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r965: added --chain-gap-scale for #540

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Heng Li
2020-01-18 10:29:33 -05:00
parent cdb7857841
commit 040f74102c
8 changed files with 19 additions and 9 deletions
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main.c
+3 -1
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@@ -7,7 +7,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.17-r963-dirty"
#define MM_VERSION "2.17-r965-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -67,6 +67,7 @@ static ko_longopt_t long_options[] = {
{ "junc-bed", ko_required_argument, 340 },
{ "junc-bonus", ko_required_argument, 341 },
{ "sam-hit-only", ko_no_argument, 342 },
{ "chain-gap-scale",ko_required_argument, 343 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
@@ -211,6 +212,7 @@ int main(int argc, char *argv[])
else if (c == 340) junc_bed = o.arg; // --junc-bed
else if (c == 341) opt.junc_bonus = atoi(o.arg); // --junc-bonus
else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
else if (c == 343) opt.chain_gap_scale = atof(o.arg); // --chain-gap-scale
else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary