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r677: reduce the change of missing hits 

that are close to end of alignments. It is still possible to create examples
that fail the heuristic.
This commit is contained in:
Heng Li 2018-02-02 10:35:33 -05:00
parent 997ab9bb2e
commit 35d3e064bf
2 changed files with 12 additions and 8 deletions
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18
align.c
View File

@ -291,33 +291,37 @@ static void mm_filter_bad_seeds(void *km, int as1, int cnt1, mm128_t *a, int min
kfree(km, K);
}
static void mm_fix_bad_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int32_t *as, int32_t *cnt)
static void mm_fix_bad_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int min_match, int32_t *as, int32_t *cnt)
{
int32_t i, l;
int32_t i, l, m;
*as = r->as, *cnt = r->cnt;
if (r->cnt < 3) return;
l = a[r->as].y >> 32 & 0xff;
m = l = a[r->as].y >> 32 & 0xff;
for (i = r->as + 1; i < r->as + r->cnt - 1; ++i) {
int32_t lq, lr, min, max;
int32_t q_span = a[i].y >> 32 & 0xff;
lr = (int32_t)a[i].x - (int32_t)a[i-1].x;
lq = (int32_t)a[i].y - (int32_t)a[i-1].y;
min = lr < lq? lr : lq;
max = lr > lq? lr : lq;
if (max - min > l >> 1) *as = i;
l += min;
if (l >= bw << 1) break;
m += min < q_span? min : q_span;
if (l >= bw << 1 || m >= min_match) break;
}
*cnt = r->as + r->cnt - *as;
l = a[r->as + r->cnt - 1].y >> 32 & 0xff;
m = l = a[r->as + r->cnt - 1].y >> 32 & 0xff;
for (i = r->as + r->cnt - 2; i > *as; --i) {
int32_t lq, lr, min, max;
int32_t q_span = a[i+1].y >> 32 & 0xff;
lr = (int32_t)a[i+1].x - (int32_t)a[i].x;
lq = (int32_t)a[i+1].y - (int32_t)a[i].y;
min = lr < lq? lr : lq;
max = lr > lq? lr : lq;
if (max - min > l >> 1) *cnt = i + 1 - *as;
l += min;
if (l >= bw) break;
m += min < q_span? min : q_span;
if (l >= bw << 1 || m >= min_match) break;
}
}
@ -418,7 +422,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
if (is_splice) {
mm_fix_bad_ends_splice(km, opt, mi, r, mat, qlen, qseq0, a, &as1, &cnt1);
} else {
mm_fix_bad_ends(r, a, opt->bw, &as1, &cnt1);
mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score, &as1, &cnt1);
}
mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.8-r672"
#define MM_VERSION "2.8-r677-dirty"
#ifdef __linux__
#include <sys/resource.h>