X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fcall1.c;h=15f6f8bcc7095c37ea5fb589efdce630680b07b7;hb=f560d9a2a23f21b1376a186b04d99099ac5b07f9;hp=a5c03f452ed044cea0867812d33d95eb499a74c8;hpb=82e06ed4289c179c7a0da9b8ffa31b15836ae763;p=samtools.git diff --git a/bcftools/call1.c b/bcftools/call1.c index a5c03f4..15f6f8b 100644 --- a/bcftools/call1.c +++ b/bcftools/call1.c @@ -13,7 +13,6 @@ KHASH_SET_INIT_INT64(set64) #include "kseq.h" KSTREAM_INIT(gzFile, gzread, 16384) -#define VC_NO_PL 1 #define VC_NO_GENO 2 #define VC_BCFOUT 4 #define VC_CALL 8 @@ -25,11 +24,12 @@ KSTREAM_INIT(gzFile, gzread, 16384) #define VC_ACGT_ONLY 512 #define VC_QCALL 1024 #define VC_CALL_GT 2048 +#define VC_ADJLD 4096 typedef struct { int flag, prior_type, n1; char *fn_list, *prior_file; - double theta, pref; + double theta, pref, indel_frac; } viewconf_t; khash_t(set64) *bcf_load_pos(const char *fn, bcf_hdr_t *_h) @@ -161,7 +161,8 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s); kputs(b->info, &s); if (b->info[0]) kputc(';', &s); - ksprintf(&s, "AF1=%.3lf;AFE=%.3lf", 1.-pr->f_em, 1.-pr->f_exp); +// ksprintf(&s, "AF1=%.4lg;AFE=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, 1.-pr->f_exp, pr->cil, pr->cih); + ksprintf(&s, "AF1=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, pr->cil, pr->cih); ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq); if (a.is_tested) { if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%lg,%lg,%lg,%lg", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]); @@ -194,11 +195,14 @@ static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p return is_var; } +double bcf_ld_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); bcf_t *bp, *bout = 0; - bcf1_t *b; + bcf1_t *b, *blast; int c; uint64_t n_processed = 0; viewconf_t vc; @@ -210,25 +214,26 @@ int bcfview(int argc, char *argv[]) tid = begin = end = -1; memset(&vc, 0, sizeof(viewconf_t)); - vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; - while ((c = getopt(argc, argv, "N1:l:cHAGvLbSuP:t:p:Qg")) >= 0) { + vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; + while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:")) >= 0) { switch (c) { case '1': vc.n1 = atoi(optarg); break; case 'l': vc.fn_list = strdup(optarg); break; case 'N': vc.flag |= VC_ACGT_ONLY; break; case 'G': vc.flag |= VC_NO_GENO; break; - case 'L': vc.flag |= VC_NO_PL; 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 'v': vc.flag |= VC_VARONLY; break; + case 'v': vc.flag |= VC_VARONLY | VC_CALL; break; case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break; case 'H': vc.flag |= VC_HWE; break; - case 'g': vc.flag |= VC_CALL_GT; break; + case 'g': vc.flag |= VC_CALL_GT | VC_CALL; 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 'P': if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL; else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2; @@ -241,20 +246,21 @@ int bcfview(int argc, char *argv[]) fprintf(stderr, "\n"); fprintf(stderr, "Usage: bcftools view [options] [reg]\n\n"); fprintf(stderr, "Options: -c SNP calling\n"); + fprintf(stderr, " -v output potential variant sites only (force -c)\n"); + fprintf(stderr, " -g call genotypes at variant sites (force -c)\n"); fprintf(stderr, " -b output BCF instead of VCF\n"); - fprintf(stderr, " -u uncompressed BCF output\n"); + fprintf(stderr, " -u uncompressed BCF output (force -b)\n"); fprintf(stderr, " -S input is VCF\n"); fprintf(stderr, " -A keep all possible alternate alleles at variant sites\n"); fprintf(stderr, " -G suppress all individual genotype information\n"); - fprintf(stderr, " -g call genotypes for variant sites\n"); - fprintf(stderr, " -L discard the PL genotype field\n"); fprintf(stderr, " -H perform Hardy-Weinberg test (slower)\n"); - fprintf(stderr, " -v output potential variant sites only\n"); fprintf(stderr, " -N skip sites where REF is not A/C/G/T\n"); fprintf(stderr, " -Q output the QCALL likelihood format\n"); + fprintf(stderr, " -L calculate LD for adjacent sites\n"); fprintf(stderr, " -1 INT number of group-1 samples [0]\n"); fprintf(stderr, " -l FILE list of sites to output [all sites]\n"); - fprintf(stderr, " -t FLOAT scaled mutation rate [%.4lg]\n", vc.theta); + fprintf(stderr, " -t FLOAT scaled substitution mutation rate [%.4lg]\n", vc.theta); + fprintf(stderr, " -i FLOAT indel-to-substitution ratio [%.4lg]\n", vc.indel_frac); fprintf(stderr, " -p FLOAT variant if P(ref|D) 0.) bcf_p1_indel_prior(p1, vc.indel_frac); } if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h); if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) { @@ -327,9 +335,9 @@ int bcfview(int argc, char *argv[]) bcf_2qcall(h, b); continue; } + if (vc.flag & (VC_CALL|VC_ADJLD)) bcf_gl2pl(b); if (vc.flag & VC_CALL) { // call variants bcf_p1rst_t pr; - bcf_gl2pl(b); bcf_p1_cal(b, p1, &pr); // pr.g[3] is not calculated here if (vc.flag&VC_HWE) bcf_p1_cal_g3(p1, pr.g); if (n_processed % 100000 == 0) { @@ -339,6 +347,18 @@ int bcfview(int argc, char *argv[]) if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue; update_bcf1(h->n_smpl, b, p1, &pr, vc.pref, vc.flag); } + if (vc.flag & VC_ADJLD) { // compute LD + double f[4], r2; + if ((r2 = bcf_ld_freq(blast, b, f)) >= 0) { + kstring_t s; + s.m = s.l = 0; s.s = 0; + if (*b->info) kputc(';', &s); + ksprintf(&s, "NEIR=%.3lf;NEIF=%.3lf,%.3lf", r2, f[0]+f[2], f[0]+f[1]); + bcf_append_info(b, s.s, s.l); + free(s.s); + } + bcf_cpy(blast, b); + } if (vc.flag & VC_NO_GENO) { // do not output GENO fields b->n_gi = 0; b->fmt[0] = '\0'; @@ -348,11 +368,10 @@ int bcfview(int argc, char *argv[]) if (vc.prior_file) free(vc.prior_file); if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1); bcf_hdr_destroy(h); - bcf_destroy(b); + bcf_destroy(b); bcf_destroy(blast); vcf_close(bp); vcf_close(bout); if (hash) kh_destroy(set64, hash); if (vc.fn_list) free(vc.fn_list); if (p1) bcf_p1_destroy(p1); return 0; } -