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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, bam_no_B = 0;
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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 int k, end = c->pos;
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20 for (k = 0; k < c->n_cigar; ++k) {
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21 int op = bam_cigar_op(cigar[k]);
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22 int len = bam_cigar_oplen(cigar[k]);
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23 if (op == BAM_CBACK) { // move backward
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24 int l, u, v;
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25 if (k == c->n_cigar - 1) break; // skip trailing 'B'
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26 for (l = k - 1, u = v = 0; l >= 0; --l) {
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27 int op1 = bam_cigar_op(cigar[l]);
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28 int len1 = bam_cigar_oplen(cigar[l]);
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29 if (bam_cigar_type(op1)&1) { // consume query
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30 if (u + len1 >= len) { // stop
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31 if (bam_cigar_type(op1)&2) v += len - u;
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32 break;
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33 } else u += len1;
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34 }
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35 if (bam_cigar_type(op1)&2) v += len1;
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36 }
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37 end = l < 0? c->pos : end - v;
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38 } else if (bam_cigar_type(op)&2) end += bam_cigar_oplen(cigar[k]);
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39 }
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40 return end;
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41 }
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42
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43 int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
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44 {
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45 uint32_t k;
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46 int32_t l = 0;
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47 for (k = 0; k < c->n_cigar; ++k)
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48 if (bam_cigar_type(bam_cigar_op(cigar[k]))&1)
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49 l += bam_cigar_oplen(cigar[k]);
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50 return l;
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51 }
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52
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53 /********************
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54 * BAM I/O routines *
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55 ********************/
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56
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57 bam_header_t *bam_header_init()
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58 {
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59 bam_is_be = bam_is_big_endian();
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60 return (bam_header_t*)calloc(1, sizeof(bam_header_t));
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61 }
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62
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63 void bam_header_destroy(bam_header_t *header)
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64 {
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65 int32_t i;
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66 extern void bam_destroy_header_hash(bam_header_t *header);
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67 if (header == 0) return;
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68 if (header->target_name) {
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69 for (i = 0; i < header->n_targets; ++i)
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70 free(header->target_name[i]);
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71 free(header->target_name);
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72 free(header->target_len);
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73 }
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74 free(header->text);
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75 if (header->dict) sam_header_free(header->dict);
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76 if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
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77 bam_destroy_header_hash(header);
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78 free(header);
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79 }
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80
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81 bam_header_t *bam_header_read(bamFile fp)
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82 {
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83 bam_header_t *header;
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84 char buf[4];
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85 int magic_len;
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86 int32_t i = 1, name_len;
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87 // check EOF
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88 i = bgzf_check_EOF(fp);
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89 if (i < 0) {
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90 // If the file is a pipe, checking the EOF marker will *always* fail
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91 // with ESPIPE. Suppress the error message in this case.
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92 if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
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93 }
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94 else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
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95 // read "BAM1"
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96 magic_len = bam_read(fp, buf, 4);
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97 if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
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98 fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
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99 return 0;
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100 }
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101 header = bam_header_init();
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102 // read plain text and the number of reference sequences
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103 bam_read(fp, &header->l_text, 4);
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104 if (bam_is_be) bam_swap_endian_4p(&header->l_text);
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105 header->text = (char*)calloc(header->l_text + 1, 1);
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106 bam_read(fp, header->text, header->l_text);
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107 bam_read(fp, &header->n_targets, 4);
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108 if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
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109 // read reference sequence names and lengths
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110 header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
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111 header->target_len = (uint32_t*)calloc(header->n_targets, 4);
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112 for (i = 0; i != header->n_targets; ++i) {
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113 bam_read(fp, &name_len, 4);
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114 if (bam_is_be) bam_swap_endian_4p(&name_len);
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115 header->target_name[i] = (char*)calloc(name_len, 1);
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116 bam_read(fp, header->target_name[i], name_len);
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117 bam_read(fp, &header->target_len[i], 4);
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118 if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
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119 }
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120 return header;
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121 }
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122
