diff --git a/main.c b/main.c index c35a1bd..167a6f5 100644 --- a/main.c +++ b/main.c @@ -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 { diff --git a/minimap2.1 b/minimap2.1 index b9113f1..e403731 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -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,