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r876: skip DP if taking too much RAM (#259)

This commit is contained in:
Heng Li 2018-11-05 11:43:10 -05:00
parent fd64dd26f6
commit 13981404e2
4 changed files with 13 additions and 2 deletions
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5
align.c
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@ -300,7 +300,10 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr); for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr);
fputc('\n', stderr); fputc('\n', stderr);
} }
if (opt->flag & MM_F_SPLICE) if (opt->max_sw_mat > 0 && (int64_t)tlen * qlen > opt->max_sw_mat) {
ksw_reset_extz(ez);
ez->zdropped = 1;
} else if (opt->flag & MM_F_SPLICE)
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, flag, ez); ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, flag, ez);
else if (opt->q == opt->q2 && opt->e == opt->e2) else if (opt->q == opt->q2 && opt->e == opt->e2)
ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, zdrop, end_bonus, flag, ez); ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, zdrop, end_bonus, flag, ez);

4
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.13-r875-dirty" #define MM_VERSION "2.13-r876-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>
@ -60,6 +60,7 @@ static ko_longopt_t long_options[] = {
{ "split-prefix", ko_required_argument, 334 }, { "split-prefix", ko_required_argument, 334 },
{ "no-end-flt", ko_no_argument, 335 }, { "no-end-flt", ko_no_argument, 335 },
{ "hard-mask-level",ko_no_argument, 336 }, { "hard-mask-level",ko_no_argument, 336 },
{ "cap-sw-mat", ko_required_argument, 337 },
{ "help", ko_no_argument, 'h' }, { "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' }, { "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' }, { "version", ko_no_argument, 'V' },
@ -190,6 +191,7 @@ int main(int argc, char *argv[])
else if (c == 334) opt.split_prefix = o.arg; // --split-prefix else if (c == 334) opt.split_prefix = o.arg; // --split-prefix
else if (c == 335) opt.flag |= MM_F_NO_END_FLT; // --no-end-flt else if (c == 335) opt.flag |= MM_F_NO_END_FLT; // --no-end-flt
else if (c == 336) opt.flag |= MM_F_HARD_MLEVEL; // --hard-mask-level else if (c == 336) opt.flag |= MM_F_HARD_MLEVEL; // --hard-mask-level
else if (c == 337) opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
else if (c == 314) { // --frag else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1); yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary } else if (c == 315) { // --secondary

1
minimap.h
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@ -139,6 +139,7 @@ typedef struct {
int32_t mid_occ; // ignore seeds with occurrences above this threshold int32_t mid_occ; // ignore seeds with occurrences above this threshold
int32_t max_occ; int32_t max_occ;
int mini_batch_size; // size of a batch of query bases to process in parallel int mini_batch_size; // size of a batch of query bases to process in parallel
int64_t max_sw_mat;
const char *split_prefix; const char *split_prefix;
} mm_mapopt_t; } mm_mapopt_t;

5
minimap2.1
View File

@ -373,6 +373,11 @@ It helps to avoid tiny terminal exons. [6]
.B --no-end-flt .B --no-end-flt
Don't filter seeds towards the ends of chains before performing base-level Don't filter seeds towards the ends of chains before performing base-level
alignment. alignment.
.TP
.BI --cap-sw-mat \ NUM
Skip alignment if the DP matrix size is above
.IR NUM .
Set 0 to disable [0].
.SS Input/output options .SS Input/output options
.TP 10 .TP 10
.B -a .B -a