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1 #include <unistd.h>
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2 #include <stdlib.h>
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3 #include <math.h>
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4 #include <zlib.h>
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5 #include <errno.h>
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6 #include "bcf.h"
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7 #include "prob1.h"
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8 #include "kstring.h"
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9 #include "time.h"
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10
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11 #include "kseq.h"
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12 KSTREAM_INIT(gzFile, gzread, 16384)
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13
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14 #define VC_NO_GENO 2
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15 #define VC_BCFOUT 4
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16 #define VC_CALL 8
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17 #define VC_VARONLY 16
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18 #define VC_VCFIN 32
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19 #define VC_UNCOMP 64
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20 #define VC_KEEPALT 256
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21 #define VC_ACGT_ONLY 512
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22 #define VC_QCALL 1024
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23 #define VC_CALL_GT 2048
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24 #define VC_ADJLD 4096
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25 #define VC_NO_INDEL 8192
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26 #define VC_ANNO_MAX 16384
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27 #define VC_FIX_PL 32768
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28 #define VC_EM 0x10000
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29
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30 typedef struct {
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31 int flag, prior_type, n1, n_sub, *sublist, n_perm;
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32 char *prior_file, **subsam, *fn_dict;
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33 uint8_t *ploidy;
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34 double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt;
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35 void *bed;
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36 } viewconf_t;
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37
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38 void *bed_read(const char *fn);
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39 void bed_destroy(void *_h);
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40 int bed_overlap(const void *_h, const char *chr, int beg, int end);
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41
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42 typedef struct {
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43 double p[4];
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44 int mq, depth, is_tested, d[4];
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45 } anno16_t;
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46
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47 static double ttest(int n1, int n2, int a[4])
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48 {
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49 extern double kf_betai(double a, double b, double x);
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50 double t, v, u1, u2;
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51 if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0;
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52 u1 = (double)a[0] / n1; u2 = (double)a[2] / n2;
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53 if (u1 <= u2) return 1.;
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54 t = (u1 - u2) / sqrt(((a[1] - n1 * u1 * u1) + (a[3] - n2 * u2 * u2)) / (n1 + n2 - 2) * (1./n1 + 1./n2));
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55 v = n1 + n2 - 2;
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56 // printf("%d,%d,%d,%d,%lf,%lf,%lf\n", a[0], a[1], a[2], a[3], t, u1, u2);
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57 return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t));
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58 }
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59
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60 static int test16_core(int anno[16], anno16_t *a)
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61 {
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62 extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
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63 double left, right;
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64 int i;
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65 a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
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66 memcpy(a->d, anno, 4 * sizeof(int));
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67 a->depth = anno[0] + anno[1] + anno[2] + anno[3];
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68 a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0);
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69 if (a->depth == 0) return -1;
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70 a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499);
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71 kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]);
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72 for (i = 1; i < 4; ++i)
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73 a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i);
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74 return 0;
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75 }
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76
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77 static int test16(bcf1_t *b, anno16_t *a)
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78 {
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79 char *p;
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80 int i, anno[16];
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81 a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
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82 a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.;
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83 a->mq = a->depth = a->is_tested = 0;
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84 if ((p = strstr(b->info, "I16=")) == 0) return -1;
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85 p += 4;
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86 for (i = 0; i < 16; ++i) {
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87 errno = 0; anno[i] = strtol(p, &p, 10);
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88 if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
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89 ++p;
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90 }
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91 return test16_core(anno, a);
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92 }
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93
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94 static void rm_info(bcf1_t *b, const char *key)
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95 {
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96 char *p, *q;
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97 if ((p = strstr(b->info, key)) == 0) return;
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98 for (q = p; *q && *q != ';'; ++q);
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99 if (p > b->info && *(p-1) == ';') --p;
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100 memmove(p, q, b->l_str - (q - b->str));
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101 b->l_str -= q - p;
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102 bcf_sync(b);
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103 }
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104
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105 static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[9])
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106 {
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107 kstring_t s;
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108 int has_I16, is_var;
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109 double fq, r;
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110 anno16_t a;
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111
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112 has_I16 = test16(b, &a) >= 0? 1 : 0;
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113 rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed!
