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r904: fixed a corner-case segfault. Resolves #307.

This commit is contained in:
Heng Li 2019-01-10 09:57:05 -05:00
parent 5b2fdfff9c
commit cf2bae6e9b
2 changed files with 4 additions and 2 deletions
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4
align.c
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@ -613,6 +613,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
if (++l > opt->min_cnt) { if (++l > opt->min_cnt) {
l = rs0 - x > qs0 - y? rs0 - x : qs0 - y; l = rs0 - x > qs0 - y? rs0 - x : qs0 - y;
rs1 = rs0 - l, qs1 = qs0 - l; rs1 = rs0 - l, qs1 = qs0 - l;
if (rs1 < 0) rs1 = 0; // not strictly necessary; better have this guard for explicit
break; break;
} }
} }
@ -626,6 +627,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
l = l < rs? l : rs; l = l < rs? l : rs;
rs1 = rs1 > rs - l? rs1 : rs - l; rs1 = rs1 > rs - l? rs1 : rs - l;
rs0 = rs0 < rs1? rs0 : rs1; rs0 = rs0 < rs1? rs0 : rs1;
rs0 = rs0 < rs? rs0 : rs;
} else rs0 = rs, qs0 = qs; } else rs0 = rs, qs0 = qs;
// compute re0 and qe0 // compute re0 and qe0
re0 = (int32_t)a[r->as + r->cnt - 1].x + 1; re0 = (int32_t)a[r->as + r->cnt - 1].x + 1;
@ -665,7 +667,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
assert(re0 > rs0); assert(re0 > rs0);
tseq = (uint8_t*)kmalloc(km, re0 - rs0); tseq = (uint8_t*)kmalloc(km, re0 - rs0);
if (qs > 0 && rs > 0) { // left extension if (qs > 0 && rs > 0) { // left extension; probably the condition can be changed to "qs > qs0 && rs > rs0"
qseq = &qseq0[rev][qs0]; qseq = &qseq0[rev][qs0];
mm_idx_getseq(mi, rid, rs0, rs, tseq); mm_idx_getseq(mi, rid, rs0, rs, tseq);
mm_seq_rev(qs - qs0, qseq); mm_seq_rev(qs - qs0, qseq);

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.14-r894-dirty" #define MM_VERSION "2.14-r904-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>