--- /dev/null
+#include "pysam.h"
+
+#include <unistd.h>
+#include <stdlib.h>
+#include <math.h>
+#include <zlib.h>
+#include <errno.h>
+#include "bcf.h"
+#include "prob1.h"
+#include "kstring.h"
+#include "time.h"
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define VC_NO_GENO 2
+#define VC_BCFOUT 4
+#define VC_CALL 8
+#define VC_VARONLY 16
+#define VC_VCFIN 32
+#define VC_UNCOMP 64
+#define VC_KEEPALT 256
+#define VC_ACGT_ONLY 512
+#define VC_QCALL 1024
+#define VC_CALL_GT 2048
+#define VC_ADJLD 4096
+#define VC_NO_INDEL 8192
+#define VC_ANNO_MAX 16384
+#define VC_FIX_PL 32768
+#define VC_EM 0x10000
+
+typedef struct {
+ int flag, prior_type, n1, n_sub, *sublist, n_perm;
+ char *prior_file, **subsam, *fn_dict;
+ uint8_t *ploidy;
+ double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt;
+ void *bed;
+} viewconf_t;
+
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
+
+typedef struct {
+ double p[4];
+ int mq, depth, is_tested, d[4];
+} anno16_t;
+
+static double ttest(int n1, int n2, int a[4])
+{
+ extern double kf_betai(double a, double b, double x);
+ double t, v, u1, u2;
+ if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0;
+ u1 = (double)a[0] / n1; u2 = (double)a[2] / n2;
+ if (u1 <= u2) return 1.;
+ t = (u1 - u2) / sqrt(((a[1] - n1 * u1 * u1) + (a[3] - n2 * u2 * u2)) / (n1 + n2 - 2) * (1./n1 + 1./n2));
+ v = n1 + n2 - 2;
+// printf("%d,%d,%d,%d,%lf,%lf,%lf\n", a[0], a[1], a[2], a[3], t, u1, u2);
+ return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t));
+}
+
+static int test16_core(int anno[16], anno16_t *a)
+{
+ extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+ double left, right;
+ int i;
+ a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+ memcpy(a->d, anno, 4 * sizeof(int));
+ a->depth = anno[0] + anno[1] + anno[2] + anno[3];
+ a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0);
+ if (a->depth == 0) return -1;
+ a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499);
+ kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]);
+ for (i = 1; i < 4; ++i)
+ a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i);
+ return 0;
+}
+
+static int test16(bcf1_t *b, anno16_t *a)
+{
+ char *p;
+ int i, anno[16];
+ a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+ a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.;
+ a->mq = a->depth = a->is_tested = 0;
+ if ((p = strstr(b->info, "I16=")) == 0) return -1;
+ p += 4;
+ for (i = 0; i < 16; ++i) {
+ errno = 0; anno[i] = strtol(p, &p, 10);
+ if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
+ ++p;
+ }
+ return test16_core(anno, a);
+}
+
+static void rm_info(bcf1_t *b, const char *key)
+{
+ char *p, *q;
+ if ((p = strstr(b->info, key)) == 0) return;
+ for (q = p; *q && *q != ';'; ++q);
+ if (p > b->info && *(p-1) == ';') --p;
+ memmove(p, q, b->l_str - (q - b->str));
+ b->l_str -= q - p;
+ bcf_sync(b);
+}
+
+static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[9])
+{
+ kstring_t s;
+ int has_I16, is_var;
+ double fq, r;
+ anno16_t a;
+
+ has_I16 = test16(b, &a) >= 0? 1 : 0;
+ rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed!
+
+ memset(&s, 0, sizeof(kstring_t));
+ kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
+ kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
+ kputs(b->info, &s);
+ if (b->info[0]) kputc(';', &s);
+ { // print EM
+ if (em[0] >= 0) ksprintf(&s, "AF1=%.4g", 1 - em[0]);
+ if (em[4] >= 0 && em[4] <= 0.05) ksprintf(&s, ";G3=%.4g,%.4g,%.4g;HWE=%.3g", em[3], em[2], em[1], em[4]);
+ if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
+ if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
+ }
+ if (pr == 0) { // if pr is unset, return
+ kputc('\0', &s); kputs(b->fmt, &s); kputc('\0', &s);
+ free(b->str);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+ return 1;
+ }
+
+ is_var = (pr->p_ref < pref);
+ r = is_var? pr->p_ref : pr->p_var;
+
+ ksprintf(&s, ";CI95=%.4g,%.4g", pr->cil, pr->cih); // FIXME: when EM is not used, ";" should be omitted!
