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r751: optionally output MD (#118)

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Heng Li
2018-03-22 14:15:33 -04:00
parent 623b5d9d48
commit 8766d286df
4 changed files with 70 additions and 27 deletions
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main.c
+3 -1
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@@ -10,7 +10,7 @@
#include "getopt.h"
#endif
#define MM_VERSION "2.9-r750-dirty"
#define MM_VERSION "2.9-r751-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -56,6 +56,7 @@ static struct option long_options[] = {
{ "dual", required_argument, 0, 0 }, // 26
{ "max-clip-ratio", required_argument, 0, 0 }, // 27
{ "min-occ-floor", required_argument, 0, 0 }, // 28
{ "MD", no_argument, 0, 0 }, // 29
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -170,6 +171,7 @@ int main(int argc, char *argv[])
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 ==29) opt.flag |= MM_F_OUT_MD; // --MD
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