From 8e3b3f229a04cb81b680987ce06ae1507c9d8b69 Mon Sep 17 00:00:00 2001
From: peterjc
Date: Fri, 19 Apr 2013 15:13:32 +0100
Subject: [PATCH] Verify old BIN value of reads during 'samtools index'.
This simple check catches invalid BIN values in reads which can cause
subtle bugs due to position-based retrieval missing data, and simple
out of bounds errors if a BIN is used beyond the length of the reference.
---
bam_index.c | 11 ++++++++++-
1 file changed, 10 insertions(+), 1 deletion(-)
diff --git a/bam_index.c b/bam_index.c
index f916e04..35fb5b6 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -154,7 +154,7 @@ 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;
@@ -193,6 +193,15 @@ 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 at POS %d has BIN %d but should be %d\n",
+ bam1_qname(b), c->pos + 1, 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
--
2.39.2