Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/progs/extract_seq.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 1994-1999. 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 #include <stdio.h> |
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16 #include <errno.h> |
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17 #include <string.h> |
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18 #include <strings.h> |
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19 #include <stdlib.h> |
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20 #include <unistd.h> |
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21 #include <io_lib/Read.h> |
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22 #include <io_lib/traceType.h> |
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23 #include <io_lib/expFileIO.h> |
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24 #include <io_lib/open_trace_file.h> |
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25 |
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26 /* #include "stdio_hack.h" */ |
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27 |
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28 #define LINE_LENGTH 60 |
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29 |
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30 static int do_trans(mFILE *infp, char *in_file, FILE *outfp, int format, |
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31 int good_only, int clip_cosmid, int fasta_out) { |
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32 Read *r; |
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33 char *tmp_base; |
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34 |
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35 read_sections(READ_BASES); |
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36 if (NULL == (r = mfread_reading(infp, in_file, format))) { |
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37 fprintf(stderr, "Failed to read file '%s'\n", in_file); |
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38 return 1; |
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39 } |
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40 |
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41 tmp_base = r->base; |
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42 |
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43 #ifdef IOLIB_EXP |
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44 if (good_only && r->orig_trace_format == TT_EXP) { |
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45 int left=0, right=r->NBases + 1, val, lval, rval; |
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46 Exp_info *e = (Exp_info *)r->orig_trace; |
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47 |
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48 if (0 == exp_get_int(e, EFLT_SL, &val)) |
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49 if (val > left) |
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50 left = val; |
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51 if (0 == exp_get_int(e, EFLT_QL, &val)) |
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52 if (val > left) |
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53 left = val; |
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54 |
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55 if (0 == exp_get_int(e, EFLT_SR, &val)) |
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56 if (val < right) |
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57 right = val; |
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58 if (0 == exp_get_int(e, EFLT_QR, &val)) |
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59 if (val < right) |
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60 right = val; |
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61 |
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62 /* This is horrid - see gap seqInfo.c file for explaination */ |
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63 if (clip_cosmid) { |
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64 int got_cosmid; |
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65 |
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66 if (0 == exp_get_rng(e, EFLT_CS, &lval, &rval)) { |
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67 got_cosmid = 1; |
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68 } else if (0 == exp_get_int(e, EFLT_CL, &lval) && |
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69 0 == exp_get_int(e, EFLT_CR, &rval)) { |
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70 got_cosmid = 1; |
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71 } else { |
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72 got_cosmid = 0; |
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73 } |
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74 |
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75 if (got_cosmid) { |
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76 if (lval <= left && rval <= left) ; |
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77 else if (lval <= left+1 && rval < right) left = rval; |
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78 else if (lval <= left+1 && rval >= right) right = left+1; |
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79 else if (lval < right && rval < right) right = lval; |
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80 else if (lval < right && rval >= right) right = lval; |
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81 } |
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82 } |
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83 |
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84 r->base += left; |
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85 r->NBases = right - left - 1; |
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86 } else |
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87 #endif /* IOLIB_EXP */ |
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88 if (good_only) { |
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89 r->base += r->leftCutoff; |
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90 r->NBases = r->rightCutoff - r->leftCutoff - 1; |
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91 } |
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92 |
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93 if (fasta_out) { |
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94 char *p = strrchr(in_file, '/'); |
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95 int i; |
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96 |
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97 /* Add header */ |
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98 if (NULL == p) |
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99 p = in_file; |
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100 else |
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101 p++; |
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102 fprintf(outfp, ">%s\n", p); |
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103 |
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104 /* Replace - with N */ |
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105 for (i = 0; i < r->NBases; i++) { |
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106 if (r->base[i] == '-') |
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107 r->base[i] = 'N'; |
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108 } |
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109 } |
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110 set_compression_method(0); /* We don't want to gzip the output */ |
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111 fwrite_reading(outfp, r, TT_PLN); |
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112 |
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113 r->base = tmp_base; |
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114 read_deallocate(r); |
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115 fflush(outfp); |
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116 |
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117 return 0; |
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118 } |
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119 |
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120 static void usage(void) { |
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121 fprintf(stderr, "Usage: extract_seq [-r] [-(abi|alf|scf|exp|pln|ctf|ztr)]\n" |
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122 " [-good_only] [-clip_cosmid] [-fasta_out]\n" |
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123 " [-output output_name] [input_name] ...\n"); |
