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r460: added option --no-long-join

This commit is contained in:
Heng Li 2017-10-04 12:08:44 -04:00
parent 841763ec24
commit cf55c84056
3 changed files with 5 additions and 2 deletions
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4
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r459-dirty"
#define MM_VERSION "2.2-r460-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -38,6 +38,7 @@ static struct option long_options[] = {
{ "no-sam-sq", no_argument, 0, 0 },
{ "sr", no_argument, 0, 0 },
{ "multi-seg", optional_argument, 0, 0 },
{ "no-long-join", no_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@ -116,6 +117,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_SAM_SQ; // --no-sam-sq
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
else if (c == 0 && long_idx ==15) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
else if (c == 0 && long_idx ==14) { // --multi-seg
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag |= MM_F_MULTI_SEG;

2
map.c
View File

@ -242,7 +242,7 @@ static void chain_post(const mm_mapopt_t *opt, const mm_idx_t *mi, void *km, int
mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, opt->max_gap_ref, mi->k*2, opt->best_n, n_segs, qlens, n_regs, regs);
if (!(opt->flag & MM_F_SPLICE) && !(opt->flag & MM_F_SR))
if (!(opt->flag & MM_F_SPLICE) && !(opt->flag & MM_F_SR) && !(opt->flag & MM_F_NO_LJOIN))
mm_join_long(km, opt, qlen, n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
}
}

1
minimap.h
View File

@ -15,6 +15,7 @@
#define MM_F_SPLICE 0x080 // splice mode
#define MM_F_SPLICE_FOR 0x100 // match GT-AG
#define MM_F_SPLICE_REV 0x200 // match CT-AC, the reverse complement of GT-AG
#define MM_F_NO_LJOIN 0x400
#define MM_F_NO_SAM_SQ 0x800
#define MM_F_SR 0x1000
#define MM_F_MULTI_SEG 0x2000