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r460: added option --no-long-join

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Heng Li
2017-10-04 12:08:44 -04:00
parent 841763ec24
commit cf55c84056
3 changed files with 5 additions and 2 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 "2.2-r459-dirty"
#define MM_VERSION "2.2-r460-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -38,6 +38,7 @@ static struct option long_options[] = {
{ "no-sam-sq", no_argument, 0, 0 },
{ "sr", no_argument, 0, 0 },
{ "multi-seg", optional_argument, 0, 0 },
{ "no-long-join", no_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -116,6 +117,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_SAM_SQ; // --no-sam-sq
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
else if (c == 0 && long_idx ==15) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
else if (c == 0 && long_idx ==14) { // --multi-seg
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag |= MM_F_MULTI_SEG;