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1 #include <string.h>
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2 #include <ctype.h>
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3 #include <stdio.h>
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4 #include "kstring.h"
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5 #include "bcf.h"
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6
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7 bcf_t *bcf_open(const char *fn, const char *mode)
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8 {
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9 bcf_t *b;
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10 b = calloc(1, sizeof(bcf_t));
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11 if (strchr(mode, 'w')) {
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12 b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdout), mode);
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13 } else {
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14 b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
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15 }
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16 return b;
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17 }
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18
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19 int bcf_close(bcf_t *b)
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20 {
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21 int ret;
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22 if (b == 0) return 0;
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23 ret = bgzf_close(b->fp);
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24 free(b);
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25 return ret;
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26 }
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27
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28 int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h)
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29 {
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30 if (b == 0 || h == 0) return -1;
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31 bgzf_write(b->fp, "BCF\4", 4);
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32 bgzf_write(b->fp, &h->l_nm, 4);
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33 bgzf_write(b->fp, h->name, h->l_nm);
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34 bgzf_write(b->fp, &h->l_smpl, 4);
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35 bgzf_write(b->fp, h->sname, h->l_smpl);
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36 bgzf_write(b->fp, &h->l_txt, 4);
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37 bgzf_write(b->fp, h->txt, h->l_txt);
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38 bgzf_flush(b->fp);
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39 return 16 + h->l_nm + h->l_smpl + h->l_txt;
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40 }
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41
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42 bcf_hdr_t *bcf_hdr_read(bcf_t *b)
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43 {
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44 uint8_t magic[4];
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45 bcf_hdr_t *h;
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46 if (b == 0) return 0;
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47 h = calloc(1, sizeof(bcf_hdr_t));
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48 bgzf_read(b->fp, magic, 4);
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49 bgzf_read(b->fp, &h->l_nm, 4);
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50 h->name = malloc(h->l_nm);
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51 bgzf_read(b->fp, h->name, h->l_nm);
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52 bgzf_read(b->fp, &h->l_smpl, 4);
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53 h->sname = malloc(h->l_smpl);
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54 bgzf_read(b->fp, h->sname, h->l_smpl);
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55 bgzf_read(b->fp, &h->l_txt, 4);
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56 h->txt = malloc(h->l_txt);
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57 bgzf_read(b->fp, h->txt, h->l_txt);
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58 bcf_hdr_sync(h);
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59 return h;
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60 }
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61
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62 void bcf_hdr_destroy(bcf_hdr_t *h)
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63 {
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64 if (h == 0) return;
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65 free(h->name); free(h->sname); free(h->txt); free(h->ns); free(h->sns);
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66 free(h);
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67 }
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68
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69 static inline char **cnt_null(int l, char *str, int *_n)
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70 {
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71 int n = 0;
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72 char *p, **list;
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73 *_n = 0;
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74 if (l == 0 || str == 0) return 0;
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75 for (p = str; p != str + l; ++p)
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76 if (*p == 0) ++n;
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77 *_n = n;
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78 list = calloc(n, sizeof(void*));
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79 list[0] = str;
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80 for (p = str, n = 1; p < str + l - 1; ++p)
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81 if (*p == 0) list[n++] = p + 1;
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82 return list;
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83 }
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84
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85 int bcf_hdr_sync(bcf_hdr_t *b)
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86 {
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87 if (b == 0) return -1;
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88 if (b->ns) free(b->ns);
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89 if (b->sns) free(b->sns);
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90 if (b->l_nm) b->ns = cnt_null(b->l_nm, b->name, &b->n_ref);
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91 else b->ns = 0, b->n_ref = 0;
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92 b->sns = cnt_null(b->l_smpl, b->sname, &b->n_smpl);
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93 return 0;
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94 }
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95
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96 int bcf_sync(bcf1_t *b)
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97 {
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98 char *p, *tmp[5];
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99 int i, n, n_smpl = b->n_smpl;
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100 ks_tokaux_t aux;
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101 // set ref, alt, flt, info, fmt
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102 b->ref = b->alt = b->flt = b->info = b->fmt = 0;
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103 for (p = b->str, n = 0; p < b->str + b->l_str; ++p) {
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104 if (*p == 0 && p+1 != b->str + b->l_str) {
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105 if (n == 5) {
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106 ++n;
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107 break;
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108 } else tmp[n++] = p + 1;
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109 }
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110 }
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111 if (n != 5) {
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112 fprintf(stderr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos);
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113 return -1;
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114 }
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115 b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
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116 // set n_alleles
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117 if (*b->alt == 0) b->n_alleles = 1;
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118 else {
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119 for (p = b->alt, n = 1; *p; ++p)
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120 if (*p == ',') ++n;
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121 b->n_alleles = n + 1;
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122 }
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123 // set n_gi and gi[i].fmt
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124 for (p = b->fmt, n = 1; *p; ++p)
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125 if (*p == ':') ++n;
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126 if (n > b->m_gi) {
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127 int old_m = b->m_gi;
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128 b->m_gi = n;
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129 kroundup32(b->m_gi);
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130 b->gi = realloc(b->gi, b->m_gi * sizeof(bcf_ginfo_t));
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131 memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
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132 }
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133 b->n_gi = n;
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134 for (p = kstrtok(b->fmt, ":", &aux), n = 0; p; p = kstrtok(0, 0, &aux))
