Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/io_lib/seqIOALF.c @ 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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0
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1 /* |
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2 * Copyright (c) Medical Research Council 1994. All rights reserved. |
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3 * |
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4 * Permission to use, copy, modify and distribute this software and its |
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5 * documentation for any purpose is hereby granted without fee, provided that |
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6 * this copyright and notice appears in all copies. |
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7 * |
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8 * This file was written by James Bonfield, Simon Dear, Rodger Staden, |
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9 * as part of the Staden Package at the MRC Laboratory of Molecular |
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10 * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom. |
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11 * |
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12 * MRC disclaims all warranties with regard to this software. |
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13 */ |
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14 |
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15 /* |
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16 * Title: seqIOALF |
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17 * |
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18 * File: seqIOALF.c |
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19 * Purpose: IO of ALF sequences |
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20 * Last update: 9th September 1994 |
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21 */ |
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22 |
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23 /* |
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24 * Change Log :- |
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25 * 14.01.91 SD |
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26 * when complimenting the sequence with an odd number of bases, |
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27 * the middle base position was not adjusted. |
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28 * 15.01.91 SD Put StLouis stuff on compilation flag |
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29 * 15.01.91 SD New include file (opp.h) |
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30 * 02.08.91 SD Changes the mapping of uncertainty codes so that we |
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31 * now only generate A C G T and - |
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32 * Previously... bug in interpreting ALF integer fields. |
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33 * We now treat them as unsigned. |
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34 * 17.09.91 LFW changed STLOUIS compilation flag to SAVE_EDITS |
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35 * and AUTO_CLIP |
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36 * 25.10.91 SD Machine independant I/O...removed BIGENDIAN flag |
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37 * 25.11.91 SD There was a hard limit (of 1024) for allocation of |
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38 * space for number of bases, yet program would |
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39 * read in more if there were any, causing nasties to happen. |
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40 * |
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41 * 11.11.92 LFW added section to actually check that the trace it |
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42 * is trying to open is an ALF file using traceType sub |
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43 * |
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44 * 10.11.92 SD SCF comments now stored in seq data structure |
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45 * 09.09.94 JKB Update to use Read instead of Seq library. |
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46 * 04.03.98 JKB Look for "Raw data" when "Processed data" is not found. |
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47 */ |
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48 |
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49 /* RMD I made substantial changes to this file 12/28/90 so as to |
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50 * read sequence data more freely (necessary when reading data from |
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51 * multiple trace files). |
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52 * The affected area is indicated by comments starting RMD, like |
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53 * this one. |
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54 */ |
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55 |
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56 /* This file was adapted by LFW from seqIOABI.c. |
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57 * The ALF results file is a concatenation of many files with an |
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58 * index structure at the beginning, consisting of a 512 byte |
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59 * block that we ignore, followed by 128 byte blocks describing |
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60 * each file. All files, including the header region, are rounded |
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61 * up to a multiple of 512 bytes long. |
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62 * The getIndexEntry routines identify the 128 byte index component |
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63 * of interest by matching 4 chars of its ASCII label, then extract |
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64 * the field of choice from that entry. |
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65 * |
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66 * Note that the SUN and PC are of opposite endian-ness, so that |
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67 * we have to provide special routines to read words and longwords |
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68 * from the results file. Luckily the floating point numbers are |
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69 * written out in ASCII. |
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70 */ |
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71 |
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72 |
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73 /* ---- Imports ---- */ |
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74 |
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75 |
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76 #include <ctype.h> |
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77 #include <stdio.h> |
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78 #include <string.h> |
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79 |
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80 #include "io_lib/stdio_hack.h" |
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81 |
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82 #include "io_lib/Read.h" |
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83 #include "io_lib/mach-io.h" |
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84 #include "io_lib/xalloc.h" |
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85 |
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86 /* ---- Constants ---- */ |
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87 |
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88 #define BasesPerLine 50 /* For output formatting */ |
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89 |
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90 #define IndexEntryLength ((off_t)128) |
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91 |
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92 |
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93 /* |
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94 * Here are some labels we will be looking for, four chars packed |
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95 * into a long word. |
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96 */ |
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97 #define EntryLabel ((uint_4) ((((('A'<<8)+'L')<<8)+'F')<<8)+' ') |
