X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_index.c;h=8c0d85414ba36475b68e9c98f79e02af7678377c;hb=698a60f0225ea0d46364522db77a559d64b3052a;hp=1ad2e93e5051972b084513d5d7391c45c6cf7bf2;hpb=ccd987169ea085165fe156e1727fbb9a33057f7b;p=samtools.git

diff --git a/bam_index.c b/bam_index.c
index 1ad2e93..8c0d854 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -154,37 +154,58 @@ 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));
 
 	save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
 	save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
-    n_mapped = n_unmapped = n_no_coor = off_end = 0;
+	n_mapped = n_unmapped = n_no_coor = off_end = 0;
 	off_beg = off_end = bam_tell(fp);
 	while ((ret = bam_read1(fp, b)) >= 0) {
 		if (c->tid < 0) ++n_no_coor;
-		if (last_tid != c->tid) { // change of chromosomes
+		if (last_tid < c->tid || (last_tid >= 0 && c->tid < 0)) { // change of chromosomes
 			last_tid = c->tid;
 			last_bin = 0xffffffffu;
-		} else if (last_coor > c->pos) {
+		} else if ((uint32_t)last_tid > (uint32_t)c->tid) {
+			fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %d-th chr > %d-th chr\n",
+					bam1_qname(b), last_tid+1, c->tid+1);
+			return NULL;
+		} else if ((int32_t)c->tid >= 0 && last_coor > c->pos) {
 			fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n",
 					bam1_qname(b), last_coor, c->pos, c->tid+1);
-			exit(1);
+			return NULL;
+		}
+		if (c->tid >= 0) {
+			if (c->n_cigar) {
+				recalculated_bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
+			} else {
+				recalculated_bin = bam_reg2bin(c->pos, c->pos + 1);
+			}
+			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) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+		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
 				insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
@@ -203,22 +224,30 @@ bam_index_t *bam_index_core(bamFile fp)
 		if (bam_tell(fp) <= last_off) {
 			fprintf(stderr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n",
 					(unsigned long long)bam_tell(fp), (unsigned long long)last_off);
-			exit(1);
+			return NULL;
 		}
 		if (c->flag & BAM_FUNMAP) ++n_unmapped;
 		else ++n_mapped;
 		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, off_end);
+		insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, bam_tell(fp));
 		insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
 	}
 	merge_chunks(idx);
 	fill_missing(idx);
-	if (ret >= 0)
-		while ((ret = bam_read1(fp, b)) >= 0) ++n_no_coor;
+	if (ret >= 0) {
+		while ((ret = bam_read1(fp, b)) >= 0) {
+			++n_no_coor;
+			if (c->tid >= 0 && n_no_coor) {
+				fprintf(stderr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
+				return NULL;
+			}
+		}
+	}
 	if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
 	free(b->data); free(b);
 	idx->n_no_coor = n_no_coor;
@@ -448,6 +477,7 @@ 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");
@@ -466,6 +496,10 @@ int bam_index_build2(const char *fn, const char *_fnidx)
 	}
 	idx = bam_index_core(fp);
 	bam_close(fp);
+	if(idx == 0) {
+		fprintf(stderr, "[bam_index_build2] fail to index the BAM file.\n");
+		return -1;
+	}
 	if (_fnidx == 0) {
 		fnidx = (char*)calloc(strlen(fn) + 5, 1);
 		strcpy(fnidx, fn); strcat(fnidx, ".bai");
@@ -474,6 +508,7 @@ 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);
@@ -608,6 +643,9 @@ bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end)
 		}
 	}
 	free(bins);
+	if (n_off == 0) {
+		free(off); return iter;
+	}
 	{
 		bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
 		int l;
@@ -695,6 +733,7 @@ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, voi
 	b = bam_init1();
 	iter = bam_iter_query(idx, tid, beg, end);
 	while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
+	bam_iter_destroy(iter);
 	bam_destroy1(b);
 	return (ret == -1)? 0 : ret;
 }