Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/io_lib/Read.h @ 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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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 #ifndef _Read_h_ |
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16 #define _Read_h_ |
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17 |
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18 /* |
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19 * Title: Read |
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20 * |
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21 * File: Read.h |
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22 * Purpose: Read data type |
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23 * Last update: June 14 1994 |
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24 */ |
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25 |
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26 /* |
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27 * This module encodes the `Read' sequence data structure. |
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28 * |
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29 * A `Read' contains information about bases and traces which are laid |
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30 * out along a single dimension of points. The number of points in a |
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31 * paricular sequence is given by `getNPoints', and these are numbered |
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32 * 0..getNPoints-1. At each point there are four trace readings, one |
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33 * for each base. |
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34 * |
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35 * The number of bases is `getNBases' which are numbered 0..N-1. |
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36 * Bases are represented by `char's. Every base is located at a |
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37 * particular point. |
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38 * |
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39 * The behaviour of these routines is undefined if given NULLRead or |
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40 * an undefined sequence. |
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41 */ |
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42 |
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43 #include "io_lib/os.h" |
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44 #include "io_lib/scf.h" |
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45 #include "io_lib/mFILE.h" |
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46 |
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47 #ifdef __cplusplus |
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48 extern "C" { |
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49 #endif |
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50 |
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51 /* |
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52 * The autoconf setup doesn't use options.mk as the Makefile is rebuilt. |
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53 * I haven't worked out how to do the analogous via autoconf, so for now |
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54 * I take the easy approach and hard-code all formats to be enabled |
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55 */ |
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56 #ifdef HAVE_CONFIG_H |
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57 #include "io_lib_config.h" |
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58 #define IOLIB_ABI |
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59 #define IOLIB_SCF |
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60 #define IOLIB_ALF |
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61 #define IOLIB_PLN |
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62 #define IOLIB_CTF |
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63 #define IOLIB_EXP |
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64 #define IOLIB_SFF |
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65 #endif |
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66 |
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67 /* Only add ZTR support if we've got ZLIB installed */ |
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68 #ifdef HAVE_ZLIB |
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69 # ifndef IOLIB_ZTR |
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70 # define IOLIB_ZTR |
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71 # endif |
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72 #endif |
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73 |
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74 /* |
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75 *----------------------------------------------------------------------------- |
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76 * Macros |
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77 *----------------------------------------------------------------------------- |
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78 */ |
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79 |
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80 #define NULLRead ((Read *)NULL) |
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81 |
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82 /* Trace file formats */ |
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83 #define TT_ERR -1 |
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84 #define TT_UNK 0 |
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85 #define TT_SCF 1 |
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86 #define TT_ABI 2 |
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87 #define TT_ALF 3 |
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88 #define TT_PLN 4 |
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89 #define TT_EXP 5 |
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90 #define TT_CTF 6 |
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91 #define TT_ZTR 7 |
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92 #define TT_ZTR1 8 |
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93 #define TT_ZTR2 9 |
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94 #define TT_ZTR3 10 |
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95 #define TT_BIO 11 |
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96 #define TT_SFF 12 |
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97 #define TT_ANY TT_UNK |
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98 /* ANYTR is specifically any *trace* type and not EXP or PLN format */ |
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99 #define TT_ANYTR 13 |
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100 |
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101 #define READ_BASES (1<<0) |
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102 #define READ_SAMPLES (1<<1) |
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103 #define READ_COMMENTS (1<<2) |
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104 #define READ_ALL (READ_BASES | READ_SAMPLES | READ_COMMENTS) |
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105 |
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106 /* |
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107 *----------------------------------------------------------------------------- |
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108 * Structures and typedefs |
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109 *----------------------------------------------------------------------------- |
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110 */ |
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111 |
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112 typedef uint_2 TRACE; /* for trace heights */ |
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113 |
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114 typedef struct |
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115 { |
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116 int format; /* Trace file format */ |
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117 char *trace_name; /* Trace file name */ |
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118 |
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119 int NPoints; /* No. of points of data */ |
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120 int NBases; /* No. of bases */ |
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121 |
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122 /* Traces */ |
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123 TRACE *traceA; /* Array of length `NPoints' */ |
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124 TRACE *traceC; /* Array of length `NPoints' */ |
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125 TRACE *traceG; /* Array of length `NPoints' */ |
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126 TRACE *traceT; /* Array of length `NPoints' */ |
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127 TRACE maxTraceVal; /* The maximal value in any trace */ |
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128 int baseline; /* The zero offset for TRACE values */ |
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129 |
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130 /* Bases */ |
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131 char *base; /* Array of length `NBases' */ |
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132 uint_2 *basePos; /* Array of length `NBases' */ |
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133 |
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134 /* Cutoffs */ |
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135 int leftCutoff; /* Number of unwanted bases */ |
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136 int rightCutoff; /* First unwanted base at right end */ |
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137 |
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138 /* Miscellaneous Sequence Information */ |
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139 char *info; /* misc seq info, eg comments */ |
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140 |
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141 /* Probability information */ |
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142 char *prob_A; /* Array of length 'NBases' */ |
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143 char *prob_C; /* Array of length 'NBases' */ |