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135 b->gi[n++].fmt = bcf_str2int(p, aux.p - p);
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136 // set gi[i].len
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137 for (i = 0; i < b->n_gi; ++i) {
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138 if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
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139 b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
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140 } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
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141 b->gi[i].len = 2;
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142 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
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143 b->gi[i].len = 1;
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144 } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
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145 b->gi[i].len = 4;
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146 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
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147 b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
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148 }
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149 b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
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150 }
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151 return 0;
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152 }
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153
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154 int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
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155 {
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156 int i, l = 0;
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157 if (b == 0) return -1;
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158 bgzf_write(bp->fp, &b->tid, 4);
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159 bgzf_write(bp->fp, &b->pos, 4);
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160 bgzf_write(bp->fp, &b->qual, 4);
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161 bgzf_write(bp->fp, &b->l_str, 4);
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162 bgzf_write(bp->fp, b->str, b->l_str);
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163 l = 12 + b->l_str;
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164 for (i = 0; i < b->n_gi; ++i) {
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165 bgzf_write(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
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166 l += b->gi[i].len * h->n_smpl;
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167 }
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168 return l;
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169 }
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170
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171 int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
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172 {
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173 int i, l = 0;
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174 if (b == 0) return -1;
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175 if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
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176 b->n_smpl = h->n_smpl;
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177 bgzf_read(bp->fp, &b->pos, 4);
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178 bgzf_read(bp->fp, &b->qual, 4);
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179 bgzf_read(bp->fp, &b->l_str, 4);
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180 if (b->l_str > b->m_str) {
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181 b->m_str = b->l_str;
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182 kroundup32(b->m_str);
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183 b->str = realloc(b->str, b->m_str);
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184 }
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185 bgzf_read(bp->fp, b->str, b->l_str);
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186 l = 12 + b->l_str;
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187 if (bcf_sync(b) < 0) return -2;
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188 for (i = 0; i < b->n_gi; ++i) {
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189 bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
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190 l += b->gi[i].len * h->n_smpl;
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191 }
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192 return l;
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193 }
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194
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195 int bcf_destroy(bcf1_t *b)
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196 {
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197 int i;
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198 if (b == 0) return -1;
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199 free(b->str);
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200 for (i = 0; i < b->m_gi; ++i)
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201 free(b->gi[i].data);
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202 free(b->gi);
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203 free(b);
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204 return 0;
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205 }
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206
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207 static inline void fmt_str(const char *p, kstring_t *s)
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208 {
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209 if (*p == 0) kputc('.', s);
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210 else kputs(p, s);
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211 }
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212
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213 void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
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214 {
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215 int i, j, x;
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216 s->l = 0;
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217 if (h->n_ref) kputs(h->ns[b->tid], s);
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218 else kputw(b->tid, s);
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219 kputc('\t', s);
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220 kputw(b->pos + 1, s); kputc('\t', s);
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221 fmt_str(b->str, s); kputc('\t', s);
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222 fmt_str(b->ref, s); kputc('\t', s);
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223 fmt_str(b->alt, s); kputc('\t', s);
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224 ksprintf(s, "%.3g", b->qual); kputc('\t', s);
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225 fmt_str(b->flt, s); kputc('\t', s);
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226 fmt_str(b->info, s);
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227 if (b->fmt[0]) {
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228 kputc('\t', s);
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229 fmt_str(b->fmt, s);
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230 }
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231 x = b->n_alleles * (b->n_alleles + 1) / 2;
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232 if (b->n_gi == 0) return;
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233 int iPL = -1;
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234 if ( b->n_alleles > 2 ) {
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235 for (i=0; i<b->n_gi; i++) {
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236 if ( b->gi[i].fmt == bcf_str2int("PL", 2) ) {
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237 iPL = i;
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238 break;
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239 }
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240 }
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241 }
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242 for (j = 0; j < h->n_smpl; ++j) {
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243 int ploidy = b->ploidy ? b->ploidy[j] : 2;
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244 kputc('\t', s);
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245 for (i = 0; i < b->n_gi; ++i) {
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246 if (i) kputc(':', s);
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247 if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
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248 uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
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249 int k;
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250 if ( ploidy==1 )
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251 for (k=0; k<b->n_alleles; k++)
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252 {
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253 if (k>0) kputc(',', s);
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254 kputw(d[(k+1)*(k+2)/2-1], s);
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255 }
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256 else
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257 for (k = 0; k < x; ++k) {
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258 if (k > 0) kputc(',', s);
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259 kputw(d[k], s);
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260 }
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261 } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
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262 kputw(((uint16_t*)b->gi[i].data)[j], s);
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263 } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
