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r273: cdna mapping mode for testing

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Differences from the typical mapping mode:

* banded alignment disabled
* log gap cost during chaining
* zero long-gap extension during alignment
* up to 100kb (by default) reference gap
* bad seeding not filtered (to tune later)
This commit is contained in:
Heng Li
2017-08-08 11:31:49 -04:00
parent 4badf2fcbf
commit 1a7d782131
6 changed files with 33 additions and 15 deletions
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main.c
+7 -1
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@@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0rc1-r238-dirty"
#define MM_VERSION "2.0rc1-r273-dirty"
void liftrlimit()
{
@@ -129,6 +129,12 @@ int main(int argc, char *argv[])
k = 19, w = 19;
opt.a = 1, opt.b = 9, opt.q = 16, opt.q2 = 41, opt.e = 2, opt.e2 = 1, opt.zdrop = 200;
opt.min_dp_max = 200;
} else if (strcmp(optarg, "cdna") == 0) {
k = 15, w = 5;
opt.flag |= MM_F_CDNA;
opt.max_gap = 2000, opt.max_gap_ref = opt.bw = 100000;
opt.a = 1, opt.b = 2, opt.q = 2, opt.e = 1, opt.q2 = 70, opt.e2 = 0;
opt.zdrop = 200;
} else {
fprintf(stderr, "[E::%s] unknown preset '%s'\n", __func__, optarg);
return 1;