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98 #define BaseEntryLabel ((uint_4) ((((('S'<<8)+'e')<<8)+'q')<<8)+'u') |
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99 #define DataEntryLabel ((uint_4) ((((('P'<<8)+'r')<<8)+'o')<<8)+'c') |
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100 #define RawDataEntryLabel ((uint_4) ((((('R'<<8)+'a')<<8)+'w')<<8)+' ') |
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101 |
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102 /* RMD make enough space for bases - hard limit */ |
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103 #define BASELIMIT 4096 |
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104 |
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105 |
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106 /* ---- Internal functions ---- */ |
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107 |
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108 /* |
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109 * From the ALF results file connected to `fp' whose index starts |
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110 * at byte offset `indexO', return in `val' the `lw'th long word |
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111 * from the entry labelled `label'. |
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112 * The result is 0 for failure, 1 for success. |
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113 */ |
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114 static int getIndexEntryLW(FILE *fp, off_t indexO, |
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115 uint_4 label, int lw, |
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116 uint_4 *val) { |
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117 off_t entryNum=-1; |
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118 int i; |
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119 uint_4 entryLabel; |
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120 |
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121 do { |
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122 entryNum++; |
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123 if (fseek(fp, indexO+(entryNum*IndexEntryLength), 0) != 0) |
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124 return 0; |
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125 |
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126 if (!be_read_int_4(fp, &entryLabel)) |
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127 return 0; |
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128 } while (!(entryLabel == label)); |
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129 |
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130 for(i=2; i<lw; i++) |
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131 if (!be_read_int_4(fp, val)) |
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132 return 0; |
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133 |
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134 |
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135 /* when i = lw read in the 4 bytes backwards */ |
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136 if (!le_read_int_4(fp,val)) |
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137 return 0; |
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138 |
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139 return 1; |
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140 } |
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141 |
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142 /* |
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143 * From the ALF results file connected to `fp' whose index starts |
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144 * at byte offset `indexO', return in `val' the `lw'th word (int2) |
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145 * from the entry labelled `label'. |
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146 * The result is 0 for failure, 1 for success. |
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147 */ |
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148 static int getIndexEntryW(FILE *fp, off_t indexO, |
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149 uint_4 label, int lw, |
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150 uint_2 *val) { |
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151 off_t entryNum=-1; |
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152 int i; |
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153 uint_4 entryLabel; |
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154 uint_4 jval; |
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155 |
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156 do { |
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157 entryNum++; |
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158 if (fseek(fp, indexO+(entryNum*IndexEntryLength), 0) != 0) |
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159 return 0; |
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160 |
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161 if (!be_read_int_4(fp, &entryLabel)) |
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162 return 0; |
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163 } while (!(entryLabel == label)); |
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164 |
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165 |
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166 for(i=2; i<lw; i++) |
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167 if (!be_read_int_4(fp, &jval)) |
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168 return 0; |
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169 |
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170 if (!le_read_int_2(fp, val)) |
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171 return 0; |
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172 |
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173 return 1; |
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174 } |
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175 |
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176 |
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177 /* ---- Exports ---- */ |
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178 |
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179 |
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180 /* |
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181 * Read the ALF format sequence from FILE *fp into a Read structure. |
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182 * All printing characters (as defined by ANSII C `isprint') |
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183 * are accepted, but `N's are translated to `-'s. In this respect we |
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184 * are adhering (more or less) to the CSET_DEFAULT uncertainty code set. |
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185 * |
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186 * Returns: |
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187 * Read * - Success, the Read structure read. |
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188 * NULLRead - Failure. |
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189 */ |
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190 Read *fread_alf(FILE *fp) { |
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191 Read *read = NULLRead; |
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192 int i; |
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193 int numPoints; |
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194 int sections = read_sections(0); |
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195 |
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196 uint_4 data_size; |
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197 uint_4 dataO; |
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198 uint_4 header_size=396; /* size of the header of the processed data |
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199 section */ |
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200 uint_2 actBaseDataSize; /* actual number of bytes of data of information |
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201 containing the base and basePos information */ |
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202 int num_points; /* keeps track of the actual number of points, |
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203 rather than the early guess of numPoints */ |
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204 |
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205 off_t indexO; /* File offset where the index is */ |
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206 uint_4 baseO; /* File offset where the bases are stored */ |
