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