X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_index.c;h=f250907039156c5559d92bfff9254ef0d8c401c8;hb=be1abba58b415b449a7a9230f2221fd3960781db;hp=9610a2656031657b796abc68bf32c1b6f1564745;hpb=cb5f44947629a68d16a48d32eef6e42a66e482fe;p=samtools.git

diff --git a/bam_index.c b/bam_index.c
index 9610a26..f250907 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -154,18 +154,22 @@ bam_index_t *bam_index_core(bamFile fp)
 	bam_header_t *h;
 	int i, ret;
 	bam_index_t *idx;
-	uint32_t last_bin, save_bin;
+	uint32_t last_bin, save_bin, recalculated_bin;
 	int32_t last_coor, last_tid, save_tid;
 	bam1_core_t *c;
 	uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
 
+	h = bam_header_read(fp);
+	if(h == 0) {
+	    fprintf(stderr, "[bam_index_core] Invalid BAM header.");
+	    return NULL;
+	}
+
 	idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
 	b = (bam1_t*)calloc(1, sizeof(bam1_t));
-	h = bam_header_read(fp);
 	c = &b->core;
 
 	idx->n = h->n_targets;
-	bam_header_destroy(h);
 	idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
 	for (i = 0; i < idx->n; ++i) idx->index[i] = kh_init(i);
 	idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
@@ -188,6 +192,15 @@ bam_index_t *bam_index_core(bamFile fp)
 					bam1_qname(b), last_coor, c->pos, c->tid+1);
 			return NULL;
 		}
+		if (c->tid >= 0) {
+			recalculated_bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
+			if (c->bin != recalculated_bin) {
+				fprintf(stderr, "[bam_index_core] read '%s' mapped to '%s' at POS %d to %d has BIN %d but should be %d\n",
+					bam1_qname(b), h->target_name[c->tid], c->pos + 1, bam_calend(c, bam1_cigar(b)), c->bin, recalculated_bin);
+				fprintf(stderr, "[bam_index_core] Fix it by using BAM->SAM->BAM to force a recalculation of the BIN field\n");
+				return NULL;
+			}
+		}
 		if (c->tid >= 0 && !(c->flag & BAM_FUNMAP)) insert_offset2(&idx->index2[b->core.tid], b, last_off);
 		if (c->bin != last_bin) { // then possibly write the binning index
 			if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
@@ -214,6 +227,7 @@ bam_index_t *bam_index_core(bamFile fp)
 		last_off = bam_tell(fp);
 		last_coor = b->core.pos;
 	}
+        bam_header_destroy(h);
 	if (save_tid >= 0) {
 		insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
 		insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, bam_tell(fp));
@@ -459,6 +473,7 @@ bam_index_t *bam_index_load(const char *fn)
 		strcat(strcpy(fnidx, fn), ".bai");
 		fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
 		download_from_remote(fnidx);
+        free(fnidx);
 		idx = bam_index_load_local(fn);
 	}
 	if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
@@ -489,6 +504,7 @@ int bam_index_build2(const char *fn, const char *_fnidx)
 	if (fpidx == 0) {
 		fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
 		free(fnidx);
+        bam_index_destroy(idx);
 		return -1;
 	}
 	bam_index_save(idx, fpidx);