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r894: added --max-qlen to filter out long query

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This commit is contained in:
Heng Li
2018-12-12 12:27:32 -05:00
parent eef1cee9b7
commit ea2b1c5b2a
4 changed files with 14 additions and 2 deletions
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main.c
+3 -1
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.14-r892-dirty"
#define MM_VERSION "2.14-r894-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -61,6 +61,7 @@ static ko_longopt_t long_options[] = {
{ "no-end-flt", ko_no_argument, 335 },
{ "hard-mask-level",ko_no_argument, 336 },
{ "cap-sw-mem", ko_required_argument, 337 },
{ "max-qlen", ko_required_argument, 338 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
@@ -192,6 +193,7 @@ int main(int argc, char *argv[])
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 == 337) opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
else if (c == 338) opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary