 files from the hash than directly via the directory. This was |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2976 testing with ~200,000 files, whereupon directory lookups become |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2977 slow. I'd imagine ResierFS or similar to be faster. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2978 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2979 * Added an XRLE encoding for ZTR. This is similar to the existing |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2980 RLE mechanism but it copes with run length encoding of items |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2981 larger than a single byte. It's current use is for storing the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2982 4-base repeating flow order in 454 data. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2983 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2984 * Potential incompatibilities: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2985 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2986 - The Exp_info structure now has an "mFILE *fp" member instead of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2987 "FILE *fp". |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2988 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2989 - As mentioned above, some functions are no longer external. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2990 These include many ctf functions, ztr_(de)compress, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2991 ztr_chunk_(read/write), be_read_*, be_write_*, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2992 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2993 - The default search order for RAWDATA is that the current |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2994 directory is searched after the rest of rawdata instead of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2995 before. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2996 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2997 - Removed support for the old unix "pack" program as a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2998 compression tool. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2999 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3000 * abi/abi.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3001 * abi/fpoint.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3002 * abi/seqIOABI.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3003 * abi/seqIOABI.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3004 * alf/alf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3005 * alf/seqIOALF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3006 * ctf/ctfCompress.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3007 * ctf/seqIOCTF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3008 * ctf/seqIOCTF.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3009 * exp_file/expFileIO.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3010 * exp_file/expFileIO.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3011 * plain/plain.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3012 (13:33:32) Version 1.9.0-test |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3013 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3014 * Significant speed ups, particularly when dealing with reading |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3015 gzipped files or when extracting data from tar files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3016 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3017 * New external functions for faster access via mFILE (memory-file) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3018 structs. These mimic the fread/fwrite calls, but with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3019 mfread/mfwrite etc. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3020 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3021 * Some functions previously available in external scope, but not |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3022 defined in header files, have now been made internal only |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3023 ("static"). Please contact me if you were using these and have a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3024 burning need for them to remain external. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3025 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3026 * Numerous minor tweaks and updates to fix compiler warnings on |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3027 more stricter modes of the Intel C Compiler. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3028 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3029 * Preliminary support for storing pyrosequencing style traces. This |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3030 has been modeled on the flowgram data from 454, but should be |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3031 applicable to other platforms. ZTR has been updated to incorporate |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3032 this too. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3033 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3034 The Read structure also has flow, flow_order, nflows and flow_raw |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3035 elements too. Code to convert these into the more usual |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3036 traceA/C/G/T arrays exists currently as part of Trev (in tk_utils |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3037 in the Staden Package), but this may move into io_lib for the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3038 next official release. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3039 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3040 * New hash_tar and hash_extract programs. These replace the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3041 index_tar program for rast random access. For RAWDATA include |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3042 "HASH=hashfile" as an element to get io_lib to use the archive |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3043 hash. It's possible to create hash files of most archive formats |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3044 as the hash itself contains the offset and size of each item in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3045 the archive. This means that extracting an item does not need to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3046 know the format of the original archive. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3047 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3048 Some benchmarks show that on ext3 it's actually faster to extract |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3049 files from the hash than directly via the directory. This was |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3050 testing with ~200,000 files, whereupon directory lookups become |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3051 slow. I'd imagine ResierFS or similar to be faster. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3052 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3053 * Added an XRLE encoding for ZTR. This is similar to the existing |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3054 RLE mechanism but it copes with run length encoding of items |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3055 larger than a single byte. It's current use is for storing the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3056 4-base repeating flow order in 454 data. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3057 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3058 * Potential incompatibilities: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3059 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3060 - The Exp_info structure now has an "mFILE *fp" member instead of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3061 "FILE *fp". |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3062 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3063 - As mentioned above, some functions are no longer external. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3064 These include many ctf functions, ztr_(de)compress, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3065 ztr_chunk_(read/write), be_read_*, be_write_*, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3066 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3067 - The default search order for RAWDATA is that the current |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3068 directory is searched after the rest of rawdata instead of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3069 before. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3070 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3071 - Removed support for the old unix "pack" program as a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3072 compression tool. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3073 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3074 * plain/seqIOPlain.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3075 * progs/Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3076 * progs/convert_trace.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3077 * progs/extract_seq.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3078 * progs/get_comment.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3079 * progs/hash_extract.