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1 #include <string.h>
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2 #include <math.h>
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3 #include "bcf.h"
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4 #include "kstring.h"
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5 #include "khash.h"
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6 KHASH_MAP_INIT_STR(str2id, int)
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7
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8 void *bcf_build_refhash(bcf_hdr_t *h)
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9 {
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10 khash_t(str2id) *hash;
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11 int i, ret;
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12 hash = kh_init(str2id);
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13 for (i = 0; i < h->n_ref; ++i) {
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14 khint_t k;
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15 k = kh_put(str2id, hash, h->ns[i], &ret); // FIXME: check ret
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16 kh_val(hash, k) = i;
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17 }
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18 return hash;
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19 }
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20
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21 void *bcf_str2id_init()
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22 {
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23 return kh_init(str2id);
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24 }
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25
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26 void bcf_str2id_destroy(void *_hash)
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27 {
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28 khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
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29 if (hash) kh_destroy(str2id, hash); // Note that strings are not freed.
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30 }
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31
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32 void bcf_str2id_thorough_destroy(void *_hash)
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33 {
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34 khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
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35 khint_t k;
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36 if (hash == 0) return;
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37 for (k = 0; k < kh_end(hash); ++k)
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38 if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
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39 kh_destroy(str2id, hash);
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40 }
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41
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42 int bcf_str2id(void *_hash, const char *str)
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43 {
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44 khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
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45 khint_t k;
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46 if (!hash) return -1;
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47 k = kh_get(str2id, hash, str);
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48 return k == kh_end(hash)? -1 : kh_val(hash, k);
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49 }
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50
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51 int bcf_str2id_add(void *_hash, const char *str)
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52 {
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53 khint_t k;
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54 int ret;
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55 khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
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56 if (!hash) return -1;
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57 k = kh_put(str2id, hash, str, &ret);
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58 if (ret == 0) return kh_val(hash, k);
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59 kh_val(hash, k) = kh_size(hash) - 1;
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60 return kh_val(hash, k);
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61 }
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62
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63 int bcf_shrink_alt(bcf1_t *b, int n)
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64 {
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65 char *p;
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66 int i, j, k, n_smpl = b->n_smpl;
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67 if (b->n_alleles <= n) return -1;
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68 // update ALT
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69 if (n > 1) {
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70 for (p = b->alt, k = 1; *p; ++p)
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71 if (*p == ',' && ++k == n) break;
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72 *p = '\0';
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73 } else p = b->alt, *p = '\0';
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74 ++p;
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75 memmove(p, b->flt, b->str + b->l_str - b->flt);
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76 b->l_str -= b->flt - p;
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77 // update PL
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78 for (i = 0; i < b->n_gi; ++i) {
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79 bcf_ginfo_t *g = b->gi + i;
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80 if (g->fmt == bcf_str2int("PL", 2)) {
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81 int l, x = b->n_alleles * (b->n_alleles + 1) / 2;
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82 uint8_t *d = (uint8_t*)g->data;
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83 g->len = n * (n + 1) / 2;
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84 for (l = k = 0; l < n_smpl; ++l) {
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85 uint8_t *dl = d + l * x;
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86 for (j = 0; j < g->len; ++j) d[k++] = dl[j];
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87 }
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88 } // FIXME: to add GL
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89 }
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90 b->n_alleles = n;
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91 bcf_sync(b);
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92 return 0;
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93 }
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94
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95 int bcf_gl2pl(bcf1_t *b)
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96 {
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97 char *p;
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98 int i, n_smpl = b->n_smpl;
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99 bcf_ginfo_t *g;
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100 float *d0;
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101 uint8_t *d1;
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102 if (strstr(b->fmt, "PL")) return -1;
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103 if ((p = strstr(b->fmt, "GL")) == 0) return -1;
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104 *p = 'P';
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105 for (i = 0; i < b->n_gi; ++i)
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106 if (b->gi[i].fmt == bcf_str2int("GL", 2))
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107 break;
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108 g = b->gi + i;
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109 g->fmt = bcf_str2int("PL", 2);
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110 g->len /= 4; // 4 == sizeof(float)
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111 d0 = (float*)g->data; d1 = (uint8_t*)g->data;
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112 for (i = 0; i < n_smpl * g->len; ++i) {
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113 int x = (int)(-10. * d0[i] + .499);
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114 if (x > 255) x = 255;
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115 if (x < 0) x = 0;
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116 d1[i] = x;
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117 }
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118 return 0;
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119 }
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120 /* FIXME: this function will fail given AB:GTX:GT. BCFtools never
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121 * produces such FMT, but others may do. */
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122 int bcf_fix_gt(bcf1_t *b)
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123 {
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124 char *s;
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125 int i;
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126 uint32_t tmp;
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127 bcf_ginfo_t gt;
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128 // check the presence of the GT FMT
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129 if ((s = strstr(b->fmt, ":GT")) == 0) return 0; // no GT or GT is already the first
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130 if (s[3] != '\0' && s[3] != ':') return 0; // :GTX in fact
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131 tmp = bcf_str2int("GT", 2);
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132 for (i = 0; i < b->n_gi; ++i)
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133 if (b->gi[i].fmt == tmp) break;
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134 if (i == b->n_gi) return 0; // no GT in b->gi; probably a bug...