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207 |
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208 |
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209 /* |
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210 * RMD lots of changes below here until end of data reading section |
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211 * Some are cosmetic. |
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212 * getIndexEntry calls in front of where they were needed, and made |
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213 * There is a substantive change to the inner loop of the sequence |
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214 * reading section. This now uses fscanf - much less rigid than the |
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215 * previous scheme. Note that it reads bp as a float. This is because |
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216 * it is a float in multiple trace data files! (bizarre Pharmacia |
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217 * programming!). |
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218 */ |
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219 |
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220 |
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221 /************************************************************* |
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222 * Read the various file offsets |
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223 *************************************************************/ |
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224 |
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225 /* indexO is the offset of the index. |
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226 * Or I could look for the first label, starting 'ALF' |
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227 * if I used 512 then none of the entries are on long |
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228 * word boundaries |
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229 */ |
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230 indexO = 522; |
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231 |
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232 /* offset in file of first base of sequence */ |
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233 if (! (getIndexEntryLW(fp,indexO,BaseEntryLabel,12,&baseO)) ) |
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234 goto bail_out; |
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235 |
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236 /* actual size of region containing this data */ |
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237 if (! (getIndexEntryW(fp,indexO,BaseEntryLabel,10,&actBaseDataSize)) ) |
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238 goto bail_out; |
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|
239 |
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240 /* Look for Processed data first. If we fail to find it, then look for |
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241 * the Raw data (same format). |
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242 */ |
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243 |
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244 /* offset in file to start of processed data segment - there |
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245 * is then a header of size header_size (currently 396) |
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246 */ |
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247 if (! (getIndexEntryLW(fp,indexO,DataEntryLabel,12,&dataO)) ) { |
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248 if (! (getIndexEntryLW(fp,indexO,RawDataEntryLabel,12,&dataO)) ) |
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249 goto bail_out; |
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|
250 |
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251 /* actual size of region containing this data */ |
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252 if (! (getIndexEntryLW(fp,indexO,RawDataEntryLabel,10,&data_size)) ) |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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253 goto bail_out; |
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254 } else { |
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255 /* actual size of region containing this data */ |
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256 if (! (getIndexEntryLW(fp,indexO,DataEntryLabel,10,&data_size)) ) |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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changeset
|
257 goto bail_out; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
258 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
259 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
260 /* Because each trace value is stored in a 2 byte |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
261 * integer, thus to store A C G T information |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
262 * it takes 8 bytes. So subtract off the header and |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
263 * divide by 8 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
264 */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
265 numPoints = (int)((data_size - header_size)/ 8); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
266 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
267 /* Allocate the sequence */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
268 if (NULLRead == (read = read_allocate(numPoints, BASELIMIT))) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
269 goto bail_out; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
270 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
271 /************************************************************* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
272 * Read the bases information |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
273 *************************************************************/ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
274 if (sections & READ_BASES) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
275 /* new locals introduced by LFW and/or RMD for the ALF */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
276 int numBases; /* number of nucleotides read in */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
277 float bp; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
278 char ch; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
279 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
280 if (!(fseek(fp, (off_t)baseO, 0) == 0)) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
281 goto bail_out; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
282 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
283 for (numBases = 0; (unsigned)ftell(fp) < baseO+(unsigned short)actBaseDataSize |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
284 && numBases<BASELIMIT;) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
285 char line[200]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
286 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
287 fgets(line, (int)sizeof(line), fp); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
288 sscanf(line, "%c %*d %f", &ch, &bp); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
289 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
290 /* we convert ch to Staden format here */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
291 switch (ch) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
292 case 'A': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
293 case 'C': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
294 case 'G': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
295 case 'T': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
296 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
297 default: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
298 ch = '-'; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
299 /* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
300 if (isupper(ch)) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
301 ch = '-'; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
302 else |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
303 ch = '\0'; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
304 */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
305 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
306 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
307 if (ch) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
308 read->base[numBases] = ch; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
309 read->prob_A[numBases] = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
