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r288: changed max intron length to 200k

This commit is contained in:
Heng Li 2017-08-12 12:39:21 -04:00
parent d240318741
commit 5a74088b74
2 changed files with 4 additions and 4 deletions
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4
main.c
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@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r287-dirty"
#define MM_VERSION "2.0-r288-dirty"
void liftrlimit()
{
@ -140,7 +140,7 @@ int main(int argc, char *argv[])
} else if (strcmp(optarg, "splice") == 0 || strcmp(optarg, "cdna") == 0) {
k = 15, w = 5;
opt.flag |= MM_F_SPLICE;
opt.max_gap = 2000, opt.max_gap_ref = opt.bw = 100000;
opt.max_gap = 2000, opt.max_gap_ref = opt.bw = 200000;
opt.a = 1, opt.b = 2, opt.q = 2, opt.e = 1, opt.q2 = 32, opt.e2 = 0;
opt.zdrop = 200;
} else {

4
minimap2.1
View File

@ -163,7 +163,7 @@ secondary alignments [5]. This option has no effect when
is applied.
.TP
.BI -G \ NUM
Maximal intron length in the splice mode. This option also changes the
Maximal intron length in the splice mode [200k]. This option also changes the
bandwidth to
.IR NUM .
Increasing this option slows down spliced alignment.
@ -302,7 +302,7 @@ is that this preset is not using HPC minimizers.
.B splice
Long-read spliced alignment
.RB ( -k15
.B -w5 --splice -g2000 -G100k -A1 -B2 -O2,32 -E1,0
.B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0
.BR -z200 ).
As of now, minimap2 only finds approximate exon boundaries. The true boundaries
are usually within 10bp around the reported positions. In the splice mode,