#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
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) {
+ while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:Qg")) >= 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 'Q': vc.flag |= VC_QCALL; break;
fprintf(stderr, "\n");
fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [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, " -1 INT number of group-1 samples [0]\n");