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3080 * progs/hash_tar.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3081 * progs/makeSCF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3082 * progs/trace_dump.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3083 * progs/ztr_dump.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3084 * read/Read.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3085 * read/Read.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3086 * read/scf_extras.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3087 * read/translate.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3088 * scf/misc_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3089 * scf/read_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3090 * scf/scf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3091 * scf/write_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3092 * utils/compress.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3093 * utils/compress.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3094 * utils/hash_table.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3095 * utils/hash_table.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3096 * utils/mach-io.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3097 * utils/mach-io.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3098 * utils/open_trace_file.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3099 * utils/open_trace_file.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3100 * utils/read_alloc.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3101 * utils/traceType.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3102 * utils/traceType.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3103 * ztr/FORMAT, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3104 * ztr/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3105 * ztr/compression.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3106 * ztr/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3107 * ztr/ztr.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3108 * ztr/ztr_translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3109 (13:33:33) Version 1.9.0-test |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3110 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3111 * Significant speed ups, particularly when dealing with reading |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3112 gzipped files or when extracting data from tar files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3113 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3114 * New external functions for faster access via mFILE (memory-file) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3115 structs. These mimic the fread/fwrite calls, but with |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3116 mfread/mfwrite etc. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3117 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3118 * Some functions previously available in external scope, but not |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3119 defined in header files, have now been made internal only |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3120 ("static"). Please contact me if you were using these and have a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3121 burning need for them to remain external. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3122 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3123 * Numerous minor tweaks and updates to fix compiler warnings on |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3124 more stricter modes of the Intel C Compiler. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3125 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3126 * Preliminary support for storing pyrosequencing style traces. This |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3127 has been modeled on the flowgram data from 454, but should be |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3128 applicable to other platforms. ZTR has been updated to incorporate |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3129 this too. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3130 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3131 The Read structure also has flow, flow_order, nflows and flow_raw |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3132 elements too. Code to convert these into the more usual |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3133 traceA/C/G/T arrays exists currently as part of Trev (in tk_utils |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3134 in the Staden Package), but this may move into io_lib for the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3135 next official release. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3136 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3137 * New hash_tar and hash_extract programs. These replace the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3138 index_tar program for rast random access. For RAWDATA include |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3139 "HASH=hashfile" as an element to get io_lib to use the archive |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3140 hash. It's possible to create hash files of most archive formats |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3141 as the hash itself contains the offset and size of each item in |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3142 the archive. This means that extracting an item does not need to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3143 know the format of the original archive. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3144 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3145 Some benchmarks show that on ext3 it's actually faster to extract |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3146 files from the hash than directly via the directory. This was |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3147 testing with ~200,000 files, whereupon directory lookups become |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3148 slow. I'd imagine ResierFS or similar to be faster. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3149 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3150 * Added an XRLE encoding for ZTR. This is similar to the existing |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3151 RLE mechanism but it copes with run length encoding of items |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3152 larger than a single byte. It's current use is for storing the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3153 4-base repeating flow order in 454 data. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3154 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3155 * Potential incompatibilities: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3156 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3157 - The Exp_info structure now has an "mFILE *fp" member instead of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3158 "FILE *fp". |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3159 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3160 - As mentioned above, some functions are no longer external. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3161 These include many ctf functions, ztr_(de)compress, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3162 ztr_chunk_(read/write), be_read_*, be_write_*, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3163 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3164 - The default search order for RAWDATA is that the current |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3165 directory is searched after the rest of rawdata instead of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3166 before. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3167 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3168 - Removed support for the old unix "pack" program as a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3169 compression tool. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3170 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3171 * utils/vlen.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3172 * utils/vlen.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3173 (13:35:42) vlen/vflen functions to estimate the maximum data size |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3174 written out by a printf style function. This is used by the new |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3175 mFILE functions. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3176 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3177 * utils/mFILE.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3178 * utils/mFILE.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3179 (13:39:13) mFILE struct support. This is basically a set of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3180 functions to similulate stdio file support on a block of memory |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3181 instead of a file, for purposes of speed and to avoid the need of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3182 writing data out to a file only to be opened and read back in again |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3183 (which happened a lot before). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3184 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3185 stdio_hack.h is, like it says, a hacky bunch of #defines to turn |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3186 stdio functions and io_lib functions into their mFILE equivalents. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3187 It is used internally to convert old code (eg ABI file reading) to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3188 use mFILE structures, but can also be used by the brave to update |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3189 their own code. Use with extreme caution. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3190 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3191 * utils/stdio_hack.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3192 (13:39:14) mFILE struct support. This is basically a set of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3193 functions to similulate stdio file support on a block of memory |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3194 instead of a file, for purposes of speed and to avoid the need of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3195 writing data out to a file only to be opened and read back in again |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3196 (which happened a lot before). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3197 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3198 stdio_hack.h is, like it says, a hacky bunch of #defines to turn |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3199 stdio functions and io_lib functions into their mFILE equivalents. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3200 It is used internally to convert old code (eg ABI file reading) to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3201 use mFILE structures, but can also be used by the brave to update |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3202 their own code. Use with extreme caution. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3203 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3204 2005-06-08 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3205 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3206 * utils/hash_table.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3207 * utils/hash_table.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3208 * progs/hash_extract.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3209 * progs/hash_tar.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3210 (08:37:49) Added some simple hash table functions. Layered on top |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3211 of these are HashFiles, which allow hash table indexing of files to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3212 be stored on disk. hash_tar and hash_extract test programs |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3213 illustrate its use on tar files, much like index_tar does. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3214 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3215 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3216 (08:38:22) Added support for integrating the new hashfile code via |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3217 a "HASH=hashfile" RAWDATA setting. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3218 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3219 2005-04-27 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3220 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3221 * progs/get_comment.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3222 (16:15:51) Removed "might be used uninitialised" warning messages |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3223 from the compiler. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3224 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3225 2005-02-09 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3226 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3227 * abi/seqIOABI.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3228 (10:08:03) Added getABIIndexEntrySW and modified getABIString to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3229 correctly determine the string type (pascal vs C-string). This |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3230 means MODL numbers now come out as 3730 instead of 730 (for |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3231 example). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3232 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3233 2004-12-06 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3234 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3235 * progs/ztr_dump.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3236 (17:41:58) Corrected minor compiler warnings. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3237 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3238 2004-11-16 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3239 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3240 * exp_file/expFileIO.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3241 (12:10:16) Major speed up of reading large experiment files. Tested |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3242 on a 1Mb sequence with AV, ON and SQ lines the new code is 1000 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3243 times faster on the Alpha. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3244 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3245 Primarily the difference comes from removing O(N^2) complexities by |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3246 removing strcat & strlen type of operations. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3247 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3248 2004-10-29 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3249 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3250 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3251 (10:42:10) Automatically create binary output directories. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3252 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3253 2004-10-21 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3254 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3255 * dependencies: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3256 (11:39:28) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3257 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3258 2004-10-14 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3259 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3260 * progs/convert_trace.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3261 (15:38:18) Added a "-subtract <amount>" option to allow removal of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3262 a specific DC offset. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3263 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3264 2004-10-08 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3265 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3266 * progs/convert_trace.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3267 (14:49:06) Fixed a divide-by-zero error in the normalisation code. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3268 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3269 2004-10-01 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3270 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3271 * progs/convert_trace.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3272 (10:56:07) Rewrote rescale_heights (the "-normalise" option) using |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3273 an amplitude tracker with an attack & delay model. This seems to |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3274 work well at adjusting for both gradual amplitude variations and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3275 for downscaling huge dye-blobs. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3276 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3277 2004-08-17 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3278 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3279 * progs/Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3280 * progs/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3281 * progs/ztr_dump.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3282 (13:37:17) Added a ztr_dump program. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3283 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3284 2004-08-05 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3285 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3286 * progs/index_tar.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3287 (09:32:05) Fix bug submitted by Steve Leonard. If a directory is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3288 too large to fit in the name (>100) but short enough to fit in the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3289 prefix the name field will be empty, this is not the cas for |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3290 ordinary files where the name field is always non-empty. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3291 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3292 2004-07-26 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3293 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3294 * exp_file/expFileIO.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3295 (14:24:35) MinGW port |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3296 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3297 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3298 (14:26:13) MinGW port |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3299 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3300 =============================================================================== |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3301 2004-06-01 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3302 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3303 * CHANGES, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3304 * Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3305 * Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3306 * README, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3307 * Attic/config.guess, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3308 * Attic/config.h.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3309 * Attic/config.sub, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3310 * Attic/configure, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3311 * configure.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3312 * Attic/depcomp, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3313 * Attic/install-sh, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3314 * Attic/ltmain.sh, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3315 * Attic/missing, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3316 * Attic/mkinstalldirs: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3317 * abi/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3318 * alf/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3319 * ctf/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3320 * exp_file/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3321 * plain/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3322 * progs/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3323 * progs/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3324 * read/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3325 * scf/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3326 * utils/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3327 * ztr/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3328 (08:54:51) Updated notes to claim this is version 1.8.12 and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3329 rebuilt all the automake/autoconf/libtool generated files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3330 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3331 2004-05-13 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3332 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3333 * abi/seqIOABI.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3334 (16:14:10) Improved spacing fix. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3335 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3336 2004-05-12 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3337 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3338 * abi/seqIOABI.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3339 (08:27:40) Applied change suggested by Saul A. Kravitz. The |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3340 fallback fspacing is now calculated over the range that basecalls |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3341 exist rather than the total length of trace. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3342 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3343 2004-03-03 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3344 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3345 * ztr/ztr_translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3346 (17:45:52) Treat Read->basePos as 16-bit, which means hard-coding |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3347 the first two bytes in ztr_encode_positions for each pos as zero. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3348 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3349 2004-02-19 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3350 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3351 * exp_file/expFileIO.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3352 (12:13:52) Fixed typo in LG qualifier (was LF). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3353 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3354 * exp_file/expFileIO.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3355 (13:48:59) More type fixes; EFLT_LG was given the same number as |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3356 _FT. Now diff. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3357 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3358 2004-02-12 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3359 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3360 * dependencies: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3361 (10:32:01) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3362 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3363 2004-02-09 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3364 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3365 * exp_file/expFileIO.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3366 * exp_file/expFileIO.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3367 (14:39:52) Added LG (LiGation) to experiment file definition. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3368 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3369 2004-01-13 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3370 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3371 * read/translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3372 (17:02:00) In read2exp only set the file format to be TT_EXP when |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3373 'redirection to trace' is not enabled (ie it indicates where the |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3374 sequence came from, EXP or SCF/ZTR/...). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3375 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3376 2003-11-17 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3377 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3378 * utils/open_trace_file.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3379 (14:52:28) Added ARC= and URL= RAWDATA search methods to fetch |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3380 traces via the ensembl trace archive and via a URL. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3381 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3382 2003-10-24 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3383 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3384 * abi/seqIOABI.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3385 (08:24:07) Protect against the base spacing being listed as a |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3386 negative number in the ABI file. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3387 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3388 * progs/extract_seq.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3389 (08:24:29) Added a -fofn option |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3390 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3391 * utils/compress.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3392 (08:24:57) More error checking on writing compressed files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3393 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3394 2003-07-10 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3395 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3396 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3397 (11:14:14) Put back the Staden Makefile as I accidently overwrote |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3398 this with the autoconf generate one. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3399 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3400 * progs/Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3401 (11:14:18) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3402 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3403 2003-07-07 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3404 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3405 * abi/seqIOABI.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3406 * abi/seqIOABI.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3407 (11:20:37) Confidence values (PCON 1) are now loaded from ABI |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3408 files. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3409 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3410 * Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3411 * Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3412 * Attic/config.guess, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3413 * Attic/config.h.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3414 * Attic/config.sub, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3415 * Attic/configure, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3416 * configure.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3417 * Attic/install-sh, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3418 * Attic/ltconfig, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3419 * Attic/ltmain.sh, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3420 * Attic/missing, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3421 * Attic/mkinstalldirs, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3422 * Attic/stamp-h.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3423 (11:24:47) Added automake/autoconf/libtool files to CVS tree. Not |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3424 all of these are 'source' files as some are generated by others, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3425 but for ease of compilation the output from these tools is |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3426 distribute too, meaning that only './configure' needs to be run. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3427 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3428 * abi/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3429 * abi/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3430 (11:24:52) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3431 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3432 * alf/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3433 * alf/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3434 * ctf/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3435 * ctf/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3436 * exp_file/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3437 * exp_file/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3438 * plain/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3439 * plain/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3440 * progs/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3441 (11:25:02) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3442 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3443 * progs/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3444 * read/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3445 * read/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3446 * scf/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3447 * scf/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3448 * utils/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3449 * utils/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3450 * ztr/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3451 * ztr/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3452 (11:25:03) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3453 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3454 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3455 (11:48:43) Updates to automake/conf system. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3456 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3457 * Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3458 * Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3459 * Attic/config.guess, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3460 * Attic/config.h.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3461 * Attic/config.sub, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3462 * Attic/configure, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3463 * Attic/depcomp, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3464 * Attic/ltmain.sh: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3465 (11:48:44) Updates to automake/conf system. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3466 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3467 * abi/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3468 * abi/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3469 * alf/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3470 * alf/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3471 * ctf/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3472 * ctf/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3473 * exp_file/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3474 * exp_file/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3475 * plain/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3476 * plain/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3477 * progs/Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3478 * progs/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3479 (11:48:50) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3480 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3481 * progs/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3482 * read/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3483 * read/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3484 * read/Read.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3485 * scf/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3486 * scf/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3487 * utils/Attic/Makefile.am, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3488 * utils/Attic/Makefile.in, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3489 * ztr/Attic/Makefile.am: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3490 (11:48:51) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3491 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3492 * ztr/Attic/Makefile.in: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3493 (11:48:54) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3494 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3495 * read/Read.h: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3496 (11:56:56) *** empty log message *** |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3497 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3498 2003-06-09 James Bonfield <jkb@sanger.ac.uk> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3499 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3500 * CHANGES, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3501 * COPYRIGHT, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3502 * Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3503 * README, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3504 * options.mk, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3505 * abi/abi.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3506 * abi/fpoint.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3507 * abi/fpoint.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3508 * abi/seqIOABI.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3509 (11:24:36) Import of Staden Package 2003.0b2 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3510 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3511 * CHANGES, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3512 * COPYRIGHT, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3513 * Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3514 * README, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3515 * options.mk, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3516 * abi/abi.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3517 * abi/fpoint.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3518 * abi/fpoint.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3519 * abi/seqIOABI.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3520 (11:24:36) branches: 1.1.1; Initial revision |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3521 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3522 * abi/seqIOABI.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3523 * alf/alf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3524 * alf/seqIOALF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3525 * ctf/ctfCompress.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3526 * ctf/seqIOCTF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3527 * ctf/seqIOCTF.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3528 * exp_file/expFileIO.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3529 * exp_file/expFileIO.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3530 * plain/plain.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3531 * plain/seqIOPlain.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3532 * progs/Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3533 * progs/convert_trace.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3534 * progs/extract_seq.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3535 * progs/get_comment.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3536 * progs/index_tar.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3537 * progs/makeSCF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3538 * progs/scf_dump.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3539 * progs/scf_info.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3540 * progs/scf_update.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3541 * progs/trace_dump.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3542 * read/Read.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3543 * read/Read.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3544 * read/scf_extras.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3545 * read/scf_extras.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3546 * read/translate.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3547 * read/translate.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3548 * scf/misc_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3549 * scf/read_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3550 * scf/scf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3551 * scf/write_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3552 * utils/array.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3553 * utils/array.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3554 * utils/compress.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3555 * utils/compress.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3556 * utils/error.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3557 * utils/error.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3558 * utils/files.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3559 * utils/find.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3560 * utils/mach-io.