From be1abba58b415b449a7a9230f2221fd3960781db Mon Sep 17 00:00:00 2001 From: peterjc Date: Wed, 24 Apr 2013 11:10:44 +0100 Subject: [PATCH] Show reference name in bad BIN error message --- bam_index.c | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bam_index.c b/bam_index.c index 2fac746..f250907 100644 --- a/bam_index.c +++ b/bam_index.c @@ -170,7 +170,6 @@ bam_index_t *bam_index_core(bamFile 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)); @@ -196,8 +195,8 @@ bam_index_t *bam_index_core(bamFile fp) 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 to %d has BIN %d but should be %d\n", - bam1_qname(b), c->pos + 1, bam_calend(c, bam1_cigar(b)), 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; } @@ -228,6 +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)); -- 2.39.2