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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 #ifdef _WIN32
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12 #define srand48(x) srand(x)
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13 #define lrand48() rand()
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14 #endif
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15
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16 #include "kseq.h"
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17 KSTREAM_INIT(gzFile, gzread, 16384)
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18
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19 #define VC_NO_GENO 2
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20 #define VC_BCFOUT 4
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21 #define VC_CALL 8
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22 #define VC_VARONLY 16
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23 #define VC_VCFIN 32
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24 #define VC_UNCOMP 64
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25 #define VC_KEEPALT 256
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26 #define VC_ACGT_ONLY 512
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27 #define VC_QCALL 1024
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28 #define VC_CALL_GT 2048
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29 #define VC_ADJLD 4096
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30 #define VC_NO_INDEL 8192
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31 #define VC_ANNO_MAX 16384
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32 #define VC_FIX_PL 32768
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33 #define VC_EM 0x10000
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34 #define VC_PAIRCALL 0x20000
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35 #define VC_QCNT 0x40000
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36 #define VC_INDEL_ONLY 0x80000
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37
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38 typedef struct {
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39 int flag, prior_type, n1, n_sub, *sublist, n_perm;
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40 uint32_t *trio_aux;
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41 char *prior_file, **subsam, *fn_dict;
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42 uint8_t *ploidy;
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43 double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt, min_ma_lrt;
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44 void *bed;
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45 } viewconf_t;
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46
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47 void *bed_read(const char *fn);
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48 void bed_destroy(void *_h);
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49 int bed_overlap(const void *_h, const char *chr, int beg, int end);
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50
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51 static double ttest(int n1, int n2, int a[4])
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52 {
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53 extern double kf_betai(double a, double b, double x);
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54 double t, v, u1, u2;
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55 if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0;
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56 u1 = (double)a[0] / n1; u2 = (double)a[2] / n2;
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57 if (u1 <= u2) return 1.;
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58 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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59 v = n1 + n2 - 2;
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60 // printf("%d,%d,%d,%d,%lf,%lf,%lf\n", a[0], a[1], a[2], a[3], t, u1, u2);
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61 return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t));
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62 }
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63
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64 static int test16_core(int anno[16], anno16_t *a)
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65 {
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66 extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
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67 double left, right;
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68 int i;
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69 a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
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70 memcpy(a->d, anno, 4 * sizeof(int));
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71 a->depth = anno[0] + anno[1] + anno[2] + anno[3];
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72 a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0);
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73 if (a->depth == 0) return -1;
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74 a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499);
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75 kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]);
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76 for (i = 1; i < 4; ++i)
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77 a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i);
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78 return 0;
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79 }
