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r463: optionally disable secondary hits

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Heng Li
2017-10-04 13:24:41 -04:00
parent 5babf41a38
commit 2581c44a21
3 changed files with 11 additions and 2 deletions
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main.c
+6 -1
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r462-dirty"
#define MM_VERSION "2.2-r463-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -40,6 +40,7 @@ static struct option long_options[] = {
{ "multi", optional_argument, 0, 0 },
{ "no-long-join", no_argument, 0, 0 },
{ "seed", required_argument, 0, 0 },
{ "print-2nd", optional_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -124,6 +125,10 @@ int main(int argc, char *argv[])
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag |= MM_F_MULTI_SEG;
else opt.flag &= ~MM_F_MULTI_SEG;
} else if (c == 0 && long_idx ==17) { // --print-2nd
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag &= ~MM_F_NO_PRINT_2ND;
else opt.flag |= MM_F_NO_PRINT_2ND;
} else if (c == 'V') {
puts(MM_VERSION);
return 0;