zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

r822: added option --no-end-flt

This commit is contained in:
Heng Li 2018-08-05 19:42:12 -04:00
parent b32296e18f
commit 5ab6538757
4 changed files with 14 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
align.c
View File

@ -563,11 +563,12 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
re = (int32_t)a[as1+cnt1-1].x + 1;
qe = (int32_t)a[as1+cnt1-1].y + 1;
} else {
if (is_splice) {
mm_fix_bad_ends_splice(km, opt, mi, r, mat, qlen, qseq0, a, &as1, &cnt1);
} else {
mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score * 2, &as1, &cnt1);
}
if (!(opt->flag & MM_F_NO_END_FLT)) {
if (is_splice)
mm_fix_bad_ends_splice(km, opt, mi, r, mat, qlen, qseq0, a, &as1, &cnt1);
else
mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score * 2, &as1, &cnt1);
} else as1 = r->as, cnt1 = r->cnt;
mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
mm_filter_bad_seeds_alt(km, as1, cnt1, a, 30, opt->max_gap>>1);
mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);

4
main.c
View File

@ -10,7 +10,7 @@
#include "getopt.h"
#endif
#define MM_VERSION "2.11-r821-dirty"
#define MM_VERSION "2.11-r822-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -62,6 +62,7 @@ static struct option long_options[] = {
{ "eqx", no_argument, 0, 0 }, // 32
{ "paf-no-hit", no_argument, 0, 0 }, // 33
{ "split-prefix", required_argument, 0, 0 }, // 34
{ "no-end-flt", no_argument, 0, 0 }, // 35
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@ -183,6 +184,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==32) opt.flag |= MM_F_EQX; // --eqx
else if (c == 0 && long_idx ==33) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
else if (c == 0 && long_idx ==34) opt.split_prefix = optarg; // --split-prefix
else if (c == 0 && long_idx ==35) opt.flag |= MM_F_NO_END_FLT; // --no-end-flt
else if (c == 0 && long_idx == 14) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
} else if (c == 0 && long_idx == 15) { // --secondary

1
minimap.h
View File

@ -33,6 +33,7 @@
#define MM_F_COPY_COMMENT 0x2000000
#define MM_F_EQX 0x4000000 // use =/X instead of M
#define MM_F_PAF_NO_HIT 0x8000000 // output unmapped reads to PAF
#define MM_F_NO_END_FLT 0x10000000
#define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2

4
minimap2.1
View File

@ -360,6 +360,10 @@ the length of the terminal gap in the chain. This option is only effective
with
.BR --splice .
It helps to avoid tiny terminal exons. [6]
.TP
.B --no-end-flt
Don't filter seeds towards the ends of chains before performing base-level
alignment.
.SS Input/output options
.TP 10
.B -a