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80
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81 int test16(bcf1_t *b, anno16_t *a)
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82 {
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83 char *p;
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84 int i, anno[16];
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85 a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
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86 a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.;
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87 a->mq = a->depth = a->is_tested = 0;
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88 if ((p = strstr(b->info, "I16=")) == 0) return -1;
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89 p += 4;
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90 for (i = 0; i < 16; ++i) {
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91 errno = 0; anno[i] = strtol(p, &p, 10);
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92 if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
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93 ++p;
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94 }
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95 return test16_core(anno, a);
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96 }
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97
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98 static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[10], int cons_llr, int64_t cons_gt)
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99 {
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100 kstring_t s;
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101 int has_I16, is_var;
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102 double fq, r;
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103 anno16_t a;
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104
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105 has_I16 = test16(b, &a) >= 0? 1 : 0;
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106 //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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107
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108 memset(&s, 0, sizeof(kstring_t));
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109 kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
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110 kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
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111 kputs(b->info, &s);
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112 if (b->info[0]) kputc(';', &s);
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113 { // print EM
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114 if (em[0] >= 0) ksprintf(&s, "AF1=%.4g", 1 - em[0]);
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115 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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116 if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
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117 if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
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118 if (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]);
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119 }
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120 if (cons_llr > 0) {
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121 ksprintf(&s, ";CLR=%d", cons_llr);
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122 if (cons_gt > 0)
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123 ksprintf(&s, ";UGT=%c%c%c;CGT=%c%c%c", cons_gt&0xff, cons_gt>>8&0xff, cons_gt>>16&0xff,
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124 cons_gt>>32&0xff, cons_gt>>40&0xff, cons_gt>>48&0xff);
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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 ksprintf(&s, ";AC1=%d", pr->ac);
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139 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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140 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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141 if (fq < -999) fq = -999;
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142 if (fq > 999) fq = 999;
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143 ksprintf(&s, ";FQ=%.3g", fq);
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144 if (pr->cmp[0] >= 0.) { // two sample groups
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145 int i, q[3];
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146 for (i = 1; i < 3; ++i) {
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147 double x = pr->cmp[i] + pr->cmp[0]/2.;
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148 q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499);
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149 if (q[i] > 255) q[i] = 255;
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150 }
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151 if (pr->perm_rank >= 0) ksprintf(&s, ";PR=%d", pr->perm_rank);
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152 // ksprintf(&s, ";LRT3=%.3g", pr->lrt);
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153 ksprintf(&s, ";PCHI2=%.3g;PC2=%d,%d", q[1], q[2], pr->p_chi2);
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154 }
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155 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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156 kputc('\0', &s);
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157 rm_info(&s, "QS=");
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158 rm_info(&s, "I16=");
