Dear SAM tools developers, here is a patch proposed by a Debian user on our bug tracker, that prevents samtools mpileup to crash when a read is aligned outside of the reference.
Please consider including it to your next release, and do not hesitate to send us comments if there are potential problems with this patch. You can refer to the email quoted below or to the following URL for more information. http://bugs.debian.org/653042 Have a nice day, -- Charles Plessy, Debian Med team, Illkirch-Graffenstaden, France. Le Thu, Dec 22, 2011 at 05:42:44PM -0800, Don Armstrong a écrit : > Package: samtools > Version: 0.1.18-1 > Severity: important > Tag: patch > > If a read is aligned outside of the reference (possibly due to > reference mismatch or truncation), samtools mpileup will segfault. It > should instead warn, and continue on. The attached patch fixes this. > Description: Fix segfault if position is outside of the reference sequence > length > Origin: Don Armstrong <d...@donarmstrong.com> > > Index: samtools-0.1.18/bam_plcmd.c > =================================================================== > --- samtools-0.1.18.orig/bam_plcmd.c 2011-07-06 20:41:26.000000000 -0700 > +++ samtools-0.1.18/bam_plcmd.c 2011-12-22 14:44:05.000000000 -0800 > @@ -93,6 +93,7 @@ > bam_iter_t iter; > bam_header_t *h; > int ref_id; > + int ref_len; > char *ref; > const mplp_conf_t *conf; > } mplp_aux_t; > @@ -134,6 +135,11 @@ > qual[i] = qual[i] > 31? qual[i] - 31 : 0; > } > has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0; > + if (has_ref && (ma->ref_len <= b->core.pos)) { // exclude reads > outside of the reference sequence > + fprintf(stderr,"[%s] Skipping because %d is outside of %d > [ref:%s]\n",__func__,b->core.pos,ma->ref_len,ma->ref_id); > + skip = 1; > + continue; > + } > skip = 0; > if (has_ref && (ma->conf->flag&MPLP_REALN)) > bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1); > if (has_ref && ma->conf->capQ_thres > 10) { > @@ -277,7 +283,11 @@ > if (tid0 >= 0 && conf->fai) { // region is set > ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, > 0x7fffffff, &ref_len); > ref_tid = tid0; > - for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = > tid0; > + for (i = 0; i < n; ++i) { > + data[i]->ref = ref; > + data[i]->ref_id = tid0; > + data[i]->ref_len = ref_len; > + } > } else ref_tid = -1, ref = 0; > iter = bam_mplp_init(n, mplp_func, (void**)data); > max_depth = conf->max_depth; > @@ -295,7 +305,11 @@ > if (tid != ref_tid) { > free(ref); ref = 0; > if (conf->fai) ref = faidx_fetch_seq(conf->fai, > h->target_name[tid], 0, 0x7fffffff, &ref_len); > - for (i = 0; i < n; ++i) data[i]->ref = ref, > data[i]->ref_id = tid; > + for (i = 0; i < n; ++i) { > + data[i]->ref = ref; > + data[i]->ref_id = tid; > + data[i]->ref_len = ref_len; > + } > ref_tid = tid; > } > if (conf->flag & MPLP_GLF) { -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
