* added prelimiary VCF parser (not finished)

[samtools.git] / bcftools / index.c

diff --git a/bcftools/index.c b/bcftools/index.c
index b2663d40838b5144936871b9bff22ce460e01d24..768519cb170c2663c5b1b0e6d88c0bf43eaa7751 100644 (file)
--- a/bcftools/index.c
+++ b/bcftools/index.c
@@ -56,7 +56,7 @@ static void fill_missing(bcf_idx_t *idx)
        }
 }
 
-bcf_idx_t *bcf_idx_core(bcf_t *bp)
+bcf_idx_t *bcf_idx_core(bcf_t *bp, bcf_hdr_t *h)
 {
        bcf_idx_t *idx;
        int32_t last_coor, last_tid;
@@ -69,12 +69,12 @@ bcf_idx_t *bcf_idx_core(bcf_t *bp)
        b = calloc(1, sizeof(bcf1_t));
        str = calloc(1, sizeof(kstring_t));
        idx = (bcf_idx_t*)calloc(1, sizeof(bcf_idx_t));
-       idx->n = bp->h.n_ref;
-       idx->index2 = calloc(bp->h.n_ref, sizeof(bcf_lidx_t));
+       idx->n = h->n_ref;
+       idx->index2 = calloc(h->n_ref, sizeof(bcf_lidx_t));
 
        last_tid = 0xffffffffu;
        last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
-       while ((ret = bcf_read(bp, b)) > 0) {
+       while ((ret = bcf_read(bp, h, b)) > 0) {
                int end, tmp;
                if (last_tid != b->tid) { // change of chromosomes
                        last_tid = b->tid;
@@ -255,11 +255,13 @@ int bcf_idx_build2(const char *fn, const char *_fnidx)
        BGZF *fpidx;
        bcf_t *bp;
        bcf_idx_t *idx;
+       bcf_hdr_t *h;
        if ((bp = bcf_open(fn, "r")) == 0) {
                fprintf(stderr, "[bcf_idx_build2] fail to open the BAM file.\n");
                return -1;
        }
-       idx = bcf_idx_core(bp);
+       h = bcf_hdr_read(bp);
+       idx = bcf_idx_core(bp, h);
        bcf_close(bp);
        if (_fnidx == 0) {
                fnidx = (char*)calloc(strlen(fn) + 5, 1);