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159 kputs(b->fmt, &s); kputc('\0', &s);
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160 free(b->str);
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161 b->m_str = s.m; b->l_str = s.l; b->str = s.s;
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162 b->qual = r < 1e-100? 999 : -4.343 * log(r);
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163 if (b->qual > 999) b->qual = 999;
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164 bcf_sync(b);
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165 if (!is_var) bcf_shrink_alt(b, 1);
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166 else if (!(flag&VC_KEEPALT))
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167 bcf_shrink_alt(b, pr->rank0 < 2? 2 : pr->rank0+1);
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168 if (is_var && (flag&VC_CALL_GT)) { // call individual genotype
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169 int i, x, old_n_gi = b->n_gi;
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170 s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
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171 kputs(":GT:GQ", &s); kputc('\0', &s);
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172 b->m_str = s.m; b->l_str = s.l; b->str = s.s;
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173 bcf_sync(b);
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174 for (i = 0; i < b->n_smpl; ++i) {
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175 x = bcf_p1_call_gt(pa, pr->f_exp, i);
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176 ((uint8_t*)b->gi[old_n_gi].data)[i] = (x&3) == 0? 1<<3|1 : (x&3) == 1? 1 : 0;
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177 ((uint8_t*)b->gi[old_n_gi+1].data)[i] = x>>2;
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178 }
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179 }
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180 return is_var;
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181 }
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182
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183 static char **read_samples(const char *fn, int *_n)
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184 {
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185 gzFile fp;
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186 kstream_t *ks;
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187 kstring_t s;
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188 int dret, n = 0, max = 0;
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189 char **sam = 0;
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190 *_n = 0;
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191 s.l = s.m = 0; s.s = 0;
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192 fp = gzopen(fn, "r");
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193 if (fp == 0)
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194 {
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195 // interpret as sample names, not as a file name
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196 const char *t = fn, *p = t;
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197 while (*t)
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198 {
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199 t++;
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200 if ( *t==',' || !*t )
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201 {
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202 sam = realloc(sam, sizeof(void*)*(n+1));
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203 sam[n] = (char*) malloc(sizeof(char)*(t-p+2));
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204 memcpy(sam[n], p, t-p);
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205 sam[n][t-p] = 0;
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206 sam[n][t-p+1] = 2; // assume diploid
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207 p = t+1;
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208 n++;
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209 }
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210 }
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211 *_n = n;
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212 return sam; // fail to open file
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213 }
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214 ks = ks_init(fp);
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215 while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
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216 int l;
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217 if (max == n) {
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218 max = max? max<<1 : 4;
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219 sam = realloc(sam, sizeof(void*)*max);
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220 }
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221 l = s.l;
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222 sam[n] = malloc(s.l + 2);
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223 strcpy(sam[n], s.s);
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224 sam[n][l+1] = 2; // by default, diploid
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225 if (dret != '\n') {
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226 if (ks_getuntil(ks, 0, &s, &dret) >= 0) { // read ploidy, 1 or 2
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227 int x = (int)s.s[0] - '0';
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228 if (x == 1 || x == 2) sam[n][l+1] = x;
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229 else fprintf(stderr, "(%s) ploidy can only be 1 or 2; assume diploid\n", __func__);
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230 }
