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1 #include <stdio.h>
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2 #include <ctype.h>
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3 #include <errno.h>
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4 #include <assert.h>
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5 #include "bam.h"
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6 #include "bam_endian.h"
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7 #include "kstring.h"
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8 #include "sam_header.h"
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9
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10 int bam_is_be = 0, bam_verbose = 2;
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11 char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
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12
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13 /**************************
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14 * CIGAR related routines *
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15 **************************/
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16
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17 uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
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18 {
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19 uint32_t k, end;
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20 end = c->pos;
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21 for (k = 0; k < c->n_cigar; ++k) {
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22 int op = cigar[k] & BAM_CIGAR_MASK;
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23 if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
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24 end += cigar[k] >> BAM_CIGAR_SHIFT;
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25 }
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26 return end;
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27 }
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28
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29 int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
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30 {
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31 uint32_t k;
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32 int32_t l = 0;
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33 for (k = 0; k < c->n_cigar; ++k) {
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34 int op = cigar[k] & BAM_CIGAR_MASK;
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35 if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP)
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36 l += cigar[k] >> BAM_CIGAR_SHIFT;
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37 }
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38 return l;
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39 }
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40
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41 /********************
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42 * BAM I/O routines *
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43 ********************/
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44
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45 bam_header_t *bam_header_init()
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46 {
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47 bam_is_be = bam_is_big_endian();
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48 return (bam_header_t*)calloc(1, sizeof(bam_header_t));
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49 }
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50
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51 void bam_header_destroy(bam_header_t *header)
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52 {
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53 int32_t i;
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54 extern void bam_destroy_header_hash(bam_header_t *header);
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55 if (header == 0) return;
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56 if (header->target_name) {
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57 for (i = 0; i < header->n_targets; ++i)
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58 free(header->target_name[i]);
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59 free(header->target_name);
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60 free(header->target_len);
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61 }
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62 free(header->text);
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63 if (header->dict) sam_header_free(header->dict);
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64 if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
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65 bam_destroy_header_hash(header);
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66 free(header);
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67 }
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68
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69 bam_header_t *bam_header_read(bamFile fp)
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70 {
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71 bam_header_t *header;
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72 char buf[4];
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73 int magic_len;
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74 int32_t i = 1, name_len;
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75 // check EOF
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76 i = bgzf_check_EOF(fp);
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77 if (i < 0) {
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78 // If the file is a pipe, checking the EOF marker will *always* fail
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79 // with ESPIPE. Suppress the error message in this case.
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80 if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
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81 }
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82 else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
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83 // read "BAM1"
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84 magic_len = bam_read(fp, buf, 4);
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85 if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
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86 fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
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87 return 0;
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88 }
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89 header = bam_header_init();
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90 // read plain text and the number of reference sequences
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91 bam_read(fp, &header->l_text, 4);
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92 if (bam_is_be) bam_swap_endian_4p(&header->l_text);
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93 header->text = (char*)calloc(header->l_text + 1, 1);
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94 bam_read(fp, header->text, header->l_text);
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95 bam_read(fp, &header->n_targets, 4);
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96 if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
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97 // read reference sequence names and lengths
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98 header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
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99 header->target_len = (uint32_t*)calloc(header->n_targets, 4);
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100 for (i = 0; i != header->n_targets; ++i) {
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101 bam_read(fp, &name_len, 4);
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102 if (bam_is_be) bam_swap_endian_4p(&name_len);
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103 header->target_name[i] = (char*)calloc(name_len, 1);
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104 bam_read(fp, header->target_name[i], name_len);
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105 bam_read(fp, &header->target_len[i], 4);
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106 if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
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107 }
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108 return header;
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109 }
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110
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111 int bam_header_write(bamFile fp, const bam_header_t *header)
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112 {
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113 char buf[4];
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114 int32_t i, name_len, x;
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115 // write "BAM1"
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116 strncpy(buf, "BAM\001", 4);
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117 bam_write(fp, buf, 4);
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118 // write plain text and the number of reference sequences
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119 if (bam_is_be) {
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120 x = bam_swap_endian_4(header->l_text);
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121 bam_write(fp, &x, 4);
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122 if (header->l_text) bam_write(fp, header->text, header->l_text);
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123 x = bam_swap_endian_4(header->n_targets);
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124 bam_write(fp, &x, 4);
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125 } else {
