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r89: added minimal number of minimizer counts

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This commit is contained in:
Heng Li
2017-06-27 18:43:15 -04:00
parent 8977f07269
commit fa80177e58
5 changed files with 19 additions and 11 deletions
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main.c
+9 -4
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@@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r88-pre"
#define MM_VERSION "2.0-r89-pre"
void liftrlimit()
{
@@ -46,6 +46,9 @@ static struct option long_options[] = {
{ "mb-size", required_argument, 0, 0 },
{ "int-rname", no_argument, 0, 0 },
{ "version", no_argument, 0, 'V' },
{ "min-count", required_argument, 0, 'n' },
{ "min-chain-score",required_argument, 0, 's' },
{ "mask-level", required_argument, 0, 'M' },
{ 0, 0, 0, 0}
};
@@ -63,7 +66,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt_long(argc, argv, "w:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:m:z:F:", long_options, &long_idx)) >= 0) {
while ((c = getopt_long(argc, argv, "w:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:F:", long_options, &long_idx)) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'H') is_hpc = 1;
@@ -74,10 +77,11 @@ int main(int argc, char *argv[])
else if (c == 'v') mm_verbose = atoi(optarg);
else if (c == 'g') opt.max_gap = atoi(optarg);
else if (c == 'p') opt.pri_ratio = atof(optarg);
else if (c == 'm') opt.mask_level = atof(optarg);
else if (c == 'M') opt.mask_level = atof(optarg);
else if (c == 'c') opt.flag |= MM_F_CIGAR;
else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
else if (c == 'T') opt.sdust_thres = atoi(optarg);
else if (c == 'n') opt.min_cnt = atoi(optarg);
else if (c == 's') opt.min_score = atoi(optarg);
else if (c == 'z') opt.zdrop = atoi(optarg);
else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // bucket-bits
@@ -123,7 +127,8 @@ int main(int argc, char *argv[])
fprintf(stderr, " Mapping:\n");
fprintf(stderr, " -f FLOAT filter out top FLOAT fraction of repetitive minimizers [%.3f]\n", opt.mid_occ_frac);
fprintf(stderr, " -r INT bandwidth [%d]\n", opt.bw);
fprintf(stderr, " -s INT min score [%d]\n", opt.min_score);
fprintf(stderr, " -n INT minimal number of minimizers [%d]\n", opt.min_cnt);
fprintf(stderr, " -s INT minimal chaining score (this is not SW score) [%d]\n", opt.min_score);
fprintf(stderr, " -g INT split a mapping if there is a gap longer than INT [%d]\n", opt.max_gap);
fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres);
fprintf(stderr, " -S skip self and dual mappings\n");