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231 if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
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232 }
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233 ++n;
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234 }
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235 ks_destroy(ks);
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236 gzclose(fp);
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237 free(s.s);
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238 *_n = n;
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239 return sam;
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240 }
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241
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242 static void write_header(bcf_hdr_t *h)
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243 {
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244 kstring_t str;
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245 str.l = h->l_txt? h->l_txt - 1 : 0;
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246 str.m = str.l + 1; str.s = h->txt;
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247 if (!strstr(str.s, "##INFO=<ID=DP,"))
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248 kputs("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">\n", &str);
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249 if (!strstr(str.s, "##INFO=<ID=DP4,"))
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250 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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251 if (!strstr(str.s, "##INFO=<ID=MQ,"))
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252 kputs("##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Root-mean-square mapping quality of covering reads\">\n", &str);
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253 if (!strstr(str.s, "##INFO=<ID=FQ,"))
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254 kputs("##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability of all samples being the same\">\n", &str);
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255 if (!strstr(str.s, "##INFO=<ID=AF1,"))
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256 kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele frequency (assuming HWE)\">\n", &str);
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257 if (!strstr(str.s, "##INFO=<ID=AC1,"))
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258 kputs("##INFO=<ID=AC1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele count (no HWE assumption)\">\n", &str);
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259 if (!strstr(str.s, "##INFO=<ID=AN,"))
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260 kputs("##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">\n", &str);
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261 if (!strstr(str.s, "##INFO=<ID=IS,"))
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262 kputs("##INFO=<ID=IS,Number=2,Type=Float,Description=\"Maximum number of reads supporting an indel and fraction of indel reads\">\n", &str);
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263 if (!strstr(str.s, "##INFO=<ID=AC,"))
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264 kputs("##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes for each ALT allele, in the same order as listed\">\n", &str);
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265 if (!strstr(str.s, "##INFO=<ID=G3,"))
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266 kputs("##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n", &str);
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267 if (!strstr(str.s, "##INFO=<ID=HWE,"))
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268 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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269 if (!strstr(str.s, "##INFO=<ID=CLR,"))
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270 kputs("##INFO=<ID=CLR,Number=1,Type=Integer,Description=\"Log ratio of genotype likelihoods with and without the constraint\">\n", &str);
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271 if (!strstr(str.s, "##INFO=<ID=UGT,"))
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272 kputs("##INFO=<ID=UGT,Number=1,Type=String,Description=\"The most probable unconstrained genotype configuration in the trio\">\n", &str);
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273 if (!strstr(str.s, "##INFO=<ID=CGT,"))
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274 kputs("##INFO=<ID=CGT,Number=1,Type=String,Description=\"The most probable constrained genotype configuration in the trio\">\n", &str);
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275 // if (!strstr(str.s, "##INFO=<ID=CI95,"))
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276 // 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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277 if (!strstr(str.s, "##INFO=<ID=PV4,"))
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278 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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279 if (!strstr(str.s, "##INFO=<ID=INDEL,"))
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280 kputs("##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">\n", &str);
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281 if (!strstr(str.s, "##INFO=<ID=PC2,"))
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282 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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283 if (!strstr(str.s, "##INFO=<ID=PCHI2,"))
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284 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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285 if (!strstr(str.s, "##INFO=<ID=QCHI2,"))