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114
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115 memset(&s, 0, sizeof(kstring_t));
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116 kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
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117 kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
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118 kputs(b->info, &s);
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119 if (b->info[0]) kputc(';', &s);
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120 { // print EM
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121 if (em[0] >= 0) ksprintf(&s, "AF1=%.4g", 1 - em[0]);
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122 if (em[4] >= 0 && em[4] <= 0.05) ksprintf(&s, ";G3=%.4g,%.4g,%.4g;HWE=%.3g", em[3], em[2], em[1], em[4]);
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123 if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
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124 if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
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125 }
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126 if (pr == 0) { // if pr is unset, return
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127 kputc('\0', &s); kputs(b->fmt, &s); kputc('\0', &s);
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128 free(b->str);
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129 b->m_str = s.m; b->l_str = s.l; b->str = s.s;
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130 bcf_sync(b);
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131 return 1;
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132 }
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133
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134 is_var = (pr->p_ref < pref);
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135 r = is_var? pr->p_ref : pr->p_var;
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136
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137 ksprintf(&s, ";CI95=%.4g,%.4g", pr->cil, pr->cih); // FIXME: when EM is not used, ";" should be omitted!
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138 if (has_I16) ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
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139 fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded);
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140 if (fq < -999) fq = -999;
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141 if (fq > 999) fq = 999;
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142 ksprintf(&s, ";FQ=%.3g", fq);
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143 if (pr->cmp[0] >= 0.) { // two sample groups
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144 int i, q[3];
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145 for (i = 1; i < 3; ++i) {
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146 double x = pr->cmp[i] + pr->cmp[0]/2.;
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147 q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499);
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148 if (q[i] > 255) q[i] = 255;
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149 }
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150 if (pr->perm_rank >= 0) ksprintf(&s, ";PR=%d", pr->perm_rank);
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151 ksprintf(&s, ";PCHI2=%.3g;PC2=%d,%d", q[1], q[2], pr->p_chi2);
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152 }
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153 if (has_I16 && a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
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154 kputc('\0', &s);
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155 kputs(b->fmt, &s); kputc('\0', &s);
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156 free(b->str);
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157 b->m_str = s.m; b->l_str = s.l; b->str = s.s;
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158 b->qual = r < 1e-100? 999 : -4.343 * log(r);
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159 if (b->qual > 999) b->qual = 999;
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160 bcf_sync(b);
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161 if (!is_var) bcf_shrink_alt(b, 1);
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162 else if (!(flag&VC_KEEPALT))
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163 bcf_shrink_alt(b, pr->rank0 < 2? 2 : pr->rank0+1);
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164 if (is_var && (flag&VC_CALL_GT)) { // call individual genotype
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165 int i, x, old_n_gi = b->n_gi;
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166 s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
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167 kputs(":GT:GQ", &s); kputc('\0', &s);
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168 b->m_str = s.m; b->l_str = s.l; b->str = s.s;
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169 bcf_sync(b);
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170 for (i = 0; i < b->n_smpl; ++i) {
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171 x = bcf_p1_call_gt(pa, pr->f_exp, i);
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172 ((uint8_t*)b->gi[old_n_gi].data)[i] = (x&3) == 0? 1<<3|1 : (x&3) == 1? 1 : 0;
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173 ((uint8_t*)b->gi[old_n_gi+1].data)[i] = x>>2;
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174 }
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175 }
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176 return is_var;
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177 }
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178
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179 static char **read_samples(const char *fn, int *_n)
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180 {
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181 gzFile fp;
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182 kstream_t *ks;
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183 kstring_t s;
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184 int dret, n = 0, max = 0;
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185 char **sam = 0;
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186 *_n = 0;
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187 s.l = s.m = 0; s.s = 0;
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188 fp = gzopen(fn, "r");
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189 if (fp == 0) return 0; // fail to open file
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190 ks = ks_init(fp);
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191 while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
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192 int l;
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193 if (max == n) {
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194 max = max? max<<1 : 4;
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195 sam = realloc(sam, sizeof(void*)*max);
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196 }
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197 l = s.l;
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198 sam[n] = malloc(s.l + 2);
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199 strcpy(sam[n], s.s);
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200 sam[n][l+1] = 2; // by default, diploid
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201 if (dret != '\n') {
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202 if (ks_getuntil(ks, 0, &s, &dret) >= 0) { // read ploidy, 1 or 2
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203 int x = (int)s.s[0] - '0';
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204 if (x == 1 || x == 2) sam[n][l+1] = x;
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205 else fprintf(stderr, "(%s) ploidy can only be 1 or 2; assume diploid\n", __func__);
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206 }
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207 if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
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208 }
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209 ++n;
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210 }
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211 ks_destroy(ks);
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212 gzclose(fp);
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213 free(s.s);
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214 *_n = n;
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215 return sam;
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216 }
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217
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218 static void write_header(bcf_hdr_t *h)
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219 {
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220 kstring_t str;
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221 str.l = h->l_txt? h->l_txt - 1 : 0;
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222 str.m = str.l + 1; str.s = h->txt;
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223 if (!strstr(str.s, "##INFO=<ID=DP,"))
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224 kputs("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">\n", &str);
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225 if (!strstr(str.s, "##INFO=<ID=DP4,"))
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226 kputs("##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\n", &str);
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227 if (!strstr(str.s, "##INFO=<ID=MQ,"))
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228 kputs("##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Root-mean-square mapping quality of covering reads\">\n", &str);
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229 if (!strstr(str.s, "##INFO=<ID=FQ,"))
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230 kputs("##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability of all samples being the same\">\n", &str);
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231 if (!strstr(str.s, "##INFO=<ID=AF1,"))
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232 kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the site allele frequency of the first ALT allele\">\n", &str);
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233 if (!strstr(str.s, "##INFO=<ID=G3,"))
