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r777: avoid skipping too many seeds

This commit is contained in:
Heng Li 2018-05-11 10:25:18 -04:00
parent 463f9309f9
commit 9f4309c376
2 changed files with 4 additions and 4 deletions
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6
align.c
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@ -325,7 +325,7 @@ static void mm_filter_bad_seeds(void *km, int as1, int cnt1, mm128_t *a, int min
kfree(km, K);
}
static void mm_filter_bad_seeds_alt(void *km, int as1, int cnt1, mm128_t *a, int min_gap)
static void mm_filter_bad_seeds_alt(void *km, int as1, int cnt1, mm128_t *a, int min_gap, int max_ext)
{
int n, k, *K;
K = collect_long_gaps(km, as1, cnt1, a, min_gap, &n);
@ -336,7 +336,7 @@ static void mm_filter_bad_seeds_alt(void *km, int as1, int cnt1, mm128_t *a, int
int re1 = (int32_t)a[as1 + i].x;
int qe1 = (int32_t)a[as1 + i].y;
gap1 = gap1 > 0? gap1 : -gap1;
for (l = k + 1; l < n; ++l) {
for (l = k + 1; l < n && a[as1 + K[l]].y - a[as1 + i].y <= max_ext; ++l) {
int j = K[l];
int gap2 = ((int32_t)a[as1 + j].y - a[as1 + j - 1].y) - ((int32_t)a[as1 + j].x - a[as1 + j - 1].x);
int q_span_pre = a[as1 + j - 1].y >> 32 & 0xff;
@ -496,7 +496,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score * 2, &as1, &cnt1);
}
mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
mm_filter_bad_seeds_alt(km, as1, cnt1, a, 30);
mm_filter_bad_seeds_alt(km, as1, cnt1, a, 30, opt->max_gap);
mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);
mm_adjust_minier(mi, qseq0, &a[as1 + cnt1 - 1], &re, &qe);
}

2
main.c
View File

@ -10,7 +10,7 @@
#include "getopt.h"
#endif
#define MM_VERSION "2.10-r774-dirty"
#define MM_VERSION "2.10-r777-dirty"
#ifdef __linux__
#include <sys/resource.h>