+ 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);
+ fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded);
+ if (fq < -999) fq = -999;
+ if (fq > 999) fq = 999;
+ ksprintf(&s, ";FQ=%.3g", fq);
+ if (pr->cmp[0] >= 0.) { // two sample groups
+ int i, q[3];
+ for (i = 1; i < 3; ++i) {
+ double x = pr->cmp[i] + pr->cmp[0]/2.;
+ q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499);
+ if (q[i] > 255) q[i] = 255;
+ }
+ if (pr->perm_rank >= 0) ksprintf(&s, ";PR=%d", pr->perm_rank);
+ ksprintf(&s, ";PCHI2=%.3g;PC2=%d,%d", q[1], q[2], pr->p_chi2);
+ }
+ 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]);
+ kputc('\0', &s);
+ kputs(b->fmt, &s); kputc('\0', &s);
+ free(b->str);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ b->qual = r < 1e-100? 999 : -4.343 * log(r);
+ if (b->qual > 999) b->qual = 999;
+ bcf_sync(b);
+ if (!is_var) bcf_shrink_alt(b, 1);
+ else if (!(flag&VC_KEEPALT))
+ bcf_shrink_alt(b, pr->rank0 < 2? 2 : pr->rank0+1);
+ if (is_var && (flag&VC_CALL_GT)) { // call individual genotype
+ int i, x, old_n_gi = b->n_gi;
+ s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
+ kputs(":GT:GQ", &s); kputc('\0', &s);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+ for (i = 0; i < b->n_smpl; ++i) {
+ x = bcf_p1_call_gt(pa, pr->f_exp, i);
+ ((uint8_t*)b->gi[old_n_gi].data)[i] = (x&3) == 0? 1<<3|1 : (x&3) == 1? 1 : 0;
+ ((uint8_t*)b->gi[old_n_gi+1].data)[i] = x>>2;
+ }
+ }
+ return is_var;
+}
+
+static char **read_samples(const char *fn, int *_n)
+{
+ gzFile fp;
+ kstream_t *ks;
+ kstring_t s;
+ int dret, n = 0, max = 0;
+ char **sam = 0;
+ *_n = 0;
+ s.l = s.m = 0; s.s = 0;
+ fp = gzopen(fn, "r");
+ if (fp == 0) return 0; // fail to open file
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
+ int l;
+ if (max == n) {
+ max = max? max<<1 : 4;
+ sam = realloc(sam, sizeof(void*)*max);
+ }
+ l = s.l;
+ sam[n] = malloc(s.l + 2);
+ strcpy(sam[n], s.s);
+ sam[n][l+1] = 2; // by default, diploid
+ if (dret != '\n') {
+ if (ks_getuntil(ks, 0, &s, &dret) >= 0) { // read ploidy, 1 or 2
+ int x = (int)s.s[0] - '0';
+ if (x == 1 || x == 2) sam[n][l+1] = x;
+ else fprintf(pysamerr, "(%s) ploidy can only be 1 or 2; assume diploid\n", __func__);
+ }
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ }
+ ++n;
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(s.s);
+ *_n = n;
+ return sam;
+}
+
+static void write_header(bcf_hdr_t *h)
+{
+ kstring_t str;
+ str.l = h->l_txt? h->l_txt - 1 : 0;
+ str.m = str.l + 1; str.s = h->txt;
+ if (!strstr(str.s, "##INFO=<ID=DP,"))
+ kputs("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=DP4,"))
+ kputs("##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=MQ,"))
+ kputs("##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Root-mean-square mapping quality of covering reads\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=FQ,"))
+ kputs("##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability of all samples being the same\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=AF1,"))
+ kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the site allele frequency of the first ALT allele\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=G3,"))
+ kputs("##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=HWE,"))
+ kputs("##INFO=<ID=HWE,Number=1,Type=Float,Description=\"Chi^2 based HWE test P-value based on G3\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=CI95,"))
+ 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);
+ if (!strstr(str.s, "##INFO=<ID=PV4,"))
+ kputs("##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=INDEL,"))
+ kputs("##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=PC2,"))
+ 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);