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126 bam_write(fp, &header->l_text, 4);
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127 if (header->l_text) bam_write(fp, header->text, header->l_text);
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128 bam_write(fp, &header->n_targets, 4);
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129 }
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130 // write sequence names and lengths
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131 for (i = 0; i != header->n_targets; ++i) {
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132 char *p = header->target_name[i];
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133 name_len = strlen(p) + 1;
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134 if (bam_is_be) {
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135 x = bam_swap_endian_4(name_len);
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136 bam_write(fp, &x, 4);
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137 } else bam_write(fp, &name_len, 4);
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138 bam_write(fp, p, name_len);
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139 if (bam_is_be) {
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140 x = bam_swap_endian_4(header->target_len[i]);
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141 bam_write(fp, &x, 4);
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142 } else bam_write(fp, &header->target_len[i], 4);
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143 }
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144 bgzf_flush(fp);
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145 return 0;
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146 }
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147
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148 static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
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149 {
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150 uint8_t *s;
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151 uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
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152 s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
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153 for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
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154 while (s < data + data_len) {
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155 uint8_t type;
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156 s += 2; // skip key
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157 type = toupper(*s); ++s; // skip type
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158 if (type == 'C' || type == 'A') ++s;
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159 else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
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160 else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
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161 else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
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162 else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
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163 else if (type == 'B') {
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164 int32_t n, Bsize = bam_aux_type2size(*s);
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165 memcpy(&n, s + 1, 4);
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166 if (1 == Bsize) {
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167 } else if (2 == Bsize) {
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168 for (i = 0; i < n; i += 2)
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169 bam_swap_endian_2p(s + 5 + i);
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170 } else if (4 == Bsize) {
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171 for (i = 0; i < n; i += 4)
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172 bam_swap_endian_4p(s + 5 + i);
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173 }
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174 bam_swap_endian_4p(s+1);
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175 }
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176 }
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177 }
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178
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179 int bam_read1(bamFile fp, bam1_t *b)
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180 {
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181 bam1_core_t *c = &b->core;
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182 int32_t block_len, ret, i;
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183 uint32_t x[8];
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184
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185 assert(BAM_CORE_SIZE == 32);
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186 if ((ret = bam_read(fp, &block_len, 4)) != 4) {
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187 if (ret == 0) return -1; // normal end-of-file
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188 else return -2; // truncated
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189 }
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190 if (bam_read(fp, x, BAM_CORE_SIZE) != BAM_CORE_SIZE) return -3;
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191 if (bam_is_be) {
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192 bam_swap_endian_4p(&block_len);
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193 for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
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194 }
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195 c->tid = x[0]; c->pos = x[1];
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196 c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
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197 c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
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198 c->l_qseq = x[4];
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199 c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
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200 b->data_len = block_len - BAM_CORE_SIZE;
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201 if (b->m_data < b->data_len) {
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202 b->m_data = b->data_len;
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203 kroundup32(b->m_data);
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204 b->data = (uint8_t*)realloc(b->data, b->m_data);
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205 }
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206 if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
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207 b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
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208 if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
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209 return 4 + block_len;
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210 }
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211
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212 inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data)
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213 {
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214 uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y;
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215 int i;
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216 assert(BAM_CORE_SIZE == 32);
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217 x[0] = c->tid;
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218 x[1] = c->pos;
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219 x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
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220 x[3] = (uint32_t)c->flag<<16 | c->n_cigar;
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221 x[4] = c->l_qseq;
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222 x[5] = c->mtid;
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223 x[6] = c->mpos;
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224 x[7] = c->isize;
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225 bgzf_flush_try(fp, 4 + block_len);
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226 if (bam_is_be) {
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227 for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
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228 y = block_len;
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229 bam_write(fp, bam_swap_endian_4p(&y), 4);
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230 swap_endian_data(c, data_len, data);
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231 } else bam_write(fp, &block_len, 4);
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232 bam_write(fp, x, BAM_CORE_SIZE);
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233 bam_write(fp, data, data_len);
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234 if (bam_is_be) swap_endian_data(c, data_len, data);
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235 return 4 + block_len;
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236 }
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237
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238 int bam_write1(bamFile fp, const bam1_t *b)
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239 {
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240 return bam_write1_core(fp, &b->core, b->data_len, b->data);
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241 }
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242
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243 char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
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244 {
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245 uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
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246 int i;
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247 const bam1_core_t *c = &b->core;
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248 kstring_t str;
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249 str.l = str.m = 0; str.s = 0;
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250
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251 kputsn(bam1_qname(b), c->l_qname-1, &str); kputc('\t', &str);
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252 if (of == BAM_OFDEC) { kputw(c->flag, &str); kputc('\t', &str); }
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253 else if (of == BAM_OFHEX) ksprintf(&str, "0x%x\t", c->flag);
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254 else { // BAM_OFSTR
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255 for (i = 0; i < 16; ++i)
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256 if ((c->flag & 1<<i) && bam_flag2char_table[i])
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257 kputc(bam_flag2char_table[i], &str);
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258 kputc('\t', &str);
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259 }
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260 if (c->tid < 0) kputsn("*\t", 2, &str);
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261 else {
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262 if (header) kputs(header->target_name[c->tid] , &str);
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263 else kputw(c->tid, &str);
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264 kputc('\t', &str);
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265 }
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266 kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str);
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267 if (c->n_cigar == 0) kputc('*', &str);
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268 else {
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269 for (i = 0; i < c->n_cigar; ++i) {
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270 kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
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271 kputc("MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
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272 }
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273 }
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274 kputc('\t', &str);
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275 if (c->mtid < 0) kputsn("*\t", 2, &str);
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276 else if (c->mtid == c->tid) kputsn("=\t", 2, &str);
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277 else {
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278 if (header) kputs(header->target_name[c->mtid], &str);
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279 else kputw(c->mtid, &str);
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280 kputc('\t', &str);
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281 }
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282 kputw(c->mpos + 1, &str); kputc('\t', &str); kputw(c->isize, &str); kputc('\t', &str);
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283 if (c->l_qseq) {
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284 for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
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285 kputc('\t', &str);
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286 if (t[0] == 0xff) kputc('*', &str);
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287 else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
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288 } else kputsn("*\t*", 3, &str);
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289 s = bam1_aux(b);
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290 while (s < b->data + b->data_len) {
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291 uint8_t type, key[2];
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292 key[0] = s[0]; key[1] = s[1];
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293 s += 2; type = *s; ++s;
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294 kputc('\t', &str); kputsn((char*)key, 2, &str); kputc(':', &str);
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295 if (type == 'A') { kputsn("A:", 2, &str); kputc(*s, &str); ++s; }
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296 else if (type == 'C') { kputsn("i:", 2, &str); kputw(*s, &str); ++s; }
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297 else if (type == 'c') { kputsn("i:", 2, &str); kputw(*(int8_t*)s, &str); ++s; }
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298 else if (type == 'S') { kputsn("i:", 2, &str); kputw(*(uint16_t*)s, &str); s += 2; }
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299 else if (type == 's') { kputsn("i:", 2, &str); kputw(*(int16_t*)s, &str); s += 2; }
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300 else if (type == 'I') { kputsn("i:", 2, &str); kputuw(*(uint32_t*)s, &str); s += 4; }
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301 else if (type == 'i') { kputsn("i:", 2, &str); kputw(*(int32_t*)s, &str); s += 4; }
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302 else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
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303 else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; }
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304 else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
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305 else if (type == 'B') {
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306 uint8_t sub_type = *(s++);
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307 int32_t n;
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308 memcpy(&n, s, 4);
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309 s += 4; // no point to the start of the array
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310 kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing
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311 for (i = 0; i < n; ++i) {
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312 kputc(',', &str);
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313 if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; }
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314 else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
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315 else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
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316 else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
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317 else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
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318 else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
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319 else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
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320 }
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321 }
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322 }
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323 return str.s;
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324 }
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325
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326 char *bam_format1(const bam_header_t *header, const bam1_t *b)
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327 {
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328 return bam_format1_core(header, b, BAM_OFDEC);
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329 }
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330
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331 void bam_view1(const bam_header_t *header, const bam1_t *b)
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332 {
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333 char *s = bam_format1(header, b);
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334 puts(s);
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335 free(s);
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336 }
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337
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338 int bam_validate1(const bam_header_t *header, const bam1_t *b)
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339 {
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340 char *s;
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341
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342 if (b->core.tid < -1 || b->core.mtid < -1) return 0;
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343 if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0;
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344
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345 if (b->data_len < b->core.l_qname) return 0;
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346 s = memchr(bam1_qname(b), '\0', b->core.l_qname);
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347 if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0;
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348
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349 // FIXME: Other fields could also be checked, especially the auxiliary data
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350
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351 return 1;
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352 }
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353
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354 // FIXME: we should also check the LB tag associated with each alignment
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355 const char *bam_get_library(bam_header_t *h, const bam1_t *b)
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356 {
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357 const uint8_t *rg;
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358 if (h->dict == 0) h->dict = sam_header_parse2(h->text);
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359 if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
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360 rg = bam_aux_get(b, "RG");
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361 return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
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362 }
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