* fixed a bug in kstrtok@kstring.c

[samtools.git] / bcftools / vcfout.c

diff --git a/bcftools/vcfout.c b/bcftools/vcfout.c
index dfcb25a4c0a40cadda0cadf1c702545e0aa1a01b..58f11a2e8499ec9f0e888feae7c8aaba6543dfa1 100644 (file)
--- a/bcftools/vcfout.c
+++ b/bcftools/vcfout.c
@@ -15,9 +15,11 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 
 #define VC_NO_PL   1
 #define VC_NO_GENO 2
-#define VC_BCF     4
+#define VC_BCFOUT  4
 #define VC_CALL    8
 #define VC_VARONLY 16
+#define VC_VCFIN   32
+#define VC_UNCOMP  64
 
 typedef struct {
        int flag, prior_type;
@@ -149,19 +151,22 @@ int bcfview(int argc, char *argv[])
        bcf_p1aux_t *p1 = 0;
        bcf_hdr_t *h;
        int tid, begin, end;
+       char moder[4], modew[4];
        khash_t(set64) *hash = 0;
 
        tid = begin = end = -1;
        memset(&vc, 0, sizeof(viewconf_t));
        vc.prior_type = -1; vc.theta = 1e-3; vc.pref = 0.9;
-       while ((c = getopt(argc, argv, "l:cGvLbP:t:p:")) >= 0) {
+       while ((c = getopt(argc, argv, "l:cGvLbSuP:t:p:")) >= 0) {
                switch (c) {
                case 'l': vc.fn_list = strdup(optarg); break;
                case 'G': vc.flag |= VC_NO_GENO; break;
                case 'L': vc.flag |= VC_NO_PL; break;
-               case 'b': vc.flag |= VC_BCF; 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 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
                case 't': vc.theta = atof(optarg); break;
                case 'p': vc.pref = atof(optarg); break;
                case 'P':
@@ -176,6 +181,8 @@ int bcfview(int argc, char *argv[])
                fprintf(stderr, "Usage:   bcftools view [options] <in.bcf> [reg]\n\n");
                fprintf(stderr, "Options: -c        SNP calling\n");
                fprintf(stderr, "         -b        output BCF instead of VCF\n");
+               fprintf(stderr, "         -u        uncompressed BCF output\n");
+               fprintf(stderr, "         -S        input is VCF\n");
                fprintf(stderr, "         -G        suppress all individual genotype information\n");
                fprintf(stderr, "         -L        discard the PL genotype field\n");
                fprintf(stderr, "         -v        output potential variant sites only\n");
@@ -188,18 +195,21 @@ int bcfview(int argc, char *argv[])
        }
 
        b = calloc(1, sizeof(bcf1_t));
-       bp = bcf_open(argv[optind], "r");
-       h = bcf_hdr_read(bp);
-       if (vc.flag & VC_BCF) {
-               bout = bcf_open("-", "w");
-               bcf_hdr_write(bout, h);
-       }
+       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);
+       h = vcf_hdr_read(bp);
+       bout = vcf_open("-", modew);
+       vcf_hdr_write(bout, h);
        if (vc.flag & VC_CALL) {
                p1 = bcf_p1_init(h->n_smpl);
                bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
        }
        if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
-       if (optind + 1 < argc) {
+       if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
                void *str2id = bcf_build_refhash(h);
                if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
                        bcf_idx_t *idx;
@@ -212,7 +222,7 @@ int bcfview(int argc, char *argv[])
                        }
                }
        }
-       while (bcf_read(bp, h, b) > 0) {
+       while (vcf_read(bp, h, b) > 0) {
                if (hash) {
                        uint64_t x = (uint64_t)b->tid<<32 | b->pos;
                        khint_t k = kh_get(set64, hash, x);
@@ -231,23 +241,17 @@ 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_BCF) bcf_write(bout, h, b);
-               else {
-                       char *vcf;
-                       if (vc.flag & VC_NO_GENO) {
-                               b->n_gi = 0;
-                               b->fmt[0] = '\0';
-                       }
-                       vcf = bcf_fmt(h, b);
-                       puts(vcf);
-                       free(vcf);
+               if (vc.flag & VC_NO_GENO) {
+                       b->n_gi = 0;
+                       b->fmt[0] = '\0';
                }
+               vcf_write(bout, h, b);
                ++n_processed;
        }
        if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
        bcf_hdr_destroy(h);
-       bcf_close(bp); bcf_close(bout);
        bcf_destroy(b);
+       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);