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r93: fixed various small issues

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This commit is contained in:
Heng Li
2017-06-28 10:35:21 -04:00
parent cdc2a1e29f
commit bcd9b1c621
4 changed files with 64 additions and 23 deletions
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main.c
+10 -7
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@@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r92-pre"
#define MM_VERSION "2.0-r93-pre"
void liftrlimit()
{
@@ -47,8 +47,9 @@ static struct option long_options[] = {
{ "int-rname", no_argument, 0, 0 },
{ "version", no_argument, 0, 'V' },
{ "min-count", required_argument, 0, 'n' },
{ "min-chain-score",required_argument, 0, 's' },
{ "min-chain-score",required_argument, 0, 'm' },
{ "mask-level", required_argument, 0, 'M' },
{ "min-dp-score", required_argument, 0, 's' },
{ 0, 0, 0, 0}
};
@@ -66,7 +67,7 @@ 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:n:z:F:A:B:O:E:", 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:A:B:O:E:m:", 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;
@@ -82,12 +83,13 @@ int main(int argc, char *argv[])
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 == 'm') opt.min_chain_score = atoi(optarg);
else if (c == 'A') opt.a = atoi(optarg);
else if (c == 'B') opt.b = atoi(optarg);
else if (c == 'O') opt.q = atoi(optarg);
else if (c == 'E') opt.e = atoi(optarg);
else if (c == 'z') opt.zdrop = atoi(optarg);
else if (c == 's') opt.min_dp_score = atoi(optarg);
else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // bucket-bits
else if (c == 0 && long_idx == 2) keep_name = 0; // int-rname
else if (c == 'V') {
@@ -112,7 +114,7 @@ int main(int argc, char *argv[])
} else if (c == 'x') {
if (strcmp(optarg, "ava10k") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF;
opt.min_score = 100, opt.pri_ratio = 0.0f;
opt.min_chain_score = 100, opt.pri_ratio = 0.0f;
is_hpc = 1, k = 19, w = 5;
}
}
@@ -132,19 +134,20 @@ int main(int argc, char *argv[])
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, " -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, " -m INT minimal chaining score [%d]\n", opt.min_chain_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");
fprintf(stderr, " -p FLOAT threshold to output a mapping [%g]\n", opt.pri_ratio);
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
fprintf(stderr, " ava10k: -Hk19 -Sw5 -p0 -s100 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " ava10k: -Hk19 -Sw5 -p0 -m100 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " Alignment:\n");
fprintf(stderr, " -A INT matching score [%d]\n", opt.a);
fprintf(stderr, " -B INT mismatch penalty [%d]\n", opt.b);
fprintf(stderr, " -O INT gap open penalty [%d]\n", opt.q);
fprintf(stderr, " -E INT gap extension penalty; a k-long gap costs {-O}+k*{-E} [%d]\n", opt.e);
fprintf(stderr, " -z INT Z-drop score [%d]\n", opt.zdrop);
fprintf(stderr, " -s INT minimal DP alignment score [%d]\n", opt.min_dp_score);
fprintf(stderr, " Input/Output:\n");
fprintf(stderr, " -F STR output format: sam or paf [paf]\n");
fprintf(stderr, " -c output CIGAR in PAF\n");