310 read->prob_C[numBases] = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
311 read->prob_G[numBases] = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
312 read->prob_T[numBases] = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
313 read->basePos[numBases] = bp; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
314 ++numBases; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
315 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
316 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
317 read->base[numBases] = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
318 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
319 read->NBases = numBases; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
320 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
321 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
322 /************************************************************* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
323 * Read the trace information |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
324 *************************************************************/ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
325 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
326 if (sections & READ_SAMPLES) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
327 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
328 /* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
329 * Traces are stored as 2 byte integers in records in the order of |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
330 * A C G T 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
|
331 */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
332 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
333 if (fseek(fp, (off_t)(dataO+header_size), 0) != 0) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
334 goto bail_out; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
335 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
336 num_points = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
337 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
338 for (i=0; i < read->NPoints; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
339 if (!le_read_int_2(fp, &(read->traceA[i]))) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
340 goto bail_out; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
341 if (read->maxTraceVal < read->traceA[i]) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
342 read->maxTraceVal = read->traceA[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
343 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
344 if (!le_read_int_2(fp, &(read->traceC[i]))) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
345 goto bail_out; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
346 if (read->maxTraceVal < read->traceC[i]) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
347 read->maxTraceVal = read->traceC[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
348 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
349 if (!le_read_int_2(fp, &(read->traceG[i]))) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
350 goto bail_out; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
351 if (read->maxTraceVal < read->traceG[i]) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
352 read->maxTraceVal = read->traceG[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
353 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
354 if (!le_read_int_2(fp, &(read->traceT[i]))) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
355 goto bail_out; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
356 if (read->maxTraceVal < read->traceT[i]) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
357 read->maxTraceVal = read->traceT[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
358 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
359 if (read->traceA[i]==0 && read->traceT[i]==0 && |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
360 read->traceC[i]==0 && read->traceG[i]==0 && |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
361 i > (numPoints-64)) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
362 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
363 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
364 num_points++; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
365 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
366 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
367 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
368 /* SUCCESS */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
369 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
370 read->format = TT_ALF; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
371 return(read); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
372 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
373 /* FAILURE */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
374 bail_out: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
375 if (read) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
376 read_deallocate(read); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
377 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
378 return NULLRead; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
379 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
380 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
381 /* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
382 * Read the ALF format sequence with name `fn' into a Read structure. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
383 * All printing characters (as defined by ANSII C `isprint') |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
384 * are accepted, but `N's are translated to `-'s. In this respect we |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
385 * are adhering (more or less) to the CSET_DEFAULT uncertainty code set. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
386 * |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
387 * Returns: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
388 * Read * - Success, the Read structure read. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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389 * NULLRead - Failure. |
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390 */ |
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391 Read *read_alf(char *fn) { |
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392 FILE *fp; |
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393 Read *read; |
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394 |
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395 /* Open file */ |
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396 if ((fp = fopen(fn, "rb")) == NULL) |
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397 return NULLRead; |
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398 |
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399 read = fread_alf(fp); |
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400 fclose(fp); |
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401 |
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402 if (read && (read->trace_name = (char *)xmalloc(strlen(fn)+1))) |
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403 strcpy(read->trace_name, fn); |
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404 |
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405 return read; |
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406 } |
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407 |
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408 /* |
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409 * Write to an ALF file - unsupported. |
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410 */ |
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411 /* ARGSUSED */ |
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412 int write_alf(char *fn, Read *read) { |
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413 fprintf(stderr, "ALF write support is unavailable\n"); |
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414 return -1; |
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415 } |
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416 |
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417 /* |
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418 * Write to an ALF file - unsupported. |
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419 */ |
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420 /* ARGSUSED */ |
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421 int fwrite_alf(FILE *fp, Read *read) { |
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422 fprintf(stderr, "ALF write support is unavailable\n"); |
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423 return -1; |
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424 } |