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r167: long join threshold depends on gap 

also caught a bug for reverse strand join
This commit is contained in:
Heng Li 2017-07-09 10:38:51 -04:00
parent 34ed85d46a
commit 1ac48556ae
3 changed files with 5 additions and 4 deletions
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5
hit.c
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@ -235,12 +235,11 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
for (i = n_aux - 1; i >= 1; --i) { for (i = n_aux - 1; i >= 1; --i) {
mm_reg1_t *r0 = &regs[(int32_t)aux[i-1]], *r1 = &regs[(int32_t)aux[i]]; mm_reg1_t *r0 = &regs[(int32_t)aux[i-1]], *r1 = &regs[(int32_t)aux[i]];
mm128_t *a0e, *a1s; mm128_t *a0e, *a1s;
int max_gap, min_gap; int max_gap, min_gap, sc_thres;
// test // test
if (r0->as + r0->cnt != r1->as) continue; // not adjacent in a[] if (r0->as + r0->cnt != r1->as) continue; // not adjacent in a[]
if (r0->rid != r1->rid || r0->rev != r1->rev) continue; // make sure on the same target and strand if (r0->rid != r1->rid || r0->rev != r1->rev) continue; // make sure on the same target and strand
if (r0->score < opt->min_join_flank_sc || r1->score < opt->min_join_flank_sc) continue; // require good flanking chains
a0e = &a[r0->as + r0->cnt - 1]; a0e = &a[r0->as + r0->cnt - 1];
a1s = &a[r1->as]; a1s = &a[r1->as];
if (a1s->x <= a0e->x || (int32_t)a1s->y <= (int32_t)a0e->y) continue; // keep colinearity if (a1s->x <= a0e->x || (int32_t)a1s->y <= (int32_t)a0e->y) continue; // keep colinearity
@ -248,6 +247,8 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
max_gap = max_gap > a1s->x - a0e->x? max_gap : a1s->x - a0e->x; max_gap = max_gap > a1s->x - a0e->x? max_gap : a1s->x - a0e->x;
min_gap = min_gap < a1s->x - a0e->x? min_gap : a1s->x - a0e->x; min_gap = min_gap < a1s->x - a0e->x? min_gap : a1s->x - a0e->x;
if (max_gap > opt->max_join_long || min_gap > opt->max_join_short) continue; if (max_gap > opt->max_join_long || min_gap > opt->max_join_short) continue;
sc_thres = (int)((float)opt->min_join_flank_sc / opt->max_join_long * max_gap + .499); // TODO: also require length
if (r0->score < sc_thres || r1->score < sc_thres) continue; // require good flanking chains
// all conditions satisfied; join // all conditions satisfied; join
a[r1->as].y |= 1ULL<<40; a[r1->as].y |= 1ULL<<40;

2
main.c
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@ -10,7 +10,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r164-pre" #define MM_VERSION "2.0-r167-pre"
void liftrlimit() void liftrlimit()
{ {

2
map.c
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@ -28,7 +28,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->max_join_long = 20000; opt->max_join_long = 20000;
opt->max_join_short = 2000; opt->max_join_short = 2000;
opt->min_join_flank_sc = 500; opt->min_join_flank_sc = 1000;
opt->a = 2, opt->b = 4, opt->q = 4, opt->e = 2, opt->q2 = 24, opt->e2 = 1; opt->a = 2, opt->b = 4, opt->q = 4, opt->e = 2, opt->q2 = 24, opt->e2 = 1;
opt->zdrop = 400; opt->zdrop = 400;