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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 "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r287-dirty" #define MM_VERSION "2.0-r288-dirty"
void liftrlimit() void liftrlimit()
{ {
@ -140,7 +140,7 @@ int main(int argc, char *argv[])
} else if (strcmp(optarg, "splice") == 0 || strcmp(optarg, "cdna") == 0) { } else if (strcmp(optarg, "splice") == 0 || strcmp(optarg, "cdna") == 0) {
k = 15, w = 5; k = 15, w = 5;
opt.flag |= MM_F_SPLICE; 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.a = 1, opt.b = 2, opt.q = 2, opt.e = 1, opt.q2 = 32, opt.e2 = 0;
opt.zdrop = 200; opt.zdrop = 200;
} else { } else {

4
minimap2.1
View File

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