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234 kputs("##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n", &str);
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235 if (!strstr(str.s, "##INFO=<ID=HWE,"))
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236 kputs("##INFO=<ID=HWE,Number=1,Type=Float,Description=\"Chi^2 based HWE test P-value based on G3\">\n", &str);
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237 if (!strstr(str.s, "##INFO=<ID=CI95,"))
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238 kputs("##INFO=<ID=CI95,Number=2,Type=Float,Description=\"Equal-tail Bayesian credible interval of the site allele frequency at the 95% level\">\n", &str);
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239 if (!strstr(str.s, "##INFO=<ID=PV4,"))
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240 kputs("##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n", &str);
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241 if (!strstr(str.s, "##INFO=<ID=INDEL,"))
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242 kputs("##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">\n", &str);
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243 if (!strstr(str.s, "##INFO=<ID=PC2,"))
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244 kputs("##INFO=<ID=PC2,Number=2,Type=Integer,Description=\"Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.\">\n", &str);
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245 if (!strstr(str.s, "##INFO=<ID=PCHI2,"))
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246 kputs("##INFO=<ID=PCHI2,Number=1,Type=Float,Description=\"Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.\">\n", &str);
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247 if (!strstr(str.s, "##INFO=<ID=QCHI2,"))
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248 kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
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249 if (!strstr(str.s, "##INFO=<ID=RP,"))
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250 kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
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251 if (!strstr(str.s, "##FORMAT=<ID=GT,"))
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252 kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
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253 if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
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254 kputs("##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n", &str);
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255 if (!strstr(str.s, "##FORMAT=<ID=GL,"))
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256 kputs("##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)\">\n", &str);
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257 if (!strstr(str.s, "##FORMAT=<ID=DP,"))
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258 kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality bases\">\n", &str);
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259 if (!strstr(str.s, "##FORMAT=<ID=SP,"))
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260 kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
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261 if (!strstr(str.s, "##FORMAT=<ID=PL,"))
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262 kputs("##FORMAT=<ID=PL,Number=-1,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2\">\n", &str);
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263 h->l_txt = str.l + 1; h->txt = str.s;
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264 }
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265
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266 double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
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267
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268 int bcfview(int argc, char *argv[])
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269 {
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270 extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
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271 extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x);
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272 extern int bcf_fix_gt(bcf1_t *b);
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273 extern int bcf_anno_max(bcf1_t *b);
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274 extern int bcf_shuffle(bcf1_t *b, int seed);
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275 bcf_t *bp, *bout = 0;
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276 bcf1_t *b, *blast;
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277 int c, *seeds = 0;
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278 uint64_t n_processed = 0;
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279 viewconf_t vc;
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280 bcf_p1aux_t *p1 = 0;
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281 bcf_hdr_t *hin, *hout;
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282 int tid, begin, end;
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283 char moder[4], modew[4];
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284
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285 tid = begin = end = -1;
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286 memset(&vc, 0, sizeof(viewconf_t));