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286 kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
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287 if (!strstr(str.s, "##INFO=<ID=RP,"))
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288 kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
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289 if (!strstr(str.s, "##INFO=<ID=QBD,"))
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290 kputs("##INFO=<ID=QBD,Number=1,Type=Float,Description=\"Quality by Depth: QUAL/#reads\">\n", &str);
|
|
|
291 //if (!strstr(str.s, "##INFO=<ID=RPS,"))
|
|
|
292 // kputs("##INFO=<ID=RPS,Number=3,Type=Float,Description=\"Read Position Stats: depth, average, stddev\">\n", &str);
|
|
|
293 if (!strstr(str.s, "##INFO=<ID=RPB,"))
|
|
|
294 kputs("##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Read Position Bias\">\n", &str);
|
|
|
295 if (!strstr(str.s, "##INFO=<ID=MDV,"))
|
|
|
296 kputs("##INFO=<ID=MDV,Number=1,Type=Integer,Description=\"Maximum number of high-quality nonRef reads in samples\">\n", &str);
|
|
|
297 if (!strstr(str.s, "##INFO=<ID=VDB,"))
|
|
|
298 kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. Note: this version may be broken.\">\n", &str);
|
|
|
299 if (!strstr(str.s, "##FORMAT=<ID=GT,"))
|
|
|
300 kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
|
|
|
301 if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
|
|
|
302 kputs("##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n", &str);
|
|
|
303 if (!strstr(str.s, "##FORMAT=<ID=GL,"))
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|
|
304 kputs("##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)\">\n", &str);
|
|
|
305 if (!strstr(str.s, "##FORMAT=<ID=DP,"))
|
|
|
306 kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality bases\">\n", &str);
|
|
|
307 if (!strstr(str.s, "##FORMAT=<ID=DV,"))
|
|
|
308 kputs("##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"# high-quality non-reference bases\">\n", &str);
|
|
|
309 if (!strstr(str.s, "##FORMAT=<ID=SP,"))
|
|
|
310 kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
|
|
|
311 if (!strstr(str.s, "##FORMAT=<ID=PL,"))
|
|
|
312 kputs("##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">\n", &str);
|
|
|
313 h->l_txt = str.l + 1; h->txt = str.s;
|
|
|
314 }
|
|
|
315
|
|
|
316 double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
|
|
|
317
|
|
|
318 int bcfview(int argc, char *argv[])
|
|
|
319 {
|
|
|
320 extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
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|
|
321 extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x);
|
|
|
322 extern int bcf_fix_gt(bcf1_t *b);
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|
|
323 extern int bcf_anno_max(bcf1_t *b);
|
|
|
324 extern int bcf_shuffle(bcf1_t *b, int seed);
|
|
|
325 extern uint32_t *bcf_trio_prep(int is_x, int is_son);
|
|
|
326 extern int bcf_trio_call(uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt);
|
|
|
327 extern int bcf_pair_call(const bcf1_t *b);
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|
|
328 extern int bcf_min_diff(const bcf1_t *b);
|
|
|
329 extern int bcf_p1_get_M(bcf_p1aux_t *b);
|
|
|
330
|
|
|
331 extern gzFile bcf_p1_fp_lk;
|
|
|
332
|
|
|
333 bcf_t *bp, *bout = 0;
|
|
|
334 bcf1_t *b, *blast;
|
|
|
335 int c, *seeds = 0;
|
|
|
336 uint64_t n_processed = 0, qcnt[256];
|
|
|
337 viewconf_t vc;
|
|
|
338 bcf_p1aux_t *p1 = 0;
|
|
|
339 bcf_hdr_t *hin, *hout;
|
|
|
340 int tid, begin, end;
|
|
|
341 char moder[4], modew[4];
|
|
|
342
|
|
|
343 tid = begin = end = -1;
|
|
|
344 memset(&vc, 0, sizeof(viewconf_t));
|
|
|
345 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; vc.min_ma_lrt = -1;
|
|
|
346 memset(qcnt, 0, 8 * 256);
|
|
|
347 while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:K:")) >= 0) {
|
|
|
348 switch (c) {
|
|
|
349 case '1': vc.n1 = atoi(optarg); break;
|
|
|
350 case 'l': vc.bed = bed_read(optarg); if (!vc.bed) { fprintf(stderr,"Could not read \"%s\"\n", optarg); return 1; } break;
|
|
|
351 case 'D': vc.fn_dict = strdup(optarg); break;
|
|
|
352 case 'F': vc.flag |= VC_FIX_PL; break;
|
|
|
353 case 'N': vc.flag |= VC_ACGT_ONLY; break;
|
|
|
354 case 'G': vc.flag |= VC_NO_GENO; break;
|
|
|
355 case 'A': vc.flag |= VC_KEEPALT; break;
|
|
|
356 case 'b': vc.flag |= VC_BCFOUT; break;
|
|
|
357 case 'S': vc.flag |= VC_VCFIN; break;
|
|
|
358 case 'c': vc.flag |= VC_CALL; break;
|
|
|
359 case 'e': vc.flag |= VC_EM; break;
|
|
|
360 case 'v': vc.flag |= VC_VARONLY | VC_CALL; break;
|
|
|
361 case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
|
|
|
362 case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
|
|
|
363 case 'I': vc.flag |= VC_NO_INDEL; break;
|
|
|
364 case 'w': vc.flag |= VC_INDEL_ONLY; break;
|
|
|
365 case 'M': vc.flag |= VC_ANNO_MAX; break;
|
|
|
366 case 'Y': vc.flag |= VC_QCNT; break;
|
|
|
367 case 'm': vc.min_ma_lrt = atof(optarg); break;
|
|
|
368 case 't': vc.theta = atof(optarg); break;
|
|
|
369 case 'p': vc.pref = atof(optarg); break;
|
|
|
370 case 'i': vc.indel_frac = atof(optarg); break;
|
|
|
371 case 'Q': vc.flag |= VC_QCALL; break;
|
|
|
372 case 'L': vc.flag |= VC_ADJLD; break;
|
|
|
373 case 'U': vc.n_perm = atoi(optarg); break;
|
|
|
374 case 'C': vc.min_lrt = atof(optarg); break;
|
|
|
375 case 'X': vc.min_perm_p = atof(optarg); break;
|
|
|
376 case 'd': vc.min_smpl_frac = atof(optarg); break;
|
|
|
377 case 'K': bcf_p1_fp_lk = gzopen(optarg, "w"); break;
|
|
|
378 case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
|
|
|
379 vc.ploidy = calloc(vc.n_sub + 1, 1);
|
|
|
380 for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
|
|
|
381 tid = -1;
|
|
|
382 break;
|
|
|
383 case 'T':
|
|
|
384 if (strcmp(optarg, "trioauto") == 0) vc.trio_aux = bcf_trio_prep(0, 0);
|
|
|
385 else if (strcmp(optarg, "trioxd") == 0) vc.trio_aux = bcf_trio_prep(1, 0);