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124 exit(1); |
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125 } |
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126 |
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127 int main(int argc, char **argv) { |
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128 int from_stdin = 1; |
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129 mFILE *infp = mstdin(); |
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130 FILE *outfp = stdout; |
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131 int format = TT_ANY; |
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132 int redirect = 1; |
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133 int good_only = 0; |
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134 int clip_cosmid = 0; |
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135 int fasta_out = 0; |
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136 int ret = 0; |
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137 char *fofn = NULL; |
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138 |
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139 for (argc--, argv++; argc > 0; argc--, argv++) { |
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140 if (strcmp(*argv, "-r") == 0) { |
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141 redirect = 0; |
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142 } else if (strcasecmp(*argv, "-abi") == 0) { |
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143 format = TT_ABI; |
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144 } else if (strcasecmp(*argv, "-alf") == 0) { |
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145 format = TT_ALF; |
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146 } else if (strcasecmp(*argv, "-scf") == 0) { |
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147 format = TT_SCF; |
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148 } else if (strcasecmp(*argv, "-exp") == 0) { |
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149 format = TT_EXP; |
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150 } else if (strcasecmp(*argv, "-pln") == 0) { |
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151 format = TT_PLN; |
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152 } else if (strcasecmp(*argv, "-ztr") == 0) { |
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153 format = TT_ZTR; |
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154 } else if (strcasecmp(*argv, "-ctf") == 0) { |
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155 format = TT_CTF; |
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156 } else if (strcasecmp(*argv, "-good_only") == 0) { |
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157 good_only = 1; |
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158 } else if (strcasecmp(*argv, "-clip_cosmid") == 0) { |
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159 clip_cosmid = 1; |
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160 } else if (strcasecmp(*argv, "-fasta_out") == 0) { |
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161 fasta_out = 1; |
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162 } else if (strcmp(*argv, "-fofn") == 0) { |
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163 fofn = *++argv; |
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164 argc--; |
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165 from_stdin = 0; |
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166 } else if (strcasecmp(*argv, "-output") == 0) { |
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167 if (NULL == (outfp = fopen(*++argv, "wb"))) { |
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168 perror(*argv); |
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169 return 1; |
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170 } |
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171 argc--; |
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172 } else if (**argv != '-') { |
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173 from_stdin = 0; |
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174 break; |
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175 } else { |
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176 usage(); |
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177 } |
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178 } |
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179 |
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180 read_experiment_redirect(redirect); |
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181 |
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182 if (!from_stdin) { |
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183 if (fofn) { |
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184 FILE *fofn_fp; |
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185 char line[8192]; |
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186 |
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187 if (strcmp(fofn, "stdin") == 0) |
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188 fofn_fp = stdin; |
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189 else |
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190 fofn_fp = fopen(fofn, "r"); |
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191 |
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192 if (fofn_fp) { |
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193 while (fgets(line, 8192, fofn_fp) != NULL) { |
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194 char *cp; |
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195 if (cp = strchr(line, '\n')) |
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196 *cp = 0; |
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197 if (format == TT_EXP) { |
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198 infp = open_exp_mfile(line, NULL); |
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199 } else { |
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200 infp = open_trace_mfile(line, NULL); |
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201 } |
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202 if (NULL == infp) { |
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203 perror(line); |
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204 ret = 1; |
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205 } else { |
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206 ret |= do_trans(infp, line, outfp, format, good_only, |
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207 clip_cosmid, fasta_out); |
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208 mfclose(infp); |
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209 } |
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210 } |
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211 fclose(fofn_fp); |
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212 } |
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213 } |
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214 for (;argc > 0; argc--, argv++) { |
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215 if (format == TT_EXP) { |
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216 infp = open_exp_mfile(*argv, NULL); |
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217 } else { |
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218 infp = open_trace_mfile(*argv, NULL); |
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219 } |
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220 if (NULL == infp) { |
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221 perror(*argv); |
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222 ret = 1; |
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223 } else { |
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224 ret |= do_trans(infp, *argv, outfp, format, good_only, |
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225 clip_cosmid, fasta_out); |
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226 mfclose(infp); |
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227 } |
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228 } |
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229 } else { |
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230 ret = do_trans(infp, "<stdin>", outfp, format, good_only, clip_cosmid, |
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231 fasta_out); |
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232 } |
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233 |
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234 return ret; |
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235 } |
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236 |