X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Findex.c;h=a7db24f671d6761dbc1558ec0a8af775814a2c98;hp=b2663d40838b5144936871b9bff22ce460e01d24;hb=2fa4cde9b8806faceffb8677440b54ca4c90b6f7;hpb=fd187467e3c5f026a4d934c5b0cb68a42939f6e1

diff --git a/bcftools/index.c b/bcftools/index.c
index b2663d4..a7db24f 100644
--- a/bcftools/index.c
+++ b/bcftools/index.c
@@ -45,18 +45,7 @@ static inline void insert_offset2(bcf_lidx_t *index2, int _beg, int _end, uint64
 	if (index2->n < end + 1) index2->n = end + 1;
 }
 
-static void fill_missing(bcf_idx_t *idx)
-{
-	int i, j;
-	for (i = 0; i < idx->n; ++i) {
-		bcf_lidx_t *idx2 = &idx->index2[i];
-		for (j = 1; j < idx2->n; ++j)
-			if (idx2->offset[j] == 0)
-				idx2->offset[j] = idx2->offset[j-1];
-	}
-}
-
-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 +58,12 @@ 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;
@@ -89,7 +78,6 @@ bcf_idx_t *bcf_idx_core(bcf_t *bp)
 		last_off = bgzf_tell(fp);
 		last_coor = b->pos;
 	}
-	fill_missing(idx);
 	free(str->s); free(str); bcf_destroy(b);
 	return idx;
 }
@@ -255,11 +243,13 @@ 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);
@@ -269,6 +259,7 @@ int bcf_idx_build2(const char *fn, const char *_fnidx)
 	if (fpidx == 0) {
 		fprintf(stderr, "[bcf_idx_build2] fail to create the index file.\n");
 		free(fnidx);
+        bcf_idx_destroy(idx);
 		return -1;
 	}
 	bcf_idx_save(idx, fpidx);
@@ -323,14 +314,14 @@ int bcf_parse_region(void *str2id, const char *str, int *tid, int *begin, int *e
  * retrieve a specified region *
  *******************************/
 
-uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg, int end)
+uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg)
 {
-	uint64_t min_off;
+	uint64_t min_off, *offset;
+	int i;
 	if (beg < 0) beg = 0;
-	if (end < beg) return 0xffffffffffffffffull;
-	min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
-		: idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT];
-	assert(min_off);
+	offset = idx->index2[tid].offset;
+	for (i = beg>>TAD_LIDX_SHIFT; i < idx->index2[tid].n && offset[i] == 0; ++i);
+	min_off = (i == idx->index2[tid].n)? offset[idx->index2[tid].n-1] : offset[i];
 	return min_off;
 }