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123 int bam_header_write(bamFile fp, const bam_header_t *header)
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124 {
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125 char buf[4];
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126 int32_t i, name_len, x;
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127 // write "BAM1"
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128 strncpy(buf, "BAM\001", 4);
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129 bam_write(fp, buf, 4);
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130 // write plain text and the number of reference sequences
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131 if (bam_is_be) {
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132 x = bam_swap_endian_4(header->l_text);
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133 bam_write(fp, &x, 4);
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134 if (header->l_text) bam_write(fp, header->text, header->l_text);
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135 x = bam_swap_endian_4(header->n_targets);
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136 bam_write(fp, &x, 4);
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137 } else {
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138 bam_write(fp, &header->l_text, 4);
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139 if (header->l_text) bam_write(fp, header->text, header->l_text);
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140 bam_write(fp, &header->n_targets, 4);
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141 }
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142 // write sequence names and lengths
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143 for (i = 0; i != header->n_targets; ++i) {
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144 char *p = header->target_name[i];
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145 name_len = strlen(p) + 1;
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146 if (bam_is_be) {
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147 x = bam_swap_endian_4(name_len);
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148 bam_write(fp, &x, 4);
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149 } else bam_write(fp, &name_len, 4);
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150 bam_write(fp, p, name_len);
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151 if (bam_is_be) {
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152 x = bam_swap_endian_4(header->target_len[i]);
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153 bam_write(fp, &x, 4);
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154 } else bam_write(fp, &header->target_len[i], 4);
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155 }
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156 bgzf_flush(fp);
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157 return 0;
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158 }
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159
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160 static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
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161 {
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162 uint8_t *s;
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163 uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
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164 s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
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165 for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
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166 while (s < data + data_len) {
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167 uint8_t type;
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168 s += 2; // skip key
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169 type = toupper(*s); ++s; // skip type
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170 if (type == 'C' || type == 'A') ++s;
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171 else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
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172 else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
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173 else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
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174 else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
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175 else if (type == 'B') {
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176 int32_t n, Bsize = bam_aux_type2size(*s);
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177 memcpy(&n, s + 1, 4);
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178 if (1 == Bsize) {
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179 } else if (2 == Bsize) {
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180 for (i = 0; i < n; i += 2)
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181 bam_swap_endian_2p(s + 5 + i);
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182 } else if (4 == Bsize) {
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183 for (i = 0; i < n; i += 4)
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184 bam_swap_endian_4p(s + 5 + i);
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185 }
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186 bam_swap_endian_4p(s+1);
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187 }
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188 }
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189 }
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190
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191 int bam_read1(bamFile fp, bam1_t *b)
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192 {
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193 bam1_core_t *c = &b->core;
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194 int32_t block_len, ret, i;
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195 uint32_t x[8];
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196
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197 assert(BAM_CORE_SIZE == 32);
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198 if ((ret = bam_read(fp, &block_len, 4)) != 4) {
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199 if (ret == 0) return -1; // normal end-of-file
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200 else return -2; // truncated
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201 }
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202 if (bam_read(fp, x, BAM_CORE_SIZE) != BAM_CORE_SIZE) return -3;
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203 if (bam_is_be) {
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204 bam_swap_endian_4p(&block_len);
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205 for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
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206 }
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207 c->tid = x[0]; c->pos = x[1];
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208 c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
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209 c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
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210 c->l_qseq = x[4];
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211 c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
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212 b->data_len = block_len - BAM_CORE_SIZE;
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213 if (b->m_data < b->data_len) {
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214 b->m_data = b->data_len;
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215 kroundup32(b->m_data);
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216 b->data = (uint8_t*)realloc(b->data, b->m_data);
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217 }
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218 if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
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219 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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220 if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
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221 if (bam_no_B) bam_remove_B(b);
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222 return 4 + block_len;
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223 }
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224
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225 inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data)
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226 {
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227 uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y;
