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r92: fixed a bug for overlapping alignment

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On the PBcR example E. coli reads, miniasm gives one circular unitig.
This commit is contained in:
Heng Li
2017-06-27 22:03:31 -04:00
parent 51057ab673
commit cdc2a1e29f
3 changed files with 6 additions and 3 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-r90-pre"
#define MM_VERSION "2.0-r92-pre"
void liftrlimit()
{
@@ -112,7 +112,7 @@ 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.min_score = 100, opt.pri_ratio = 0.0f;
is_hpc = 1, k = 19, w = 5;
}
}
@@ -138,7 +138,7 @@ int main(int argc, char *argv[])
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 -s100 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " ava10k: -Hk19 -Sw5 -p0 -s100 (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);