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135 gt = b->gi[i];
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136 // move GT to the first
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137 for (; i > 0; --i) b->gi[i] = b->gi[i-1];
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138 b->gi[0] = gt;
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139 memmove(b->fmt + 3, b->fmt, s + 1 - b->fmt);
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140 b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
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141 return 0;
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142 }
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143
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144 int bcf_fix_pl(bcf1_t *b)
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145 {
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146 int i;
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147 uint32_t tmp;
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148 uint8_t *PL, *swap;
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149 bcf_ginfo_t *gi;
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150 // pinpoint PL
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151 tmp = bcf_str2int("PL", 2);
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152 for (i = 0; i < b->n_gi; ++i)
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153 if (b->gi[i].fmt == tmp) break;
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154 if (i == b->n_gi) return 0;
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155 // prepare
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156 gi = b->gi + i;
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157 PL = (uint8_t*)gi->data;
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158 swap = alloca(gi->len);
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159 // loop through individuals
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160 for (i = 0; i < b->n_smpl; ++i) {
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161 int k, l, x;
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162 uint8_t *PLi = PL + i * gi->len;
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163 memcpy(swap, PLi, gi->len);
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164 for (k = x = 0; k < b->n_alleles; ++k)
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165 for (l = k; l < b->n_alleles; ++l)
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166 PLi[l*(l+1)/2 + k] = swap[x++];
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167 }
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168 return 0;
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169 }
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170
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171 int bcf_smpl_covered(const bcf1_t *b)
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172 {
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173 int i, j, n = 0;
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174 uint32_t tmp;
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175 bcf_ginfo_t *gi;
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176 // pinpoint PL
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177 tmp = bcf_str2int("PL", 2);
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178 for (i = 0; i < b->n_gi; ++i)
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179 if (b->gi[i].fmt == tmp) break;
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180 if (i == b->n_gi) return 0;
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181 // count how many samples having PL!=[0..0]
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182 gi = b->gi + i;
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183 for (i = 0; i < b->n_smpl; ++i) {
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184 uint8_t *PLi = ((uint8_t*)gi->data) + i * gi->len;
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185 for (j = 0; j < gi->len; ++j)
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186 if (PLi[j]) break;
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187 if (j < gi->len) ++n;
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188 }
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189 return n;
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190 }
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191
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192 static void *locate_field(const bcf1_t *b, const char *fmt, int l)
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193 {
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194 int i;
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195 uint32_t tmp;
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196 tmp = bcf_str2int(fmt, l);
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197 for (i = 0; i < b->n_gi; ++i)
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198 if (b->gi[i].fmt == tmp) break;
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199 return i == b->n_gi? 0 : b->gi[i].data;
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200 }
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201
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202 int bcf_anno_max(bcf1_t *b)
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203 {
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204 int k, max_gq, max_sp, n_het;
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205 kstring_t str;
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206 uint8_t *gt, *gq;
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207 int32_t *sp;
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208 max_gq = max_sp = n_het = 0;
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209 gt = locate_field(b, "GT", 2);
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210 if (gt == 0) return -1;
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211 gq = locate_field(b, "GQ", 2);
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212 sp = locate_field(b, "SP", 2);
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213 if (sp)
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214 for (k = 0; k < b->n_smpl; ++k)
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215 if (gt[k]&0x3f)
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216 max_sp = max_sp > (int)sp[k]? max_sp : sp[k];
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217 if (gq)
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218 for (k = 0; k < b->n_smpl; ++k)
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219 if (gt[k]&0x3f)
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220 max_gq = max_gq > (int)gq[k]? max_gq : gq[k];
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221 for (k = 0; k < b->n_smpl; ++k) {
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222 int a1, a2;
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223 a1 = gt[k]&7; a2 = gt[k]>>3&7;
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224 if ((!a1 && a2) || (!a2 && a1)) { // a het