|
|
|
386 else if (strcmp(optarg, "trioxs") == 0) vc.trio_aux = bcf_trio_prep(1, 1);
|
|
|
387 else if (strcmp(optarg, "pair") == 0) vc.flag |= VC_PAIRCALL;
|
|
|
388 else {
|
|
|
389 fprintf(stderr, "[%s] Option '-T' can only take value trioauto, trioxd or trioxs.\n", __func__);
|
|
|
390 return 1;
|
|
|
391 }
|
|
|
392 break;
|
|
|
393 case 'P':
|
|
|
394 if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
|
|
|
395 else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
|
|
|
396 else if (strcmp(optarg, "flat") == 0) vc.prior_type = MC_PTYPE_FLAT;
|
|
|
397 else vc.prior_file = strdup(optarg);
|
|
|
398 break;
|
|
|
399 }
|
|
|
400 }
|
|
|
401 if (argc == optind) {
|
|
|
402 fprintf(stderr, "\n");
|
|
|
403 fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
|
|
|
404 fprintf(stderr, "Input/output options:\n\n");
|
|
|
405 fprintf(stderr, " -A keep all possible alternate alleles at variant sites\n");
|
|
|
406 fprintf(stderr, " -b output BCF instead of VCF\n");
|
|
|
407 fprintf(stderr, " -D FILE sequence dictionary for VCF->BCF conversion [null]\n");
|
|
|
408 fprintf(stderr, " -F PL generated by r921 or before (which generate old ordering)\n");
|
|
|
409 fprintf(stderr, " -G suppress all individual genotype information\n");
|
|
|
410 fprintf(stderr, " -l FILE list of sites (chr pos) or regions (BED) to output [all sites]\n");
|
|
|
411 fprintf(stderr, " -L calculate LD for adjacent sites\n");
|
|
|
412 fprintf(stderr, " -N skip sites where REF is not A/C/G/T\n");
|
|
|
413 fprintf(stderr, " -Q output the QCALL likelihood format\n");
|
|
|
414 fprintf(stderr, " -s FILE list of samples to use [all samples]\n");
|
|
|
415 fprintf(stderr, " -S input is VCF\n");
|
|
|
416 fprintf(stderr, " -u uncompressed BCF output (force -b)\n");
|
|
|
417 fprintf(stderr, "\nConsensus/variant calling options:\n\n");
|
|
|
418 fprintf(stderr, " -c SNP calling (force -e)\n");
|
|
|
419 fprintf(stderr, " -d FLOAT skip loci where less than FLOAT fraction of samples covered [0]\n");
|
|
|
420 fprintf(stderr, " -e likelihood based analyses\n");
|
|
|
421 fprintf(stderr, " -g call genotypes at variant sites (force -c)\n");
|
|
|
422 fprintf(stderr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
|
|
|
423 fprintf(stderr, " -I skip indels\n");
|
|
|
424 fprintf(stderr, " -m FLOAT alternative model for multiallelic and rare-variant calling, include if P(chi^2)>=FLOAT\n");
|
|
|
425 fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
|
|
|
426 fprintf(stderr, " -P STR type of prior: full, cond2, flat [full]\n");
|
|
|
427 fprintf(stderr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
|
|
|
428 fprintf(stderr, " -T STR constrained calling; STR can be: pair, trioauto, trioxd and trioxs (see manual) [null]\n");
|
|
|
429 fprintf(stderr, " -v output potential variant sites only (force -c)\n");
|
|
|
430 fprintf(stderr, "\nContrast calling and association test options:\n\n");
|
|
|
431 fprintf(stderr, " -1 INT number of group-1 samples [0]\n");
|
|
|
432 fprintf(stderr, " -C FLOAT posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", vc.min_lrt);
|
|
|
433 fprintf(stderr, " -U INT number of permutations for association testing (effective with -1) [0]\n");
|
|
|
434 fprintf(stderr, " -X FLOAT only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p);
|
|
|
435 fprintf(stderr, "\n");
|
|
|
436 return 1;
|
|
|
437 }
|
|
|
438
|
|
|
439 if (vc.flag & VC_CALL) vc.flag |= VC_EM;
|
|
|
440 if ((vc.flag & VC_VCFIN) && (vc.flag & VC_BCFOUT) && vc.fn_dict == 0) {
|
|
|
441 fprintf(stderr, "[%s] For VCF->BCF conversion please specify the sequence dictionary with -D\n", __func__);
|
|
|
442 return 1;
|
|
|
443 }
|
|
|
444 if (vc.n1 <= 0) vc.n_perm = 0; // TODO: give a warning here!
|
|
|
445 if (vc.n_perm > 0) {
|
|
|
446 seeds = malloc(vc.n_perm * sizeof(int));
|
|
|
447 srand48(time(0));
|
|
|
448 for (c = 0; c < vc.n_perm; ++c) seeds[c] = lrand48();
|
|
|
449 }
|
|
|
450 b = calloc(1, sizeof(bcf1_t));
|
|
|
451 blast = calloc(1, sizeof(bcf1_t));
|
|
|
452 strcpy(moder, "r");
|
|
|
453 if (!(vc.flag & VC_VCFIN)) strcat(moder, "b");
|
|
|
454 strcpy(modew, "w");
|
|
|
455 if (vc.flag & VC_BCFOUT) strcat(modew, "b");
|
|
|
456 if (vc.flag & VC_UNCOMP) strcat(modew, "u");
|
|
|
457 bp = vcf_open(argv[optind], moder);
|
|
|
458 hin = hout = vcf_hdr_read(bp);
|
|
|
459 if (vc.fn_dict && (vc.flag & VC_VCFIN))
|
|
|
460 vcf_dictread(bp, hin, vc.fn_dict);
|
|
|
461 bout = vcf_open("-", modew);
|
|
|
462 if (!(vc.flag & VC_QCALL)) {
|
|
|
463 if (vc.n_sub) {
|
|
|
464 vc.sublist = calloc(vc.n_sub, sizeof(int));
|
|
|
465 hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
|
|
|
466 }
|
|
|
467 write_header(hout); // always print the header
|
|
|
468 vcf_hdr_write(bout, hout);
|
|
|
469 }
|
|
|
470 if (vc.flag & VC_CALL) {
|
|
|
471 p1 = bcf_p1_init(hout->n_smpl, vc.ploidy);
|
|
|
472 if (vc.prior_file) {
|
|
|
473 if (bcf_p1_read_prior(p1, vc.prior_file) < 0) {
|
|
|
474 fprintf(stderr, "[%s] fail to read the prior AFS.\n", __func__);
|
|
|
475 return 1;
|
|
|
476 }
|
|
|
477 } else bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
|
|
|
478 if (vc.n1 > 0 && vc.min_lrt > 0.) { // set n1
|
|
|
479 bcf_p1_set_n1(p1, vc.n1);
|
|
|
480 bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
|
|
|
481 }
|
|
|
482 if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
|
|
|
483 }
|
|
|
484 if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
|
|
|
485 void *str2id = bcf_build_refhash(hout);
|
|
|
486 if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
|
|
|
487 bcf_idx_t *idx;
|
|
|
488 idx = bcf_idx_load(argv[optind]);
|
|
|
489 if (idx) {
|
|
|
490 uint64_t off;
|
|
|
491 off = bcf_idx_query(idx, tid, begin);
|
|
|
492 if (off == 0) {
|
|
|
493 fprintf(stderr, "[%s] no records in the query region.\n", __func__);
|
|
|
494 return 1; // FIXME: a lot of memory leaks...