+ if (!strstr(str.s, "##INFO=<ID=PCHI2,"))
+ 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);
+ if (!strstr(str.s, "##INFO=<ID=QCHI2,"))
+ kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=RP,"))
+ kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=GT,"))
+ kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
+ kputs("##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=GL,"))
+ kputs("##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=DP,"))
+ kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality bases\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=SP,"))
+ kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=PL,"))
+ 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);
+ h->l_txt = str.l + 1; h->txt = str.s;
+}
+
+double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
+
+int bcfview(int argc, char *argv[])
+{
+ extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
+ extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x);
+ extern int bcf_fix_gt(bcf1_t *b);
+ extern int bcf_anno_max(bcf1_t *b);
+ extern int bcf_shuffle(bcf1_t *b, int seed);
+ bcf_t *bp, *bout = 0;
+ bcf1_t *b, *blast;
+ int c, *seeds = 0;
+ uint64_t n_processed = 0;
+ viewconf_t vc;
+ bcf_p1aux_t *p1 = 0;
+ bcf_hdr_t *hin, *hout;
+ int tid, begin, end;
+ char moder[4], modew[4];
+
+ tid = begin = end = -1;
+ memset(&vc, 0, sizeof(viewconf_t));
+ 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;
+ while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:")) >= 0) {
+ switch (c) {
+ case '1': vc.n1 = atoi(optarg); break;
+ case 'l': vc.bed = bed_read(optarg); break;
+ case 'D': vc.fn_dict = strdup(optarg); break;
+ case 'F': vc.flag |= VC_FIX_PL; break;
+ case 'N': vc.flag |= VC_ACGT_ONLY; break;
+ case 'G': vc.flag |= VC_NO_GENO; break;
+ case 'A': vc.flag |= VC_KEEPALT; break;
+ case 'b': vc.flag |= VC_BCFOUT; break;
+ case 'S': vc.flag |= VC_VCFIN; break;
+ case 'c': vc.flag |= VC_CALL; break;
+ case 'e': vc.flag |= VC_EM; break;
+ case 'v': vc.flag |= VC_VARONLY | VC_CALL; break;
+ case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
+ case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
+ case 'I': vc.flag |= VC_NO_INDEL; break;
+ case 'M': vc.flag |= VC_ANNO_MAX; break;
+ case 't': vc.theta = atof(optarg); break;
+ case 'p': vc.pref = atof(optarg); break;
+ case 'i': vc.indel_frac = atof(optarg); break;
+ case 'Q': vc.flag |= VC_QCALL; break;
+ case 'L': vc.flag |= VC_ADJLD; break;
+ case 'U': vc.n_perm = atoi(optarg); break;
+ case 'C': vc.min_lrt = atof(optarg); break;
+ case 'X': vc.min_perm_p = atof(optarg); break;
+ case 'd': vc.min_smpl_frac = atof(optarg); break;
+ case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
+ vc.ploidy = calloc(vc.n_sub + 1, 1);
+ for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
+ tid = -1;
+ break;
+ case 'P':
+ if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
+ else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
+ else if (strcmp(optarg, "flat") == 0) vc.prior_type = MC_PTYPE_FLAT;
+ else vc.prior_file = strdup(optarg);
+ break;
+ }
+ }
+ if (argc == optind) {
+ fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
+ fprintf(pysamerr, "Input/output options:\n\n");
+ fprintf(pysamerr, " -A keep all possible alternate alleles at variant sites\n");
+ fprintf(pysamerr, " -b output BCF instead of VCF\n");
+ fprintf(pysamerr, " -D FILE sequence dictionary for VCF->BCF conversion [null]\n");
+ fprintf(pysamerr, " -F PL generated by r921 or before (which generate old ordering)\n");
+ fprintf(pysamerr, " -G suppress all individual genotype information\n");
+ fprintf(pysamerr, " -l FILE list of sites (chr pos) or regions (BED) to output [all sites]\n");
+ fprintf(pysamerr, " -L calculate LD for adjacent sites\n");
+ fprintf(pysamerr, " -N skip sites where REF is not A/C/G/T\n");
+ fprintf(pysamerr, " -Q output the QCALL likelihood format\n");
+ fprintf(pysamerr, " -s FILE list of samples to use [all samples]\n");
+ fprintf(pysamerr, " -S input is VCF\n");
+ fprintf(pysamerr, " -u uncompressed BCF output (force -b)\n");
+ fprintf(pysamerr, "\nConsensus/variant calling options:\n\n");
+ fprintf(pysamerr, " -c SNP calling (force -e)\n");
+ fprintf(pysamerr, " -d FLOAT skip loci where less than FLOAT fraction of samples covered [0]\n");
+ fprintf(pysamerr, " -e likelihood based analyses\n");
+ fprintf(pysamerr, " -g call genotypes at variant sites (force -c)\n");
+ fprintf(pysamerr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
+ fprintf(pysamerr, " -I skip indels\n");
+ fprintf(pysamerr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
+ fprintf(pysamerr, " -P STR type of prior: full, cond2, flat [full]\n");
+ fprintf(pysamerr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
+ fprintf(pysamerr, " -v output potential variant sites only (force -c)\n");
+ fprintf(pysamerr, "\nContrast calling and association test options:\n\n");
+ fprintf(pysamerr, " -1 INT number of group-1 samples [0]\n");
+ fprintf(pysamerr, " -C FLOAT posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", vc.min_lrt);
+ fprintf(pysamerr, " -U INT number of permutations for association testing (effective with -1) [0]\n");
+ fprintf(pysamerr, " -X FLOAT only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p);
+ fprintf(pysamerr, "\n");
+ return 1;
+ }
+
+ if (vc.flag & VC_CALL) vc.flag |= VC_EM;
+ if ((vc.flag & VC_VCFIN) && (vc.flag & VC_BCFOUT) && vc.fn_dict == 0) {
+ fprintf(pysamerr, "[%s] For VCF->BCF conversion please specify the sequence dictionary with -D\n", __func__);
+ return 1;
+ }
+ if (vc.n1 <= 0) vc.n_perm = 0; // TODO: give a warning here!
+ if (vc.n_perm > 0) {
+ seeds = malloc(vc.n_perm * sizeof(int));
+ srand48(time(0));
+ for (c = 0; c < vc.n_perm; ++c) seeds[c] = lrand48();
+ }
+ b = calloc(1, sizeof(bcf1_t));
+ blast = calloc(1, sizeof(bcf1_t));
+ strcpy(moder, "r");
+ if (!(vc.flag & VC_VCFIN)) strcat(moder, "b");
+ strcpy(modew, "w");
+ if (vc.flag & VC_BCFOUT) strcat(modew, "b");
+ if (vc.flag & VC_UNCOMP) strcat(modew, "u");
+ bp = vcf_open(argv[optind], moder);
+ hin = hout = vcf_hdr_read(bp);
+ if (vc.fn_dict && (vc.flag & VC_VCFIN))
+ vcf_dictread(bp, hin, vc.fn_dict);
+ bout = vcf_open("-", modew);
+ if (!(vc.flag & VC_QCALL)) {
+ if (vc.n_sub) {
+ vc.sublist = calloc(vc.n_sub, sizeof(int));
+ hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
+ }
+ if (vc.flag & VC_CALL) write_header(hout);
+ vcf_hdr_write(bout, hout);
+ }
+ if (vc.flag & VC_CALL) {
+ p1 = bcf_p1_init(hout->n_smpl, vc.ploidy);
+ if (vc.prior_file) {
+ if (bcf_p1_read_prior(p1, vc.prior_file) < 0) {
+ fprintf(pysamerr, "[%s] fail to read the prior AFS.\n", __func__);
+ return 1;
+ }
+ } else bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
+ if (vc.n1 > 0 && vc.min_lrt > 0.) { // set n1
+ bcf_p1_set_n1(p1, vc.n1);
+ bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
+ }
+ if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
+ }
+ if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
+ void *str2id = bcf_build_refhash(hout);
+ if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
+ bcf_idx_t *idx;
+ idx = bcf_idx_load(argv[optind]);
+ if (idx) {
+ uint64_t off;
+ off = bcf_idx_query(idx, tid, begin);
+ if (off == 0) {
+ fprintf(pysamerr, "[%s] no records in the query region.\n", __func__);
+ return 1; // FIXME: a lot of memory leaks...
