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r120: use max-scoring seg to control output

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much better now
This commit is contained in:
Heng Li
2017-06-30 14:21:44 -04:00
parent 08a61c3cfc
commit d11049eb32
5 changed files with 38 additions and 29 deletions
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main.c
+3 -3
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@@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r119-pre"
#define MM_VERSION "2.0-r120-pre"
void liftrlimit()
{
@@ -89,7 +89,7 @@ int main(int argc, char *argv[])
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 == 's') opt.min_dp_max = 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') {
@@ -147,7 +147,7 @@ int main(int argc, char *argv[])
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, " -s INT minimal peak DP alignment score [%d]\n", opt.min_dp_max);
fprintf(stderr, " Input/Output:\n");
fprintf(stderr, " -F STR output format: sam or paf [paf]\n");
fprintf(stderr, " -c output CIGAR in PAF\n");