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r526: fixed a bug when HPC is in use 

It happened when the query HPC minimizer is longer than the reference HPC
minimizer close to the beginning of a contig. We may get a negative coordinate,
which causes an assertion failure.
This commit is contained in:
Heng Li 2017-10-21 19:54:04 -04:00
parent be7f3c4ffe
commit beeb806829
4 changed files with 68 additions and 66 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
align.c
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@ -400,6 +400,8 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
// compute rs0 and qs0
rs0 = (int32_t)a[r->as].x + 1 - (int32_t)(a[r->as].y>>32&0xff);
qs0 = (int32_t)a[r->as].y + 1 - (int32_t)(a[r->as].y>>32&0xff);
if (rs0 < 0) rs0 = 0; // this may happen when HPC is in use
assert(qs0 >= 0); // this should never happen, or it is logic error
rs1 = qs1 = 0;
for (i = r->as - 1, l = 0; i >= 0 && a[i].x>>32 == a[r->as].x>>32; --i) { // inspect nearby seeds
int32_t x = (int32_t)a[i].x + 1 - (int32_t)(a[i].y>>32&0xff);

2
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r525-dirty"
#define MM_VERSION "2.2-r526-dirty"
#ifdef __linux__
#include <sys/resource.h>

120
tex/mm2-s3.sam.eval
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@ -1,60 +1,60 @@
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U 1703

10
tex/mm2.eval
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@ -1,9 +1,9 @@
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