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r770: matching N bases not working properly (#155)

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Heng Li
2018-04-30 19:55:23 -04:00
parent aef7b0744c
commit 734ac379bb
9 changed files with 19 additions and 10 deletions
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main.c
+3 -1
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@@ -10,7 +10,7 @@
#include "getopt.h"
#endif
#define MM_VERSION "2.10-r768-dirty"
#define MM_VERSION "2.10-r770-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -58,6 +58,7 @@ static struct option long_options[] = {
{ "min-occ-floor", required_argument, 0, 0 }, // 28
{ "MD", no_argument, 0, 0 }, // 29
{ "lj-min-ratio", required_argument, 0, 0 }, // 30
{ "score-N", required_argument, 0, 0 }, // 31
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -175,6 +176,7 @@ int main(int argc, char *argv[])
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 ==30) opt.min_join_flank_ratio = atof(optarg); // --lj-min-ratio
else if (c == 0 && long_idx ==31) opt.sc_ambi = atoi(optarg); // --score-N
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