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225 if (gq == 0) ++n_het;
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226 else if (gq[k] >= 20) ++n_het;
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227 }
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228 }
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229 if (n_het) max_sp -= (int)(4.343 * log(n_het) + .499);
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230 if (max_sp < 0) max_sp = 0;
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231 memset(&str, 0, sizeof(kstring_t));
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232 if (*b->info) kputc(';', &str);
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233 ksprintf(&str, "MXSP=%d;MXGQ=%d", max_sp, max_gq);
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234 bcf_append_info(b, str.s, str.l);
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235 free(str.s);
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236 return 0;
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237 }
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238
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239 // FIXME: only data are shuffled; the header is NOT
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240 int bcf_shuffle(bcf1_t *b, int seed)
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241 {
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242 int i, j, *a;
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243 if (seed > 0) srand48(seed);
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244 a = malloc(b->n_smpl * sizeof(int));
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245 for (i = 0; i < b->n_smpl; ++i) a[i] = i;
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246 for (i = b->n_smpl; i > 1; --i) {
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247 int tmp;
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248 j = (int)(drand48() * i);
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249 tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp;
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250 }
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251 for (j = 0; j < b->n_gi; ++j) {
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252 bcf_ginfo_t *gi = b->gi + j;
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253 uint8_t *swap, *data = (uint8_t*)gi->data;
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254 swap = malloc(gi->len * b->n_smpl);
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255 for (i = 0; i < b->n_smpl; ++i)
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256 memcpy(swap + gi->len * a[i], data + gi->len * i, gi->len);
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257 free(gi->data);
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258 gi->data = swap;
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259 }
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260 free(a);
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261 return 0;
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262 }
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263
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264 bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list)
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265 {
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266 int i, ret, j;
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267 khint_t k;
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268 bcf_hdr_t *h;
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269 khash_t(str2id) *hash;
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270 kstring_t s;
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271 s.l = s.m = 0; s.s = 0;
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272 hash = kh_init(str2id);
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273 for (i = 0; i < h0->n_smpl; ++i) {
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274 k = kh_put(str2id, hash, h0->sns[i], &ret);
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275 kh_val(hash, k) = i;
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276 }
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277 for (i = j = 0; i < n; ++i) {
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278 k = kh_get(str2id, hash, samples[i]);
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279 if (k != kh_end(hash)) {
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280 list[j++] = kh_val(hash, k);
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281 kputs(samples[i], &s); kputc('\0', &s);
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282 }
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283 }
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284 if (j < n) fprintf(stderr, "<%s> %d samples in the list but not in BCF.", __func__, n - j);
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285 kh_destroy(str2id, hash);
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286 h = calloc(1, sizeof(bcf_hdr_t));
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287 *h = *h0;
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288 h->ns = 0; h->sns = 0;
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289 h->name = malloc(h->l_nm); memcpy(h->name, h0->name, h->l_nm);
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290 h->txt = calloc(1, h->l_txt + 1); memcpy(h->txt, h0->txt, h->l_txt);
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291 h->l_smpl = s.l; h->sname = s.s;
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292 bcf_hdr_sync(h);
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293 return h;
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294 }
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295
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296 int bcf_subsam(int n_smpl, int *list, bcf1_t *b)
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297 {
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298 int i, j;
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299 for (j = 0; j < b->n_gi; ++j) {
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300 bcf_ginfo_t *gi = b->gi + j;
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301 uint8_t *swap;
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302 swap = malloc(gi->len * b->n_smpl);
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303 for (i = 0; i < n_smpl; ++i)
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304 memcpy(swap + i * gi->len, (uint8_t*)gi->data + list[i] * gi->len, gi->len);
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305 free(gi->data);
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306 gi->data = swap;
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307 }
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308 b->n_smpl = n_smpl;
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309 return 0;
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310 }
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