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r703: added --max-clip-ratio 

still testing the option
This commit is contained in:
Heng Li 2018-02-12 13:29:18 -05:00
parent f66de7df59
commit 7ef5490884
7 changed files with 12 additions and 6 deletions
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2
align.c
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@ -720,7 +720,7 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
*n_regs_ = n_regs; *n_regs_ = n_regs;
kfree(km, qseq0[0]); kfree(km, qseq0[0]);
kfree(km, ez.cigar); kfree(km, ez.cigar);
mm_filter_regs(km, opt, n_regs_, regs); mm_filter_regs(km, opt, qlen, n_regs_, regs);
mm_hit_sort_by_dp(km, n_regs_, regs); mm_hit_sort_by_dp(km, n_regs_, regs);
return regs; return regs;
} }

7
hit.c
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@ -245,16 +245,17 @@ void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_,
} }
} }
void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs) void mm_filter_regs(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs)
{ // NB: after this call, mm_reg1_t::parent can be -1 if its parent filtered out { // NB: after this call, mm_reg1_t::parent can be -1 if its parent filtered out
int i, k; int i, k;
for (i = k = 0; i < *n_regs; ++i) { for (i = k = 0; i < *n_regs; ++i) {
mm_reg1_t *r = &regs[i]; mm_reg1_t *r = &regs[i];
int flt = 0; int flt = 0;
if (!r->inv && !r->seg_split && r->cnt < opt->min_cnt) flt = 1; if (!r->inv && !r->seg_split && r->cnt < opt->min_cnt) flt = 1;
if (r->p) { if (r->p) { // these filters are only applied when base-alignment is available
if (r->mlen < opt->min_chain_score) flt = 1; if (r->mlen < opt->min_chain_score) flt = 1;
else if (r->p->dp_max < opt->min_dp_max) flt = 1; else if (r->p->dp_max < opt->min_dp_max) flt = 1;
else if (r->qs > qlen * opt->max_clip_ratio && qlen - r->qe > qlen * opt->max_clip_ratio) flt = 1;
if (flt) free(r->p); if (flt) free(r->p);
} }
if (!flt) { if (!flt) {
@ -337,7 +338,7 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
r->parent = regs[r->parent].parent; r->parent = regs[r->parent].parent;
} }
} }
mm_filter_regs(km, opt, n_regs_, regs); mm_filter_regs(km, opt, qlen, n_regs_, regs);
mm_sync_regs(km, *n_regs_, regs); mm_sync_regs(km, *n_regs_, regs);
} }
} }

4
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-r686-dirty" #define MM_VERSION "2.8-r703-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>
@ -50,6 +50,7 @@ static struct option long_options[] = {
{ "heap-sort", required_argument, 0, 0 }, // 24 { "heap-sort", required_argument, 0, 0 }, // 24
{ "all-chain", no_argument, 0, 'P' }, { "all-chain", no_argument, 0, 'P' },
{ "dual", required_argument, 0, 0 }, // 26 { "dual", required_argument, 0, 0 }, // 26
{ "max-clip-ratio", required_argument, 0, 0 }, // 27
{ "help", no_argument, 0, 'h' }, { "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' }, { "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' }, { "version", no_argument, 0, 'V' },
@ -163,6 +164,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==21) opt.anchor_ext_shift = atoi(optarg); // --end-seed-pen else if (c == 0 && long_idx ==21) opt.anchor_ext_shift = atoi(optarg); // --end-seed-pen
else if (c == 0 && long_idx ==22) opt.flag |= MM_F_FOR_ONLY; // --for-only else if (c == 0 && long_idx ==22) opt.flag |= MM_F_FOR_ONLY; // --for-only
else if (c == 0 && long_idx ==23) opt.flag |= MM_F_REV_ONLY; // --rev-only else if (c == 0 && long_idx ==23) opt.flag |= MM_F_REV_ONLY; // --rev-only
else if (c == 0 && long_idx ==27) opt.max_clip_ratio = atof(optarg); // --max-clip-ratio
else if (c == 0 && long_idx == 14) { // --frag else if (c == 0 && long_idx == 14) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1); yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
} else if (c == 0 && long_idx == 15) { // --secondary } else if (c == 0 && long_idx == 15) { // --secondary

1
minimap.h
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@ -121,6 +121,7 @@ typedef struct {
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 anchor_ext_len, anchor_ext_shift; int anchor_ext_len, anchor_ext_shift;
float max_clip_ratio; // drop an alignment if BOTH ends are clipped above this ratio
int pe_ori, pe_bonus; int pe_ori, pe_bonus;

2
mmpriv.h
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@ -75,7 +75,7 @@ int mm_set_sam_pri(int n, mm_reg1_t *r);
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff); void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff);
void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_, mm_reg1_t *r); void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_, mm_reg1_t *r);
void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int max_gap_ref, int min_diff, int best_n, int n_segs, const int *qlens, int *n_, mm_reg1_t *r); void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int max_gap_ref, int min_diff, int best_n, int n_segs, const int *qlens, int *n_, mm_reg1_t *r);
void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs); void mm_filter_regs(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs);
void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs, mm128_t *a); void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs, mm128_t *a);
void mm_hit_sort_by_dp(void *km, int *n_regs, mm_reg1_t *r); void mm_hit_sort_by_dp(void *km, int *n_regs, mm_reg1_t *r);
void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr); void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr);

1
options.c
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@ -29,6 +29,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
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->anchor_ext_len = 20, opt->anchor_ext_shift = 6; opt->anchor_ext_len = 20, opt->anchor_ext_shift = 6;
opt->max_clip_ratio = 1.0f;
opt->mini_batch_size = 500000000; opt->mini_batch_size = 500000000;
opt->pe_ori = 0; // FF opt->pe_ori = 0; // FF

1
python/cmappy.pxd
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@ -31,6 +31,7 @@ cdef extern from "minimap.h":
int min_dp_max int min_dp_max
int min_ksw_len int min_ksw_len
int anchor_ext_len, anchor_ext_shift int anchor_ext_len, anchor_ext_shift
float max_clip_ratio
int pe_ori, pe_bonus int pe_ori, pe_bonus
float mid_occ_frac float mid_occ_frac
int32_t mid_occ int32_t mid_occ