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r497: the previous change not working at the ends

This commit is contained in:
Heng Li 2017-10-10 17:32:28 -04:00
parent c217eecdb7
commit 6c78a980b6
2 changed files with 5 additions and 5 deletions
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8
align.c
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@ -373,12 +373,12 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
}
// compute rs0 and qs0
rs1 = rs0 = (int32_t)a[r->as].x + 1 - (int32_t)(a[r->as].y>>32&0xff);
qs1 = qs0 = (int32_t)a[r->as].y + 1 - (int32_t)(a[r->as].y>>32&0xff);
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 (r->as > 0 && a[r->as - 1].x>>32 == a[r->as].x>>32) {
rs1 = (int32_t)a[r->as - 1].x + 1;
qs1 = (int32_t)a[r->as - 1].y + 1;
}
} else rs1 = qs1 = 0; // no adjacent previous chain on the same chr
if (qs > 0 && rs > 0) { // actually this is always true
l = qs < max_end_ext? qs : max_end_ext;
qs1 = qs1 > qs - l? qs1 : qs - l; // choose between the max_end_ext bound and the previous seed bound
@ -396,7 +396,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
if (r->as + r->cnt < n_a && a[r->as + r->cnt].x>>32 == a[r->as + r->cnt - 1].x>>32) {
re1 = (int32_t)a[r->as + r->cnt].x + 1 - (int32_t)(a[r->as + r->cnt].y>>32&0xff);
qe1 = (int32_t)a[r->as + r->cnt].y + 1 - (int32_t)(a[r->as + r->cnt].y>>32&0xff);
}
} else re1 = mi->seq[rid].len, qe1 = qlen; // no adjacent next chain on the same chr
if (qe < qlen && re < mi->seq[rid].len) {
l = qlen - qe < max_end_ext? qlen - qe : max_end_ext;
qe1 = qe1 < qe + l? qe1 : qe + l; // choose between the max_end_ext bound and the next seed bound

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r496-dirty"
#define MM_VERSION "2.2-r497-dirty"
#ifdef __linux__
#include <sys/resource.h>