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r703: added --max-clip-ratio

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still testing the option
This commit is contained in:
Heng Li
2018-02-12 13:29:18 -05:00
parent f66de7df59
commit 7ef5490884
7 changed files with 12 additions and 6 deletions
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main.c
+3 -1
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.8-r686-dirty"
#define MM_VERSION "2.8-r703-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -50,6 +50,7 @@ static struct option long_options[] = {
{ "heap-sort", required_argument, 0, 0 }, // 24
{ "all-chain", no_argument, 0, 'P' },
{ "dual", required_argument, 0, 0 }, // 26
{ "max-clip-ratio", required_argument, 0, 0 }, // 27
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -163,6 +164,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==21) opt.anchor_ext_shift = atoi(optarg); // --end-seed-pen
else if (c == 0 && long_idx ==22) opt.flag |= MM_F_FOR_ONLY; // --for-only
else if (c == 0 && long_idx ==23) opt.flag |= MM_F_REV_ONLY; // --rev-only
else if (c == 0 && long_idx ==27) opt.max_clip_ratio = atof(optarg); // --max-clip-ratio
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