|
|
|
495 }
|
|
|
496 bgzf_seek(bp->fp, off, SEEK_SET);
|
|
|
497 bcf_idx_destroy(idx);
|
|
|
498 }
|
|
|
499 }
|
|
|
500 }
|
|
|
501 if (bcf_p1_fp_lk && p1) {
|
|
|
502 int32_t M = bcf_p1_get_M(p1);
|
|
|
503 gzwrite(bcf_p1_fp_lk, &M, 4);
|
|
|
504 }
|
|
|
505 while (vcf_read(bp, hin, b) > 0) {
|
|
|
506 int is_indel, cons_llr = -1;
|
|
|
507 int64_t cons_gt = -1;
|
|
|
508 double em[10];
|
|
|
509 if ((vc.flag & VC_VARONLY) && strcmp(b->alt, "X") == 0) continue;
|
|
|
510 if ((vc.flag & VC_VARONLY) && vc.min_smpl_frac > 0.) {
|
|
|
511 extern int bcf_smpl_covered(const bcf1_t *b);
|
|
|
512 int n = bcf_smpl_covered(b);
|
|
|
513 if ((double)n / b->n_smpl < vc.min_smpl_frac) continue;
|
|
|
514 }
|
|
|
515 if (vc.n_sub) bcf_subsam(vc.n_sub, vc.sublist, b);
|
|
|
516 if (vc.flag & VC_FIX_PL) bcf_fix_pl(b);
|
|
|
517 is_indel = bcf_is_indel(b);
|
|
|
518 if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
|
|
|
519 if ((vc.flag & VC_INDEL_ONLY) && !is_indel) continue;
|
|
|
520 if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
|
|
|
521 int x;
|
|
|
522 if (b->ref[0] == 0 || b->ref[1] != 0) continue;
|
|
|
523 x = toupper(b->ref[0]);
|
|
|
524 if (x != 'A' && x != 'C' && x != 'G' && x != 'T') continue;
|
|
|
525 }
|
|
|
526 if (vc.bed && !bed_overlap(vc.bed, hin->ns[b->tid], b->pos, b->pos + strlen(b->ref))) continue;
|
|
|
527 if (tid >= 0) {
|
|
|
528 int l = strlen(b->ref);
|
|
|
529 l = b->pos + (l > 0? l : 1);
|
|
|
530 if (b->tid != tid || b->pos >= end) break;
|
|
|
531 if (!(l > begin && end > b->pos)) continue;
|
|
|
532 }
|
|
|
533 ++n_processed;
|
|
|
534 if ((vc.flag & VC_QCNT) && !is_indel) { // summarize the difference
|
|
|
535 int x = bcf_min_diff(b);
|
|
|
536 if (x > 255) x = 255;
|
|
|
537 if (x >= 0) ++qcnt[x];
|
|
|
538 }
|
|
|
539 if (vc.flag & VC_QCALL) { // output QCALL format; STOP here
|
|
|
540 bcf_2qcall(hout, b);
|
|
|
541 continue;
|
|
|
542 }
|
|
|
543 if (vc.trio_aux) // do trio calling
|
|
|
544 bcf_trio_call(vc.trio_aux, b, &cons_llr, &cons_gt);
|
|
|
545 else if (vc.flag & VC_PAIRCALL)
|
|
|
546 cons_llr = bcf_pair_call(b);
|
|
|
547 if (vc.flag & (VC_CALL|VC_ADJLD|VC_EM)) bcf_gl2pl(b);
|
|
|
548 if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0x1ff, em);
|
|
|
549 else {
|
|
|
550 int i;
|
|
|
551 for (i = 0; i < 9; ++i) em[i] = -1.;
|
|
|
552 }
|
|
|
553 if ( !(vc.flag&VC_KEEPALT) && (vc.flag&VC_CALL) && vc.min_ma_lrt>=0 )
|
|
|
554 {
|
|
|
555 bcf_p1_set_ploidy(b, p1); // could be improved: do this per site to allow pseudo-autosomal regions
|
|
|
556 int gts = call_multiallelic_gt(b, p1, vc.min_ma_lrt, vc.flag&VC_VARONLY);
|
|
|
557 if ( gts<=1 && vc.flag & VC_VARONLY ) continue;
|
|
|
558 }
|
|
|
559 else if (vc.flag & VC_CALL) { // call variants
|
|
|
560 bcf_p1rst_t pr;
|
|
|
561 int calret;
|
|
|
562 gzwrite(bcf_p1_fp_lk, &b->tid, 4);
|
|
|
563 gzwrite(bcf_p1_fp_lk, &b->pos, 4);
|
|
|
564 gzwrite(bcf_p1_fp_lk, &em[0], sizeof(double));
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565 calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
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566 if (n_processed % 100000 == 0) {
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567 fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
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568 bcf_p1_dump_afs(p1);
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569 }
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570 if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
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571 if (vc.n_perm && vc.n1 > 0 && pr.p_chi2 < vc.min_perm_p) { // permutation test
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572 bcf_p1rst_t r;
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573 int i, n = 0;
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574 for (i = 0; i < vc.n_perm; ++i) {
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575 #ifdef BCF_PERM_LRT // LRT based permutation is much faster but less robust to artifacts
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576 double x[10];
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577 bcf_shuffle(b, seeds[i]);
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578 bcf_em1(b, vc.n1, 1<<7, x);
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579 if (x[7] < em[7]) ++n;
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580 #else
