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r684: separate end score from min_chain_score

This commit is contained in:
Heng Li 2018-02-05 11:40:38 -05:00
parent 3df5015668
commit dbf284b2d9
6 changed files with 9 additions and 4 deletions
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6
align.c
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@ -307,7 +307,7 @@ static void mm_fix_bad_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int mi
if (max - min > l >> 1) *as = i; if (max - min > l >> 1) *as = i;
l += min; l += min;
m += min < q_span? min : q_span; m += min < q_span? min : q_span;
if (l >= bw << 1 || m >= min_match) break; if (l >= bw << 1 || m >= min_match || m >= r->mlen >> 1) break;
} }
*cnt = r->as + r->cnt - *as; *cnt = r->as + r->cnt - *as;
m = l = a[r->as + r->cnt - 1].y >> 32 & 0xff; m = l = a[r->as + r->cnt - 1].y >> 32 & 0xff;
@ -321,7 +321,7 @@ static void mm_fix_bad_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int mi
if (max - min > l >> 1) *cnt = i + 1 - *as; if (max - min > l >> 1) *cnt = i + 1 - *as;
l += min; l += min;
m += min < q_span? min : q_span; m += min < q_span? min : q_span;
if (l >= bw << 1 || m >= min_match) break; if (l >= bw << 1 || m >= min_match || m >= r->mlen >> 1) break;
} }
} }
@ -422,7 +422,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
if (is_splice) { if (is_splice) {
mm_fix_bad_ends_splice(km, opt, mi, r, mat, qlen, qseq0, a, &as1, &cnt1); mm_fix_bad_ends_splice(km, opt, mi, r, mat, qlen, qseq0, a, &as1, &cnt1);
} else { } else {
mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score, &as1, &cnt1); mm_fix_bad_ends(r, a, opt->bw, opt->min_end_match, &as1, &cnt1);
} }
mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10); mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs); mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);

2
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "getopt.h" #include "getopt.h"
#define MM_VERSION "2.8-r677-dirty" #define MM_VERSION "2.8-r684-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

1
minimap.h
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@ -120,6 +120,7 @@ typedef struct {
int end_bonus; int end_bonus;
int min_dp_max; // drop an alignment if the score of the max scoring segment is below this threshold int min_dp_max; // drop an alignment if the score of the max scoring segment is below this threshold
int min_ksw_len; int min_ksw_len;
int min_end_match;
int anchor_ext_len, anchor_ext_shift; int anchor_ext_len, anchor_ext_shift;
int pe_ori, pe_bonus; int pe_ori, pe_bonus;

2
misc/mapstat.js 100644 → 100755
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@ -1,3 +1,5 @@
#!/usr/bin/env k8
var getopt = function(args, ostr) { var getopt = function(args, ostr) {
var oli; // option letter list index var oli; // option letter list index
if (typeof(getopt.place) == 'undefined') if (typeof(getopt.place) == 'undefined')

1
options.c
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@ -28,6 +28,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->end_bonus = -1; opt->end_bonus = -1;
opt->min_dp_max = opt->min_chain_score * opt->a; opt->min_dp_max = opt->min_chain_score * opt->a;
opt->min_ksw_len = 200; opt->min_ksw_len = 200;
opt->min_end_match = 200;
opt->anchor_ext_len = 20, opt->anchor_ext_shift = 6; opt->anchor_ext_len = 20, opt->anchor_ext_shift = 6;
opt->mini_batch_size = 500000000; opt->mini_batch_size = 500000000;

1
python/cmappy.pxd
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@ -30,6 +30,7 @@ cdef extern from "minimap.h":
int end_bonus int end_bonus
int min_dp_max int min_dp_max
int min_ksw_len int min_ksw_len
int min_end_match;
int anchor_ext_len, anchor_ext_shift int anchor_ext_len, anchor_ext_shift
int pe_ori, pe_bonus int pe_ori, pe_bonus
float mid_occ_frac float mid_occ_frac