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228 int i;
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229 assert(BAM_CORE_SIZE == 32);
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230 x[0] = c->tid;
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231 x[1] = c->pos;
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232 x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
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233 x[3] = (uint32_t)c->flag<<16 | c->n_cigar;
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234 x[4] = c->l_qseq;
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235 x[5] = c->mtid;
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236 x[6] = c->mpos;
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237 x[7] = c->isize;
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238 bgzf_flush_try(fp, 4 + block_len);
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239 if (bam_is_be) {
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240 for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
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241 y = block_len;
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242 bam_write(fp, bam_swap_endian_4p(&y), 4);
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243 swap_endian_data(c, data_len, data);
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244 } else bam_write(fp, &block_len, 4);
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245 bam_write(fp, x, BAM_CORE_SIZE);
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246 bam_write(fp, data, data_len);
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247 if (bam_is_be) swap_endian_data(c, data_len, data);
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248 return 4 + block_len;
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249 }
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250
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251 int bam_write1(bamFile fp, const bam1_t *b)
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252 {
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253 return bam_write1_core(fp, &b->core, b->data_len, b->data);
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254 }
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255
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256 char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
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257 {
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258 uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
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259 int i;
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260 const bam1_core_t *c = &b->core;
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261 kstring_t str;
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262 str.l = str.m = 0; str.s = 0;
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263
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264 kputsn(bam1_qname(b), c->l_qname-1, &str); kputc('\t', &str);
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265 if (of == BAM_OFDEC) { kputw(c->flag, &str); kputc('\t', &str); }
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266 else if (of == BAM_OFHEX) ksprintf(&str, "0x%x\t", c->flag);
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267 else { // BAM_OFSTR
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268 for (i = 0; i < 16; ++i)
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269 if ((c->flag & 1<<i) && bam_flag2char_table[i])
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270 kputc(bam_flag2char_table[i], &str);
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271 kputc('\t', &str);
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272 }
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273 if (c->tid < 0) kputsn("*\t", 2, &str);
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274 else {
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275 if (header) kputs(header->target_name[c->tid] , &str);
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276 else kputw(c->tid, &str);
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277 kputc('\t', &str);
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278 }
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279 kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str);
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280 if (c->n_cigar == 0) kputc('*', &str);
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281 else {
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282 uint32_t *cigar = bam1_cigar(b);
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283 for (i = 0; i < c->n_cigar; ++i) {
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284 kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
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285 kputc(bam_cigar_opchr(cigar[i]), &str);
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286 }
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287 }
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288 kputc('\t', &str);
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289 if (c->mtid < 0) kputsn("*\t", 2, &str);
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290 else if (c->mtid == c->tid) kputsn("=\t", 2, &str);
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291 else {
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292 if (header) kputs(header->target_name[c->mtid], &str);
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293 else kputw(c->mtid, &str);
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294 kputc('\t', &str);
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295 }
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296 kputw(c->mpos + 1, &str); kputc('\t', &str); kputw(c->isize, &str); kputc('\t', &str);
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297 if (c->l_qseq) {
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298 for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
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299 kputc('\t', &str);
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300 if (t[0] == 0xff) kputc('*', &str);
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301 else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
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302 } else kputsn("*\t*", 3, &str);
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303 s = bam1_aux(b);
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304 while (s < b->data + b->data_len) {
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305 uint8_t type, key[2];
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306 key[0] = s[0]; key[1] = s[1];
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307 s += 2; type = *s; ++s;
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308 kputc('\t', &str); kputsn((char*)key, 2, &str); kputc(':', &str);
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309 if (type == 'A') { kputsn("A:", 2, &str); kputc(*s, &str); ++s; }
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310 else if (type == 'C') { kputsn("i:", 2, &str); kputw(*s, &str); ++s; }
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311 else if (type == 'c') { kputsn("i:", 2, &str); kputw(*(int8_t*)s, &str); ++s; }
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312 else if (type == 'S') { kputsn("i:", 2, &str); kputw(*(uint16_t*)s, &str); s += 2; }
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313 else if (type == 's') { kputsn("i:", 2, &str); kputw(*(int16_t*)s, &str); s += 2; }
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314 else if (type == 'I') { kputsn("i:", 2, &str); kputuw(*(uint32_t*)s, &str); s += 4; }
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315 else if (type == 'i') { kputsn("i:", 2, &str); kputw(*(int32_t*)s, &str); s += 4; }
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316 else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
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317 else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; }
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318 else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
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319 else if (type == 'B') {
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320 uint8_t sub_type = *(s++);
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321 int32_t n;
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322 memcpy(&n, s, 4);
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323 s += 4; // no point to the start of the array
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324 kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing
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325 for (i = 0; i < n; ++i) {
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326 kputc(',', &str);
