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r941: set a min length for 3rd-round seeding

This commit is contained in:
Heng Li 2014-10-21 13:15:42 -04:00
parent 282130a64e
commit 60b728487a
4 changed files with 6 additions and 6 deletions
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4
bwamem.c
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@ -147,7 +147,7 @@ static void mem_collect_intv(const mem_opt_t *opt, const bwt_t *bwt, int len, co
if (seq[x] < 4) { if (seq[x] < 4) {
if (1) { if (1) {
bwtintv_t m; bwtintv_t m;
x = bwt_seed_strategy1(bwt, len, seq, x, opt->max_mem_intv, &m); x = bwt_seed_strategy1(bwt, len, seq, x, opt->min_seed_len, opt->max_mem_intv, &m);
if (m.x[2] > 0) kv_push(bwtintv_t, a->mem, m); if (m.x[2] > 0) kv_push(bwtintv_t, a->mem, m);
} else { // for now, we never come to this block which is slower } else { // for now, we never come to this block which is slower
x = bwt_smem1a(bwt, len, seq, x, start_width, opt->max_mem_intv, &a->mem1, a->tmpv); x = bwt_smem1a(bwt, len, seq, x, start_width, opt->max_mem_intv, &a->mem1, a->tmpv);
@ -274,7 +274,7 @@ mem_chain_v mem_chain(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
bwtintv_t *p = &aux->mem.a[i]; bwtintv_t *p = &aux->mem.a[i];
int step, count, slen = (uint32_t)p->info - (p->info>>32); // seed length int step, count, slen = (uint32_t)p->info - (p->info>>32); // seed length
int64_t k; int64_t k;
if (slen < opt->min_seed_len) continue; // ignore if too short or too repetitive // if (slen < opt->min_seed_len) continue; // ignore if too short or too repetitive
step = p->x[2] > opt->max_occ? p->x[2] / opt->max_occ : 1; step = p->x[2] > opt->max_occ? p->x[2] / opt->max_occ : 1;
for (k = count = 0; k < p->x[2] && count < opt->max_occ; k += step, ++count) { for (k = count = 0; k < p->x[2] && count < opt->max_occ; k += step, ++count) {
mem_chain_t tmp, *lower, *upper; mem_chain_t tmp, *lower, *upper;

4
bwt.c
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@ -355,7 +355,7 @@ int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv,
return bwt_smem1a(bwt, len, q, x, min_intv, 0, mem, tmpvec); return bwt_smem1a(bwt, len, q, x, min_intv, 0, mem, tmpvec);
} }
int bwt_seed_strategy1(const bwt_t *bwt, int len, const uint8_t *q, int x, int max_intv, bwtintv_t *mem) int bwt_seed_strategy1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_len, int max_intv, bwtintv_t *mem)
{ {
int i, c; int i, c;
bwtintv_t ik, ok[4]; bwtintv_t ik, ok[4];
@ -367,7 +367,7 @@ int bwt_seed_strategy1(const bwt_t *bwt, int len, const uint8_t *q, int x, int m
if (q[i] < 4) { // an A/C/G/T base if (q[i] < 4) { // an A/C/G/T base
c = 3 - q[i]; // complement of q[i] c = 3 - q[i]; // complement of q[i]
bwt_extend(bwt, &ik, ok, 0); bwt_extend(bwt, &ik, ok, 0);
if (ok[c].x[2] < max_intv) { if (ok[c].x[2] < max_intv && i - x >= min_len) {
*mem = ok[c]; *mem = ok[c];
mem->info = (uint64_t)x<<32 | (i + 1); mem->info = (uint64_t)x<<32 | (i + 1);
return i + 1; return i + 1;

2
bwt.h
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@ -121,7 +121,7 @@ extern "C" {
int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2]); int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2]);
int bwt_smem1a(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, uint64_t max_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2]); int bwt_smem1a(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, uint64_t max_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2]);
int bwt_seed_strategy1(const bwt_t *bwt, int len, const uint8_t *q, int x, int max_intv, bwtintv_t *mem); int bwt_seed_strategy1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_len, int max_intv, bwtintv_t *mem);
#ifdef __cplusplus #ifdef __cplusplus
} }

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r940-dirty" #define PACKAGE_VERSION "0.7.10-r941-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);