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r444: changed the way orientation is specified

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The old model doesn't work with RF or RR orientation. The new model only works
with paired-end reads. For >2 segments, only FF is supported.
This commit is contained in:
Heng Li
2017-09-27 12:33:10 -04:00
parent f611edf6f2
commit a349d85280
4 changed files with 39 additions and 13 deletions
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main.c
+1 -6
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r443-dirty"
#define MM_VERSION "2.2-r444-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -38,7 +38,6 @@ static struct option long_options[] = {
{ "no-sam-sq", no_argument, 0, 0 },
{ "sr", no_argument, 0, 0 },
{ "multi-seg", optional_argument, 0, 0 },
{ "2nd-seg-rev", optional_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -121,10 +120,6 @@ 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 ==15) { // --2nd-seg-rev
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag |= MM_F_SEG_REV;
else opt.flag &= ~MM_F_SEG_REV;
} else if (c == 'V') {
puts(MM_VERSION);
return 0;