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144 char *prob_G; /* Array of length 'NBases' */ |
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145 char *prob_T; /* Array of length 'NBases' */ |
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146 |
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147 /* The original input format data, or NULL if inapplicable */ |
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148 int orig_trace_format; |
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149 void (*orig_trace_free)(void *ptr); |
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150 void *orig_trace; |
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151 |
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152 char *ident; /* Seq id, NULL for unknown. Malloced data. |
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153 Owned and freed by io_lib. */ |
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154 |
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155 /* Pyrosequencing "peaks" (more like spikes). NULL if not used */ |
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156 int nflows; /* Number of "flows" */ |
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157 char *flow_order; /* Bases flowed across */ |
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158 float *flow; /* Processed to be 1 base unit oriented */ |
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159 unsigned int*flow_raw; /* Unprocessed data */ |
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160 |
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161 void *private_data; /* The 'private data' block and size from SCF, */ |
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162 int private_size; /* NULL & 0 if not present. */ |
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163 } Read; |
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164 |
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165 |
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166 /* |
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167 *----------------------------------------------------------------------------- |
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168 * Function prototypes |
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169 *----------------------------------------------------------------------------- |
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170 */ |
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171 |
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172 |
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173 /* ----- Main I/O routines ----- */ |
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174 |
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175 /* |
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176 * Read a sequence from a file "fn" of format "format". If "format" is 0 |
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177 * (TT_ANY), we automatically determine the correct format. |
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178 * |
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179 * Returns: |
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180 * Read * for success |
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181 * NULLRead for failure |
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182 */ |
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183 Read *read_reading(char *fn, int format); |
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184 Read *fread_reading(FILE *fp, char *fn, int format); |
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185 Read *mfread_reading(mFILE *fp, char *fn, int format); |
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186 |
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187 |
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188 /* |
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189 * Write a sequence to a file "fn" of format "format". If "format" is 0, |
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190 * we choose our favourite - SCF. |
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191 * |
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192 * Returns: |
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193 * 0 for success |
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194 * -1 for failure |
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195 */ |
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196 int write_reading(char *fn, Read *read, int format); |
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197 int fwrite_reading(FILE *fp, Read *read, int format); |
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198 int mfwrite_reading(mFILE *fp, Read *read, int format); |
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199 |
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200 |
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201 /* ----- Utility routines ----- */ |
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202 |
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203 /* |
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204 * Allocate a new sequence, with the given sizes. |
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205 * Returns: |
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206 * "Read *" for success |
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207 * "NULLRead" for failure |
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208 */ |
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209 Read *read_allocate(int num_points, int num_bases); |
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210 |
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211 |
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212 /* |
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213 * Duplicates the read structure and optionally gives it a new filename. |
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214 * The following fields are not duplicated: |
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215 * |
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216 * int orig_trace_format; |
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217 * void (*orig_trace_free)(void *ptr); |
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218 * void *orig_trace; |
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219 * char *ident; |
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220 * |
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221 * Returns: |
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222 * "Read *" for success |
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223 * "NULLRead" for failure |
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224 */ |
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225 Read* read_dup( Read* src, const char* new_name ); |
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226 |
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227 |
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228 /* |
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229 * Free memory allocated to a sequence by read_allocate(). |
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230 */ |
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231 void read_deallocate(Read *read); |
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232 |
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233 /* unix specific file deletion routine */ |
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234 |
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235 int remove_file(char *fn); |
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236 |
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237 Read *read_abi(char *fn); |
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238 Read *fread_abi(FILE *fp); |
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239 Read *mfread_abi(mFILE *fp); |
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240 int write_abi(char *fn, Read *read); |
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241 int fwrite_abi(FILE *fp, Read *read); |
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242 int mfwrite_abi(mFILE *fp, Read *read); |
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243 |
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244 int write_alf(char *fn, Read *read); |
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245 int fwrite_alf(FILE *fp, Read *read); |
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246 int mfwrite_alf(mFILE *fp, Read *read); |
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247 Read *read_alf(char *fn); |
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248 Read *fread_alf(FILE *fp); |
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249 Read *mfread_alf(mFILE *fp); |
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250 |
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251 int write_pln(char *fn, Read *read); |
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252 int fwrite_pln(FILE *fp, Read *read); |
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253 int mfwrite_pln(mFILE *fp, Read *read); |
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254 Read *read_pln(char *fn); |
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255 Read *fread_pln(FILE *fp); |
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256 Read *mfread_pln(mFILE *fp); |
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257 |
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258 Read *read_ctf(char *fn); |
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259 Read *fread_ctf(FILE *fp); |
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260 Read *mfread_ctf(mFILE *fp); |
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261 int write_ctf(char *fn, Read *read); |
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262 int fwrite_ctf(FILE *fp, Read *read); |
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263 int mfwrite_ctf(mFILE *fp, Read *read); |
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264 |
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265 int read_sections(int sec); |
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266 |
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267 #include "io_lib/translate.h" |
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268 #include "io_lib/compress.h" |
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269 |
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270 #ifdef __cplusplus |
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271 } |
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272 #endif |
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273 |
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274 #endif /* _Read_h_ */ |