* added prelimiary VCF parser (not finished)

[samtools.git] / bcftools / vcfout.c

diff --git a/bcftools/vcfout.c b/bcftools/vcfout.c
index d71dfd93183b835e89b9ed49386277d66b27d7e2..075fb617acb62784cb31608a7f5f3380fe50bacd 100644 (file)
--- a/bcftools/vcfout.c
+++ b/bcftools/vcfout.c
@@ -88,6 +88,7 @@ int bcfview(int argc, char *argv[])
        uint64_t n_processed = 0;
        viewconf_t vc;
        bcf_p1aux_t *p1 = 0;
+       bcf_hdr_t *h;
        int tid, begin, end;
        khash_t(set64) *hash = 0;
 
@@ -117,18 +118,18 @@ 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_cpy(&bout->h, &bp->h);
-               bcf_hdr_write(bout);
+               bcf_hdr_write(bout, h);
        }
        if (vc.flag & VC_CALL) {
-               p1 = bcf_p1_init(bp->h.n_smpl);
+               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, &bp->h);
+       if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
        if (optind + 1 < argc) {
-               void *str2id = bcf_build_refhash(&bp->h);
+               void *str2id = bcf_build_refhash(h);
                if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
                        bcf_idx_t *idx;
                        idx = bcf_idx_load(argv[optind]);
@@ -140,7 +141,7 @@ int bcfview(int argc, char *argv[])
                        }
                }
        }
-       while (bcf_read(bp, b) > 0) {
+       while (bcf_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);
@@ -157,24 +158,25 @@ int bcfview(int argc, char *argv[])
                        int is_var;
                        bcf_p1_cal(b, p1, &pr);
                        is_var = update_bcf1(b, p1, &pr, vc.flag);
-                       bcf_sync(bp->h.n_smpl, b);
+                       bcf_sync(h->n_smpl, b);
                        if ((n_processed + 1) % 50000 == 0) bcf_p1_dump_afs(p1);
                        if ((vc.flag & VC_VARONLY) && !is_var) continue;
                }
-               if (vc.flag & VC_BCF) bcf_write(bout, b);
+               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(bp, b);
+                       vcf = bcf_fmt(h, b);
                        puts(vcf);
                        free(vcf);
                }
                ++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);
        if (hash) kh_destroy(set64, hash);