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287 vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1;
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288 while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:")) >= 0) {
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289 switch (c) {
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290 case '1': vc.n1 = atoi(optarg); break;
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291 case 'l': vc.bed = bed_read(optarg); break;
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292 case 'D': vc.fn_dict = strdup(optarg); break;
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293 case 'F': vc.flag |= VC_FIX_PL; break;
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294 case 'N': vc.flag |= VC_ACGT_ONLY; break;
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295 case 'G': vc.flag |= VC_NO_GENO; break;
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296 case 'A': vc.flag |= VC_KEEPALT; break;
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297 case 'b': vc.flag |= VC_BCFOUT; break;
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298 case 'S': vc.flag |= VC_VCFIN; break;
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299 case 'c': vc.flag |= VC_CALL; break;
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300 case 'e': vc.flag |= VC_EM; break;
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301 case 'v': vc.flag |= VC_VARONLY | VC_CALL; break;
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302 case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
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303 case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
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304 case 'I': vc.flag |= VC_NO_INDEL; break;
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305 case 'M': vc.flag |= VC_ANNO_MAX; break;
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306 case 't': vc.theta = atof(optarg); break;
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307 case 'p': vc.pref = atof(optarg); break;
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308 case 'i': vc.indel_frac = atof(optarg); break;
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309 case 'Q': vc.flag |= VC_QCALL; break;
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310 case 'L': vc.flag |= VC_ADJLD; break;
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311 case 'U': vc.n_perm = atoi(optarg); break;
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312 case 'C': vc.min_lrt = atof(optarg); break;
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313 case 'X': vc.min_perm_p = atof(optarg); break;
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314 case 'd': vc.min_smpl_frac = atof(optarg); break;
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315 case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
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316 vc.ploidy = calloc(vc.n_sub + 1, 1);
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317 for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
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318 tid = -1;
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319 break;
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320 case 'P':
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321 if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
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322 else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
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323 else if (strcmp(optarg, "flat") == 0) vc.prior_type = MC_PTYPE_FLAT;
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324 else vc.prior_file = strdup(optarg);
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325 break;
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326 }
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327 }
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328 if (argc == optind) {
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329 fprintf(stderr, "\n");
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330 fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
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331 fprintf(stderr, "Input/output options:\n\n");
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332 fprintf(stderr, " -A keep all possible alternate alleles at variant sites\n");
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333 fprintf(stderr, " -b output BCF instead of VCF\n");
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334 fprintf(stderr, " -D FILE sequence dictionary for VCF->BCF conversion [null]\n");
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335 fprintf(stderr, " -F PL generated by r921 or before (which generate old ordering)\n");
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336 fprintf(stderr, " -G suppress all individual genotype information\n");
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337 fprintf(stderr, " -l FILE list of sites (chr pos) or regions (BED) to output [all sites]\n");
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338 fprintf(stderr, " -L calculate LD for adjacent sites\n");
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339 fprintf(stderr, " -N skip sites where REF is not A/C/G/T\n");
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|
340 fprintf(stderr, " -Q output the QCALL likelihood format\n");
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|
341 fprintf(stderr, " -s FILE list of samples to use [all samples]\n");
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342 fprintf(stderr, " -S input is VCF\n");
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343 fprintf(stderr, " -u uncompressed BCF output (force -b)\n");
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|
344 fprintf(stderr, "\nConsensus/variant calling options:\n\n");
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|
345 fprintf(stderr, " -c SNP calling (force -e)\n");
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|
346 fprintf(stderr, " -d FLOAT skip loci where less than FLOAT fraction of samples covered [0]\n");
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|
347 fprintf(stderr, " -e likelihood based analyses\n");
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|
348 fprintf(stderr, " -g call genotypes at variant sites (force -c)\n");
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|
349 fprintf(stderr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
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350 fprintf(stderr, " -I skip indels\n");
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351 fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
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|
352 fprintf(stderr, " -P STR type of prior: full, cond2, flat [full]\n");
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353 fprintf(stderr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
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354 fprintf(stderr, " -v output potential variant sites only (force -c)\n");
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355 fprintf(stderr, "\nContrast calling and association test options:\n\n");
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|
356 fprintf(stderr, " -1 INT number of group-1 samples [0]\n");
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|
357 fprintf(stderr, " -C FLOAT posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", vc.min_lrt);
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|
358 fprintf(stderr, " -U INT number of permutations for association testing (effective with -1) [0]\n");
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|
359 fprintf(stderr, " -X FLOAT only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p);
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|
360 fprintf(stderr, "\n");
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|
361 return 1;
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|
|
362 }
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363
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364 if (vc.flag & VC_CALL) vc.flag |= VC_EM;
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|
365 if ((vc.flag & VC_VCFIN) && (vc.flag & VC_BCFOUT) && vc.fn_dict == 0) {
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366 fprintf(stderr, "[%s] For VCF->BCF conversion please specify the sequence dictionary with -D\n", __func__);
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|
367 return 1;
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|
|
368 }
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|
|
369 if (vc.n1 <= 0) vc.n_perm = 0; // TODO: give a warning here!
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|
370 if (vc.n_perm > 0) {
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|
371 seeds = malloc(vc.n_perm * sizeof(int));
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|
|
372 srand48(time(0));
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|
373 for (c = 0; c < vc.n_perm; ++c) seeds[c] = lrand48();
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|
|
374 }
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|
|
375 b = calloc(1, sizeof(bcf1_t));
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|
|
376 blast = calloc(1, sizeof(bcf1_t));
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|
|
377 strcpy(moder, "r");
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|
|
378 if (!(vc.flag & VC_VCFIN)) strcat(moder, "b");
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|
|
379 strcpy(modew, "w");
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|
|
380 if (vc.flag & VC_BCFOUT) strcat(modew, "b");
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|
|
381 if (vc.flag & VC_UNCOMP) strcat(modew, "u");
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|
|
382 bp = vcf_open(argv[optind], moder);
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|
|
383 hin = hout = vcf_hdr_read(bp);
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|
|
384 if (vc.fn_dict && (vc.flag & VC_VCFIN))
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|
|
385 vcf_dictread(bp, hin, vc.fn_dict);
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|
|
386 bout = vcf_open("-", modew);
|
|
|
387 if (!(vc.flag & VC_QCALL)) {
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|
|
388 if (vc.n_sub) {
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|
|
389 vc.sublist = calloc(vc.n_sub, sizeof(int));
|
|
|
390 hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
|
|
|
391 }
|
|
|
392 if (vc.flag & VC_CALL) write_header(hout);
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|
|
393 vcf_hdr_write(bout, hout);
