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r741: added --min-occ-floor to improve #107

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Heng Li
2018-03-12 14:32:27 -04:00
parent ad1beaf255
commit bdc615c1d4
5 changed files with 34 additions and 5 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 "2.9-r720"
#define MM_VERSION "2.9-r741-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -51,6 +51,7 @@ static struct option long_options[] = {
{ "all-chain", no_argument, 0, 'P' },
{ "dual", required_argument, 0, 0 }, // 26
{ "max-clip-ratio", required_argument, 0, 0 }, // 27
{ "min-occ-floor", required_argument, 0, 0 }, // 28
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -164,6 +165,7 @@ int main(int argc, char *argv[])
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 ==28) opt.min_mid_occ = atoi(optarg); // --min-occ-floor
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