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264 kputw(((uint8_t*)b->gi[i].data)[j], s);
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265 } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
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266 kputw(((int32_t*)b->gi[i].data)[j], s);
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267 } else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
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268 int y = ((uint8_t*)b->gi[i].data)[j];
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269 if ( ploidy==1 )
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270 {
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271 if ( y>>7&1 )
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272 kputc('.', s);
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273 else
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274 kputc('0' + (y>>3&7), s);
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275 }
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276 else
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277 {
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278 if ( y>>7&1 )
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279 kputsn("./.", 3, s);
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280 else {
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281 kputc('0' + (y>>3&7), s);
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282 kputc("/|"[y>>6&1], s);
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283 kputc('0' + (y&7), s);
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284 }
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285 }
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286 } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
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287 float *d = (float*)b->gi[i].data + j * x;
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288 int k;
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289 //printf("- %lx\n", d);
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290 for (k = 0; k < x; ++k) {
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291 if (k > 0) kputc(',', s);
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292 ksprintf(s, "%.2f", d[k]);
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293 }
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294 } else kputc('.', s); // custom fields
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295 }
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296 }
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297 }
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298
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299 char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
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300 {
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301 kstring_t s;
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302 s.l = s.m = 0; s.s = 0;
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303 bcf_fmt_core(h, b, &s);
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304 return s.s;
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305 }
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306
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307 int bcf_append_info(bcf1_t *b, const char *info, int l)
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308 {
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309 int shift = b->fmt - b->str;
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310 int l_fmt = b->l_str - shift;
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311 char *ori = b->str;
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312 if (b->l_str + l > b->m_str) { // enlarge if necessary
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313 b->m_str = b->l_str + l;
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314 kroundup32(b->m_str);
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315 b->str = realloc(b->str, b->m_str);
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316 }
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317 memmove(b->str + shift + l, b->str + shift, l_fmt); // move the FORMAT field
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318 memcpy(b->str + shift - 1, info, l); // append to the INFO field
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319 b->str[shift + l - 1] = '\0';
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320 b->fmt = b->str + shift + l;
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321 b->l_str += l;
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322 if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
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323 return 0;
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324 }
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325
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326 int remove_tag(char *str, const char *tag, char delim)
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327 {
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328 char *tmp = str, *p;
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329 int len_diff = 0, ori_len = strlen(str);
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330 while ( *tmp && (p = strstr(tmp,tag)) )
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331 {
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332 if ( p>str )
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333 {
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334 if ( *(p-1)!=delim ) { tmp=p+1; continue; } // shared substring
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335 p--;
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336 }
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337 char *q=p+1;
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338 while ( *q && *q!=delim ) q++;
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339 if ( p==str && *q ) q++; // the tag is first, don't move the delim char
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340 len_diff += q-p;
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341 if ( ! *q ) { *p = 0; break; } // the tag was last, no delim follows
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342 else
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343 memmove(p,q,ori_len-(int)(p-str)-(int)(q-p)); // *q==delim
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344 }
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345 if ( len_diff==ori_len )
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346 str[0]='.', str[1]=0, len_diff--;
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347
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348 return len_diff;
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349 }
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350
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351
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352 void rm_info(kstring_t *s, const char *key)
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353 {
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354 char *p = s->s;
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355 int n = 0;
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356 while ( n<4 )
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357 {
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358 if ( !*p ) n++;
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359 p++;
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360 }
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361 char *q = p+1;
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362 while ( *q && q-s->s<s->l ) q++;
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363
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364 int nrm = remove_tag(p, key, ';');
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365 if ( nrm )
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366 memmove(q-nrm, q, s->s+s->l-q+1);
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367 s->l -= nrm;
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368 }
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369
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370 int bcf_cpy(bcf1_t *r, const bcf1_t *b)
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371 {
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372 char *t1 = r->str;
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373 bcf_ginfo_t *t2 = r->gi;
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374 int i, t3 = r->m_str, t4 = r->m_gi;
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375 *r = *b;
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376 r->str = t1; r->gi = t2; r->m_str = t3; r->m_gi = t4;
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377 if (r->m_str < b->m_str) {
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378 r->m_str = b->m_str;
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379 r->str = realloc(r->str, r->m_str);
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380 }
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381 memcpy(r->str, b->str, r->m_str);
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382 bcf_sync(r); // calling bcf_sync() is simple but inefficient
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383 for (i = 0; i < r->n_gi; ++i)
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384 memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len);
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385 return 0;
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386 }
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387
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388 int bcf_is_indel(const bcf1_t *b)
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389 {
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390 char *p;
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391 if (strlen(b->ref) > 1) return 1;
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392 for (p = b->alt; *p; ++p)
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393 if (*p != ',' && p[1] != ',' && p[1] != '\0')
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394 return 1;
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395 return 0;
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396 }
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