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327 if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; }
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328 else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
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329 else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
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330 else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
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331 else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
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332 else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
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333 else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
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334 }
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335 }
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336 }
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337 return str.s;
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338 }
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339
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340 char *bam_format1(const bam_header_t *header, const bam1_t *b)
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341 {
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342 return bam_format1_core(header, b, BAM_OFDEC);
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343 }
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344
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345 void bam_view1(const bam_header_t *header, const bam1_t *b)
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346 {
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347 char *s = bam_format1(header, b);
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348 puts(s);
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349 free(s);
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350 }
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351
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352 int bam_validate1(const bam_header_t *header, const bam1_t *b)
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353 {
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354 char *s;
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355
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356 if (b->core.tid < -1 || b->core.mtid < -1) return 0;
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357 if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0;
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358
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359 if (b->data_len < b->core.l_qname) return 0;
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360 s = memchr(bam1_qname(b), '\0', b->core.l_qname);
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361 if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0;
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362
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363 // FIXME: Other fields could also be checked, especially the auxiliary data
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364
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365 return 1;
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|
366 }
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|
|
367
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|
368 // FIXME: we should also check the LB tag associated with each alignment
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369 const char *bam_get_library(bam_header_t *h, const bam1_t *b)
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370 {
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|
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371 const uint8_t *rg;
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372 if (h->dict == 0) h->dict = sam_header_parse2(h->text);
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373 if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
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374 rg = bam_aux_get(b, "RG");
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375 return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
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376 }
|
|
|
377
|
|
|
378 /************
|
|
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379 * Remove B *
|
|
|
380 ************/
|
|
|
381
|
|
|
382 int bam_remove_B(bam1_t *b)
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|
|
383 {
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|
|
384 int i, j, end_j, k, l, no_qual;
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|
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385 uint32_t *cigar, *new_cigar;
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|
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386 uint8_t *seq, *qual, *p;
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|
387 // test if removal is necessary
|
|
|
388 if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing
|
|
|
389 cigar = bam1_cigar(b);
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|
|
390 for (k = 0; k < b->core.n_cigar; ++k)
|
|
|
391 if (bam_cigar_op(cigar[k]) == BAM_CBACK) break;
|
|
|
392 if (k == b->core.n_cigar) return 0; // no 'B'
|
|
|
393 if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed
|
|
|
394 // allocate memory for the new CIGAR
|
|
|
395 if (b->data_len + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory
|
|
|
396 b->m_data = b->data_len + b->core.n_cigar * 4;
|
|
|
397 kroundup32(b->m_data);
|
|
|
398 b->data = (uint8_t*)realloc(b->data, b->m_data);
|
|
|
399 cigar = bam1_cigar(b); // after realloc, cigar may be changed
|
|
|
400 }
|
|
|
401 new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data
|
|
|
402 // the core loop
|
|
|
403 seq = bam1_seq(b); qual = bam1_qual(b);
|
|
|
404 no_qual = (qual[0] == 0xff); // test whether base quality is available
|
|
|
405 i = j = 0; end_j = -1;
|
|
|
406 for (k = l = 0; k < b->core.n_cigar; ++k) {
|
|
|
407 int op = bam_cigar_op(cigar[k]);
|
|
|
408 int len = bam_cigar_oplen(cigar[k]);
|
|
|
409 if (op == BAM_CBACK) { // the backward operation
|
|
|
410 int t, u;
|
|
|
411 if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR
|
|
|
412 if (len > j) goto rmB_err; // an excessively long backward
|
|
|
413 for (t = l - 1, u = 0; t >= 0; --t) { // look back
|
|
|
414 int op1 = bam_cigar_op(new_cigar[t]);
|
|
|
415 int len1 = bam_cigar_oplen(new_cigar[t]);
|
|
|
416 if (bam_cigar_type(op1)&1) { // consume the query
|
|
|
417 if (u + len1 >= len) { // stop
|
|
|
418 new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT;
|
|
|
419 break;
|
|
|
420 } else u += len1;
|
|
|
421 }
|
|
|
422 }
|
|
|
423 if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation
|
|
|
424 l = t + 1;
|
|
|
425 end_j = j; j -= len;
|
|
|
426 } else { // other CIGAR operations
|
|
|
427 new_cigar[l++] = cigar[k];
|
|
|
428 if (bam_cigar_type(op)&1) { // consume the query
|
|
|
429 if (i != j) { // no need to copy if i == j
|
|
|
430 int u, c, c0;
|
|
|
431 for (u = 0; u < len; ++u) { // construct the consensus
|
|
|
432 c = bam1_seqi(seq, i+u);
|
|
|
433 if (j + u < end_j) { // in an overlap
|
|
|
434 c0 = bam1_seqi(seq, j+u);
|
|
|
435 if (c != c0) { // a mismatch; choose the better base
|
|
|
436 if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better
|
|
|
437 bam1_seq_seti(seq, j+u, c);
|
|
|
438 qual[j+u] = qual[i+u] - qual[j+u];
|
|
|
439 } else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality
|
|
|
440 } else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u];
|
|
|
441 } else { // not in an overlap; copy over
|
|
|
442 bam1_seq_seti(seq, j+u, c);
|
|
|
443 qual[j+u] = qual[i+u];
|
|
|
444 }
|
|
|
445 }
|
|
|
446 }
|
|
|
447 i += len, j += len;
|
|
|
448 }
|
|
|
449 }
|
|
|
450 }
|
|
|
451 if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified
|
|
|
452 // merge adjacent operations if possible
|
|
|
453 for (k = 1; k < l; ++k)
|
|
|
454 if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1]))
|
|
|
455 new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf;
|
|
|
456 // kill zero length operations
|
|
|
457 for (k = i = 0; k < l; ++k)
|
|
|
458 if (new_cigar[k] >> BAM_CIGAR_SHIFT)
|
|
|
459 new_cigar[i++] = new_cigar[k];
|
|
|
460 l = i;
|
|
|
461 // update b
|
|
|
462 memcpy(cigar, new_cigar, l * 4); // set CIGAR
|
|
|
463 p = b->data + b->core.l_qname + l * 4;
|
|
|
464 memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ
|
|
|
465 memmove(p, qual, j); p += j; // set QUAL
|
|
|
466 memmove(p, bam1_aux(b), b->l_aux); p += b->l_aux; // set optional fields
|
|
|
467 b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length
|
|
|
468 b->data_len = p - b->data; // update record length
|
|
|
469 return 0;
|
|
|
470
|
|
|
471 rmB_err:
|
|
|
472 b->core.flag |= BAM_FUNMAP;
|
|
|
473 return -1;
|
|
|
474 }
|