+ }
+ bgzf_seek(bp->fp, off, SEEK_SET);
+ bcf_idx_destroy(idx);
+ }
+ }
+ }
+ while (vcf_read(bp, hin, b) > 0) {
+ int is_indel;
+ double em[9];
+ if ((vc.flag & VC_VARONLY) && strcmp(b->alt, "X") == 0) continue;
+ if ((vc.flag & VC_VARONLY) && vc.min_smpl_frac > 0.) {
+ extern int bcf_smpl_covered(const bcf1_t *b);
+ int n = bcf_smpl_covered(b);
+ if ((double)n / b->n_smpl < vc.min_smpl_frac) continue;
+ }
+ if (vc.n_sub) bcf_subsam(vc.n_sub, vc.sublist, b);
+ if (vc.flag & VC_FIX_PL) bcf_fix_pl(b);
+ is_indel = bcf_is_indel(b);
+ if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
+ if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
+ int x;
+ if (b->ref[0] == 0 || b->ref[1] != 0) continue;
+ x = toupper(b->ref[0]);
+ if (x != 'A' && x != 'C' && x != 'G' && x != 'T') continue;
+ }
+ if (vc.bed && !bed_overlap(vc.bed, hin->ns[b->tid], b->pos, b->pos + strlen(b->ref))) continue;
+ if (tid >= 0) {
+ int l = strlen(b->ref);
+ l = b->pos + (l > 0? l : 1);
+ if (b->tid != tid || b->pos >= end) break;
+ if (!(l > begin && end > b->pos)) continue;
+ }
+ ++n_processed;
+ if (vc.flag & VC_QCALL) { // output QCALL format; STOP here
+ bcf_2qcall(hout, b);
+ continue;
+ }
+ if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0xff, em);
+ else {
+ int i;
+ for (i = 0; i < 9; ++i) em[i] = -1.;
+ }
+ if (vc.flag & (VC_CALL|VC_ADJLD)) bcf_gl2pl(b);
+ if (vc.flag & VC_CALL) { // call variants
+ bcf_p1rst_t pr;
+ int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
+ if (n_processed % 100000 == 0) {
+ fprintf(pysamerr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
+ bcf_p1_dump_afs(p1);
+ }
+ if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
+ if (vc.n_perm && vc.n1 > 0 && pr.p_chi2 < vc.min_perm_p) { // permutation test
+ bcf_p1rst_t r;
+ int i, n = 0;
+ for (i = 0; i < vc.n_perm; ++i) {
+#ifdef BCF_PERM_LRT // LRT based permutation is much faster but less robust to artifacts
+ double x[9];
+ bcf_shuffle(b, seeds[i]);
+ bcf_em1(b, vc.n1, 1<<7, x);
+ if (x[7] < em[7]) ++n;
+#else
+ bcf_shuffle(b, seeds[i]);
+ bcf_p1_cal(b, 1, p1, &r);
+ if (pr.p_chi2 >= r.p_chi2) ++n;
+#endif
+ }
+ pr.perm_rank = n;
+ }
+ if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em);
+ } else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em);
+ if (vc.flag & VC_ADJLD) { // compute LD
+ double f[4], r2;
+ if ((r2 = bcf_pair_freq(blast, b, f)) >= 0) {
+ kstring_t s;
+ s.m = s.l = 0; s.s = 0;
+ if (*b->info) kputc(';', &s);
+ ksprintf(&s, "NEIR=%.3f;NEIF4=%.3f,%.3f,%.3f,%.3f", r2, f[0], f[1], f[2], f[3]);
+ bcf_append_info(b, s.s, s.l);
+ free(s.s);
+ }
+ bcf_cpy(blast, b);
+ }
+ if (vc.flag & VC_ANNO_MAX) bcf_anno_max(b);
+ if (vc.flag & VC_NO_GENO) { // do not output GENO fields
+ b->n_gi = 0;
+ b->fmt[0] = '\0';
+ b->l_str = b->fmt - b->str + 1;
+ } else bcf_fix_gt(b);
+ vcf_write(bout, hout, b);
+ }
+ if (vc.prior_file) free(vc.prior_file);
+ if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
+ if (hin != hout) bcf_hdr_destroy(hout);
+ bcf_hdr_destroy(hin);
+ bcf_destroy(b); bcf_destroy(blast);
+ vcf_close(bp); vcf_close(bout);
+ if (vc.fn_dict) free(vc.fn_dict);
+ if (vc.ploidy) free(vc.ploidy);
+ if (vc.n_sub) {
+ int i;
+ for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]);
+ free(vc.subsam); free(vc.sublist);
+ }
+ if (vc.bed) bed_destroy(vc.bed);
+ if (seeds) free(seeds);
+ if (p1) bcf_p1_destroy(p1);
+ return 0;
+}
projects / pysam.git / blobdiff