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Merge branch 'dev'

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This commit is contained in:
Heng Li
2017-08-08 21:30:32 -04:00
parent 6840370f3c 4badf2fcbf
commit 3dbe23b34e
30 changed files with 4436 additions and 28 deletions
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main.c
+5 -3
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@@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r275"
#define MM_VERSION "2.0-r276-dirty"
void liftrlimit()
{
@@ -54,7 +54,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt_long(argc, argv, "aw:k:K:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Q", long_options, &long_idx)) >= 0) {
while ((c = getopt_long(argc, argv, "aSw:k:K:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Q", long_options, &long_idx)) >= 0) {
if (c == 'w') w = atoi(optarg), idx_par_set = 1;
else if (c == 'k') k = atoi(optarg), idx_par_set = 1;
else if (c == 'H') is_hpc = 1, idx_par_set = 1;
@@ -67,7 +67,8 @@ int main(int argc, char *argv[])
else if (c == 'N') opt.best_n = atoi(optarg);
else if (c == 'p') opt.pri_ratio = atof(optarg);
else if (c == 'M') opt.mask_level = atof(optarg);
else if (c == 'c') opt.flag |= MM_F_CIGAR;
else if (c == 'c') opt.flag |= MM_F_OUT_CG | MM_F_CIGAR;
else if (c == 'S') opt.flag |= MM_F_OUT_CS | MM_F_CIGAR;
else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
else if (c == 'Q') opt.flag |= MM_F_NO_QUAL;
@@ -166,6 +167,7 @@ int main(int argc, char *argv[])
fprintf(stderr, " -Q ignore base quality in the input\n");
fprintf(stderr, " -a output in the SAM format (PAF by default)\n");
fprintf(stderr, " -c output CIGAR in PAF\n");
fprintf(stderr, " -S output the cs tag in PAF\n");
fprintf(stderr, " -t INT number of threads [%d]\n", n_threads);
fprintf(stderr, " -K NUM minibatch size [200M]\n");
// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose);