Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/progs/srf_extract_hash.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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rev | line source |
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0
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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 #ifdef HAVE_CONFIG_H |
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2 #include "io_lib_config.h" |
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3 #endif |
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4 |
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5 #include <stdio.h> |
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6 #include <math.h> |
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7 #include <string.h> |
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8 #include <stdlib.h> |
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9 #include <fcntl.h> |
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10 #include <io_lib/hash_table.h> |
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11 #include <io_lib/srf.h> |
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12 |
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13 static char qlookup[256]; |
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14 void init_qlookup(void) { |
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15 int i; |
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16 for (i = -128; i < 128; i++) { |
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17 qlookup[i+128] = '!' + (int)((10*log(1+pow(10, i/10.0))/log(10)+.499)); |
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18 } |
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19 } |
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20 |
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21 /* ------------------------------------------------------------------------ */ |
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22 |
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23 #define MAX_READ_LEN 10000 |
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24 void ztr2fastq(ztr_t *z, char *name, int calibrated) { |
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25 int i, nc, seq_len; |
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26 char buf[MAX_READ_LEN*2 + 512 + 6]; |
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27 char *seq, *qual, *sdata, *qdata; |
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28 ztr_chunk_t **chunks; |
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29 |
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30 /* Extract the sequence only */ |
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31 chunks = ztr_find_chunks(z, ZTR_TYPE_BASE, &nc); |
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32 if (nc != 1) { |
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33 fprintf(stderr, "Zero or greater than one BASE chunks found.\n"); |
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34 return; |
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35 } |
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36 uncompress_chunk(z, chunks[0]); |
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37 sdata = chunks[0]->data+1; |
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38 seq_len = chunks[0]->dlength-1; |
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39 |
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40 /* Extract the quality */ |
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41 if (calibrated) |
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42 chunks = ztr_find_chunks(z, ZTR_TYPE_CNF1, &nc); |
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43 else |
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44 chunks = ztr_find_chunks(z, ZTR_TYPE_CNF4, &nc); |
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45 |
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46 if (nc != 1) { |
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47 fprintf(stderr, "Zero or greater than one CNF chunks found.\n"); |
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48 return; |
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49 } |
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50 uncompress_chunk(z, chunks[0]); |
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51 qdata = chunks[0]->data+1; |
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52 |
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53 /* Construct fastq entry */ |
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54 seq = buf; |
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55 *seq++ = '@'; |
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56 while (*name) |
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57 *seq++ = *name++; |
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58 *seq++ = '\n'; |
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59 |
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60 qual = seq + seq_len; |
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61 *qual++ = '\n'; |
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62 *qual++ = '+'; |
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63 *qual++ = '\n'; |
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64 |
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65 for (i = 0; i < seq_len; i++) { |
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66 if (*sdata != '.') { |
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67 *seq++ = *sdata++; |
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68 } else { |
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69 *seq++ = 'N'; |
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70 sdata++; |
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71 } |
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72 *qual++ = calibrated |
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73 ? *qdata++ + '!' |
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74 : qlookup[*qdata++ + 128]; |
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75 } |
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76 *qual++ = '\n'; |
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77 |
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78 fwrite(buf, 1, qual - buf, stdout); |
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79 } |
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80 |
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81 /* ------------------------------------------------------------------------ */ |
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82 void usage(void) { |
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83 fprintf(stderr, "Usage: srf_extract [-fastq] [-c] archive_name trace_name ...\n"); |
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84 exit(1); |
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85 } |
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86 |
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87 int main(int argc, char **argv) { |
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88 FILE *fp; |
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89 srf_t *srf; |
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90 char *archive, *trace; |
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91 uint64_t cpos, hpos, dpos; |
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92 int fastq = 0, calibrated = 0, i; |
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93 |
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94 /* Parse args */ |
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95 for (i = 1; i < argc && argv[i][0] == '-'; i++) { |
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96 if (!strcmp(argv[i], "-")) { |
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97 break; |
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98 } else if (!strcmp(argv[i], "-c")) { |
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99 calibrated = 1; |
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100 } else if (!strcmp(argv[i], "-fastq")) { |
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101 fastq = 1; |
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102 } else { |
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103 usage(); |
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104 } |
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105 } |
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106 |
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107 if (argc < (i+2)) { |
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108 usage(); |
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109 } |
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110 |
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111 /* the SRF archive */ |
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112 archive = argv[i++]; |
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113 fp = fopen(archive, "rb"); |
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114 if (NULL == fp) { |
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115 perror(archive); |
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116 return 1; |
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117 } |
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118 srf = srf_create(fp); |
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119 |
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120 /* the trace */ |
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121 trace = argv[i]; |
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122 |
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123 if( fastq ){ |
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124 read_sections(READ_BASES); |
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125 init_qlookup(); |
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126 }else{ |
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127 #ifdef _WIN32 |
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128 _setmode(_fileno(stdout), _O_BINARY); |
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129 #endif |
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130 } |
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131 |
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132 /* Search index */ |
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133 switch (srf_find_trace(srf, trace, &cpos, &hpos, &dpos)) { |
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134 case -1: |
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135 fprintf(stderr, "Malformed or missing index hash. " |
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136 "Consider running srf_index_hash\n"); |
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137 return 1; |
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138 |
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139 case -2: |
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140 fprintf(stderr, "%s: not found\n", trace); |
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141 break; |
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142 |
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143 default: |
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144 /* The srf object holds the latest data and trace header blocks */ |
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145 if( fastq ){ |
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146 mFILE *mf = mfcreate(NULL, 0); |
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147 mfwrite(srf->th.trace_hdr, 1, srf->th.trace_hdr_size, mf); |
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148 mfwrite(srf->tb.trace, 1, srf->tb.trace_size, mf); |
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149 mfseek(mf, 0, SEEK_SET); |
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150 ztr_t *ztr = partial_decode_ztr(srf, mf, NULL); |
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151 ztr2fastq(ztr, trace, calibrated); |
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152 delete_ztr(ztr); |
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153 mfdestroy(mf); |
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154 } else { |
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155 fwrite(srf->th.trace_hdr, 1, srf->th.trace_hdr_size, stdout); |
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156 fwrite(srf->tb.trace, 1, srf->tb.trace_size, stdout); |
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157 } |
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158 break; |
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159 } |
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160 |
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161 return 0; |
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162 } |