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3561 * utils/mach-io.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3562 * utils/misc.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3563 * utils/open_trace_file.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3564 * utils/open_trace_file.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3565 * utils/read_alloc.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3566 * utils/strings.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3567 * utils/tar_format.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3568 * utils/traceType.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3569 (11:24:37) Import of Staden Package 2003.0b2 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3570 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3571 * abi/seqIOABI.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3572 * alf/alf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3573 * alf/seqIOALF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3574 * ctf/ctfCompress.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3575 * ctf/seqIOCTF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3576 * ctf/seqIOCTF.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3577 * exp_file/expFileIO.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3578 * exp_file/expFileIO.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3579 * plain/plain.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3580 * plain/seqIOPlain.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3581 * progs/Makefile, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3582 * progs/convert_trace.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3583 * progs/extract_seq.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3584 * progs/get_comment.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3585 * progs/index_tar.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3586 * progs/makeSCF.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3587 * progs/scf_dump.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3588 * progs/scf_info.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3589 * progs/scf_update.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3590 * progs/trace_dump.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3591 * read/Read.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3592 * read/Read.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3593 * read/scf_extras.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3594 * read/scf_extras.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3595 * read/translate.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3596 * read/translate.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3597 * scf/misc_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3598 * scf/read_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3599 * scf/scf.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3600 * scf/write_scf.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3601 * utils/array.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3602 * utils/array.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3603 * utils/compress.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3604 * utils/compress.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3605 * utils/error.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3606 * utils/error.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3607 * utils/files.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3608 * utils/find.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3609 * utils/mach-io.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3610 * utils/mach-io.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3611 * utils/misc.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3612 * utils/open_trace_file.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3613 * utils/open_trace_file.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3614 * utils/read_alloc.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3615 * utils/strings.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3616 * utils/tar_format.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3617 * utils/traceType.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3618 (11:24:37) branches: 1.1.1; Initial revision |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3619 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3620 * man/man3/ExperimentFile.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3621 * man/man3/exp2read.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3622 * man/man3/fread_reading.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3623 * man/man3/fread_scf.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3624 * man/man3/fwrite_reading.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3625 * man/man3/fwrite_scf.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3626 * man/man3/read2exp.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3627 * man/man3/read2scf.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3628 * man/man3/read_allocate.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3629 * man/man3/read_deallocate.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3630 * man/man3/read_reading.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3631 * man/man3/read_scf.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3632 * man/man3/read_scf_header.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3633 * man/man3/scf2read.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3634 * man/man3/write_reading.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3635 * man/man3/write_scf.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3636 * man/man3/write_scf_header.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3637 * man/man4/Read.4, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3638 * utils/traceType.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3639 * utils/xalloc.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3640 * utils/xalloc.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3641 * ztr/FORMAT, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3642 * ztr/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3643 * ztr/compression.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3644 * ztr/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3645 * ztr/ztr.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3646 * ztr/ztr_translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3647 (11:24:38) Import of Staden Package 2003.0b2 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3648 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3649 * man/man3/ExperimentFile.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3650 * man/man3/exp2read.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3651 * man/man3/fread_reading.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3652 * man/man3/fread_scf.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3653 * man/man3/fwrite_reading.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3654 * man/man3/fwrite_scf.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3655 * man/man3/read2exp.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3656 * man/man3/read2scf.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3657 * man/man3/read_allocate.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3658 * man/man3/read_deallocate.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3659 * man/man3/read_reading.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3660 * man/man3/read_scf.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3661 * man/man3/read_scf_header.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3662 * man/man3/scf2read.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3663 * man/man3/write_reading.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3664 * man/man3/write_scf.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3665 * man/man3/write_scf_header.3, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3666 * man/man4/Read.4, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3667 * utils/traceType.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3668 * utils/xalloc.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3669 * utils/xalloc.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3670 * ztr/FORMAT, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3671 * ztr/compression.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3672 * ztr/compression.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3673 * ztr/ztr.c, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3674 * ztr/ztr.h, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3675 * ztr/ztr_translate.c: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3676 (11:24:38) branches: 1.1.1; Initial revision |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3677 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3678 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3679 (11:59:11) Added include/.links target to main library instead of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3680 progs, thus making the build work cleanly from a newly checked out |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3681 copy. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3682 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3683 * Makefile: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3684 (14:22:43) Fix .links code. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3685 |