From 4e4e3fdee9dd2331d38effa3f3af29a0a2c4f268 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Fri, 17 Sep 2010 01:36:01 +0000
Subject: [PATCH] fixed a bug in indexing

---
 bcftools/bcf.h   |  2 +-
 bcftools/call1.c |  6 +++++-
 bcftools/index.c | 24 ++++++------------------
 3 files changed, 12 insertions(+), 20 deletions(-)

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index d0f9b02..b52f367 100644
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.h
@@ -75,7 +75,7 @@ extern "C" {
 	void *bcf_str2id_init();
 
 	int bcf_idx_build(const char *fn);
-	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);
 	int bcf_parse_region(void *str2id, const char *str, int *tid, int *begin, int *end);
 	bcf_idx_t *bcf_idx_load(const char *fn);
 	void bcf_idx_destroy(bcf_idx_t *idx);
diff --git a/bcftools/call1.c b/bcftools/call1.c
index 08d759d..6b5c47b 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -277,7 +277,11 @@ int bcfview(int argc, char *argv[])
 			idx = bcf_idx_load(argv[optind]);
 			if (idx) {
 				uint64_t off;
-				off = bcf_idx_query(idx, tid, begin, end);
+				off = bcf_idx_query(idx, tid, begin);
+				if (off == 0) {
+					fprintf(stderr, "[%s] no records in the query region.\n", __func__);
+					return 1; // FIXME: a lot of memory leaks...
+				}
 				bgzf_seek(bp->fp, off, SEEK_SET);
 				bcf_idx_destroy(idx);
 			}
diff --git a/bcftools/index.c b/bcftools/index.c
index 768519c..014856d 100644
--- a/bcftools/index.c
+++ b/bcftools/index.c
@@ -45,17 +45,6 @@ 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_hdr_t *h)
 {
 	bcf_idx_t *idx;
@@ -89,7 +78,6 @@ bcf_idx_t *bcf_idx_core(bcf_t *bp, bcf_hdr_t *h)
 		last_off = bgzf_tell(fp);
 		last_coor = b->pos;
 	}
-	fill_missing(idx);
 	free(str->s); free(str); bcf_destroy(b);
 	return idx;
 }
@@ -325,14 +313,14 @@ 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;
 }
 
-- 
2.39.5