zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

r145: changed default -p from 2 to 0.8 

For long reads, secondary alignments can be very information.
This commit is contained in:
Heng Li 2017-07-02 22:51:45 -04:00
parent 632b8638d2
commit 51cfb60520
3 changed files with 10 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
main.c
View File

@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r144-pre"
#define MM_VERSION "2.0-r145-pre"
void liftrlimit()
{
@ -143,6 +143,7 @@ int main(int argc, char *argv[])
// fprintf(stderr, " -T INT SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); // TODO: this option is never used; might be buggy
fprintf(stderr, " -S skip self and dual mappings (for the all-vs-all mode)\n");
fprintf(stderr, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
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 -Sw5 -p0 -m100 -D.05 (PacBio/ONT all-vs-all read mapping)\n");

2
map.c
View File

@ -23,7 +23,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->min_seedcov_ratio = 0.0f;
opt->mask_level = 0.5f;
opt->pri_ratio = 2.0f;
opt->pri_ratio = 0.8f;
opt->best_n = 5;
opt->max_join_long = 20000;

10
minimap2.1
View File

@ -1,4 +1,4 @@
.TH minimap2 1 "1 July 2017" "minimap2-2.0-r141-pre" "Bioinformatics tools"
.TH minimap2 1 "1 July 2017" "minimap2-2.0-r145-pre" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@ -149,14 +149,18 @@ will be suppressed; if the query sequence name is the same as the target name,
diagonal minimizer hits will also be suppressed.
.TP
.BI -p \ FLOAT
Minimal secondary-to-primary score ratio to output secondary mappings [2].
Minimal secondary-to-primary score ratio to output secondary mappings [0.8].
Between two chains overlaping over half of the shorter chain (controled by
.BR --mask-level ),
the chain with a lower score is secondary to the chain with a higher score.
If the ratio of the scores is below
.IR FLOAT ,
the secondary chain will not be outputted or extended with DP alignment later.
The default value suppresses all secondary chains.
.TP
.BI -N \ INT
Output at most
.I INT
secondary alignments [5]
.TP
.BI -D \ FLOAT
Discard a chain if the fraction of matching bases over the length of