|
|
|
394 }
|
|
|
395 if (vc.flag & VC_CALL) {
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|
|
396 p1 = bcf_p1_init(hout->n_smpl, vc.ploidy);
|
|
|
397 if (vc.prior_file) {
|
|
|
398 if (bcf_p1_read_prior(p1, vc.prior_file) < 0) {
|
|
|
399 fprintf(stderr, "[%s] fail to read the prior AFS.\n", __func__);
|
|
|
400 return 1;
|
|
|
401 }
|
|
|
402 } else bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
|
|
|
403 if (vc.n1 > 0 && vc.min_lrt > 0.) { // set n1
|
|
|
404 bcf_p1_set_n1(p1, vc.n1);
|
|
|
405 bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
|
|
|
406 }
|
|
|
407 if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
|
|
|
408 }
|
|
|
409 if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
|
|
|
410 void *str2id = bcf_build_refhash(hout);
|
|
|
411 if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
|
|
|
412 bcf_idx_t *idx;
|
|
|
413 idx = bcf_idx_load(argv[optind]);
|
|
|
414 if (idx) {
|
|
|
415 uint64_t off;
|
|
|
416 off = bcf_idx_query(idx, tid, begin);
|
|
|
417 if (off == 0) {
|
|
|
418 fprintf(stderr, "[%s] no records in the query region.\n", __func__);
|
|
|
419 return 1; // FIXME: a lot of memory leaks...
|
|
|
420 }
|
|
|
421 bgzf_seek(bp->fp, off, SEEK_SET);
|
|
|
422 bcf_idx_destroy(idx);
|
|
|
423 }
|
|
|
424 }
|
|
|
425 }
|
|
|
426 while (vcf_read(bp, hin, b) > 0) {
|
|
|
427 int is_indel;
|
|
|
428 double em[9];
|
|
|
429 if ((vc.flag & VC_VARONLY) && strcmp(b->alt, "X") == 0) continue;
|
|
|
430 if ((vc.flag & VC_VARONLY) && vc.min_smpl_frac > 0.) {
|
|
|
431 extern int bcf_smpl_covered(const bcf1_t *b);
|
|
|
432 int n = bcf_smpl_covered(b);
|
|
|
433 if ((double)n / b->n_smpl < vc.min_smpl_frac) continue;
|
|
|
434 }
|
|
|
435 if (vc.n_sub) bcf_subsam(vc.n_sub, vc.sublist, b);
|
|
|
436 if (vc.flag & VC_FIX_PL) bcf_fix_pl(b);
|
|
|
437 is_indel = bcf_is_indel(b);
|
|
|
438 if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
|
|
|
439 if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
|
|
|
440 int x;
|
|
|
441 if (b->ref[0] == 0 || b->ref[1] != 0) continue;
|
|
|
442 x = toupper(b->ref[0]);
|
|
|
443 if (x != 'A' && x != 'C' && x != 'G' && x != 'T') continue;
|
|
|
444 }
|
|
|
445 if (vc.bed && !bed_overlap(vc.bed, hin->ns[b->tid], b->pos, b->pos + strlen(b->ref))) continue;
|
|
|
446 if (tid >= 0) {
|
|
|
447 int l = strlen(b->ref);
|
|
|
448 l = b->pos + (l > 0? l : 1);
|
|
|
449 if (b->tid != tid || b->pos >= end) break;
|
|
|
450 if (!(l > begin && end > b->pos)) continue;
|
|
|
451 }
|
|
|
452 ++n_processed;
|
|
|
453 if (vc.flag & VC_QCALL) { // output QCALL format; STOP here
|
|
|
454 bcf_2qcall(hout, b);
|
|
|
455 continue;
|
|
|
456 }
|
|
|
457 if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0xff, em);
|
|
|
458 else {
|
|
|
459 int i;
|
|
|
460 for (i = 0; i < 9; ++i) em[i] = -1.;
|
|
|
461 }
|
|
|
462 if (vc.flag & (VC_CALL|VC_ADJLD)) bcf_gl2pl(b);
|
|
|
463 if (vc.flag & VC_CALL) { // call variants
|
|
|
464 bcf_p1rst_t pr;
|
|
|
465 int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
|
|
|
466 if (n_processed % 100000 == 0) {
|
|
|
467 fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
|
|
|
468 bcf_p1_dump_afs(p1);
|
|
|
469 }
|
|
|
470 if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
|
|
|
471 if (vc.n_perm && vc.n1 > 0 && pr.p_chi2 < vc.min_perm_p) { // permutation test
|
|
|
472 bcf_p1rst_t r;
|
|
|
473 int i, n = 0;
|
|
|
474 for (i = 0; i < vc.n_perm; ++i) {
|
|
|
475 #ifdef BCF_PERM_LRT // LRT based permutation is much faster but less robust to artifacts
|
|
|
476 double x[9];
|
|
|
477 bcf_shuffle(b, seeds[i]);
|
|
|
478 bcf_em1(b, vc.n1, 1<<7, x);
|
|
|
479 if (x[7] < em[7]) ++n;
|
|
|
480 #else
|
|
|
481 bcf_shuffle(b, seeds[i]);
|
|
|
482 bcf_p1_cal(b, 1, p1, &r);
|
|
|
483 if (pr.p_chi2 >= r.p_chi2) ++n;
|
|
|
484 #endif
|
|
|
485 }
|
|
|
486 pr.perm_rank = n;
|
|
|
487 }
|
|
|
488 if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em);
|
|
|
489 } else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em);
|
|
|
490 if (vc.flag & VC_ADJLD) { // compute LD
|
|
|
491 double f[4], r2;
|
|
|
492 if ((r2 = bcf_pair_freq(blast, b, f)) >= 0) {
|
|
|
493 kstring_t s;
|
|
|
494 s.m = s.l = 0; s.s = 0;
|
|
|
495 if (*b->info) kputc(';', &s);
|
|
|
496 ksprintf(&s, "NEIR=%.3f;NEIF4=%.3f,%.3f,%.3f,%.3f", r2, f[0], f[1], f[2], f[3]);
|
|
|
497 bcf_append_info(b, s.s, s.l);
|
|
|
498 free(s.s);
|
|
|
499 }
|
|
|
500 bcf_cpy(blast, b);
|
|
|
501 }
|
|
|
502 if (vc.flag & VC_ANNO_MAX) bcf_anno_max(b);
|
|
|
503 if (vc.flag & VC_NO_GENO) { // do not output GENO fields
|
|
|
504 b->n_gi = 0;
|
|
|
505 b->fmt[0] = '\0';
|
|
|
506 b->l_str = b->fmt - b->str + 1;
|
|
|
507 } else bcf_fix_gt(b);
|
|
|
508 vcf_write(bout, hout, b);
|
|
|
509 }
|
|
|
510 if (vc.prior_file) free(vc.prior_file);
|
|
|
511 if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
|
|
|
512 if (hin != hout) bcf_hdr_destroy(hout);
|
|
|
513 bcf_hdr_destroy(hin);
|
|
|
514 bcf_destroy(b); bcf_destroy(blast);
|
|
|
515 vcf_close(bp); vcf_close(bout);
|
|
|
516 if (vc.fn_dict) free(vc.fn_dict);
|
|
|
517 if (vc.ploidy) free(vc.ploidy);
|
|
|
518 if (vc.n_sub) {
|
|
|
519 int i;
|
|
|
520 for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]);
|
|
|
521 free(vc.subsam); free(vc.sublist);
|
|
|
522 }
|
|
|
523 if (vc.bed) bed_destroy(vc.bed);
|
|
|
524 if (seeds) free(seeds);
|
|
|
525 if (p1) bcf_p1_destroy(p1);
|
|
|
526 return 0;
|
|
|
527 }
|
