fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-05 21:48:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r168: fixed a bug in long join: a[] not sorted

Browse Source 
Also added length requirement for long join and changed -g in the ava mode
This commit is contained in:
Heng Li
2017-07-09 12:14:20 -04:00
parent 1ac48556ae
commit 782449975d
3 changed files with 28 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+3 -3
View File
@@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r167-pre"
#define MM_VERSION "2.0-r168-pre"
void liftrlimit()
{
@@ -120,7 +120,7 @@ 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_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f;
opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000;
is_hpc = 1, k = 19, w = 5;
} else if (strcmp(optarg, "map10k") == 0) {
is_hpc = 1, k = 19;
@@ -155,7 +155,7 @@ int main(int argc, char *argv[])
fprintf(stderr, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n);
fprintf(stderr, " -D FLOAT min fraction of minimizer matches [%g]\n", opt.min_seedcov_ratio);
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
fprintf(stderr, " ava10k: -Hk19 -w5 -Xp0 -m100 -D.05 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " ava10k: -Hk19 -w5 -Xp0 -m100 -D.05 -g10000 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " map10k: -Hk19 (PacBio/ONT vs reference mapping)\n");
fprintf(stderr, " asm1m: -k19 -w19 (intra-species assembly to ref mapping)\n");
fprintf(stderr, " Alignment:\n");