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581 bcf_shuffle(b, seeds[i]);
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582 bcf_p1_cal(b, 1, p1, &r);
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583 if (pr.p_chi2 >= r.p_chi2) ++n;
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584 #endif
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585 }
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586 pr.perm_rank = n;
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587 }
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588 if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em, cons_llr, cons_gt);
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589 } else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em, cons_llr, cons_gt);
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590 if (vc.flag & VC_ADJLD) { // compute LD
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591 double f[4], r2;
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592 if ((r2 = bcf_pair_freq(blast, b, f)) >= 0) {
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593 kstring_t s;
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594 s.m = s.l = 0; s.s = 0;
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595 if (*b->info) kputc(';', &s);
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596 ksprintf(&s, "NEIR=%.3f;NEIF4=%.3f,%.3f,%.3f,%.3f", r2, f[0], f[1], f[2], f[3]);
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597 bcf_append_info(b, s.s, s.l);
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598 free(s.s);
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599 }
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600 bcf_cpy(blast, b);
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601 }
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602 if (vc.flag & VC_ANNO_MAX) bcf_anno_max(b);
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603 if (vc.flag & VC_NO_GENO) { // do not output GENO fields
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604 b->n_gi = 0;
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605 b->fmt[0] = '\0';
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606 b->l_str = b->fmt - b->str + 1;
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|
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607 } else bcf_fix_gt(b);
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|
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608 vcf_write(bout, hout, b);
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609 }
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|
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610
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611 if (bcf_p1_fp_lk) gzclose(bcf_p1_fp_lk);
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|
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612 if (vc.prior_file) free(vc.prior_file);
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|
|
613 if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
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|
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614 if (hin != hout) bcf_hdr_destroy(hout);
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|
|
615 bcf_hdr_destroy(hin);
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|
|
616 bcf_destroy(b); bcf_destroy(blast);
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|
|
617 vcf_close(bp); vcf_close(bout);
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|
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618 if (vc.fn_dict) free(vc.fn_dict);
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|
|
619 if (vc.ploidy) free(vc.ploidy);
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620 if (vc.trio_aux) free(vc.trio_aux);
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|
|
621 if (vc.n_sub) {
|
|
|
622 int i;
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|
|
623 for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]);
|
|
|
624 free(vc.subsam); free(vc.sublist);
|
|
|
625 }
|
|
|
626 if (vc.bed) bed_destroy(vc.bed);
|
|
|
627 if (vc.flag & VC_QCNT)
|
|
|
628 for (c = 0; c < 256; ++c)
|
|
|
629 fprintf(stderr, "QT\t%d\t%lld\n", c, (long long)qcnt[c]);
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|
|
630 if (seeds) free(seeds);
|
|
|
631 if (p1) bcf_p1_destroy(p1);
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|
|
632 return 0;
|
|
|
633 }
|
