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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
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3
main.c
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@ -10,7 +10,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r144-pre" #define MM_VERSION "2.0-r145-pre"
void liftrlimit() 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, " -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, " -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, " -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, " -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, " -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"); fprintf(stderr, " ava10k: -Hk19 -Sw5 -p0 -m100 -D.05 (PacBio/ONT all-vs-all read mapping)\n");

2
map.c
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@ -23,7 +23,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->min_seedcov_ratio = 0.0f; opt->min_seedcov_ratio = 0.0f;
opt->mask_level = 0.5f; opt->mask_level = 0.5f;
opt->pri_ratio = 2.0f; opt->pri_ratio = 0.8f;
opt->best_n = 5; opt->best_n = 5;
opt->max_join_long = 20000; opt->max_join_long = 20000;

10
minimap2.1
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@ -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 .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences 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. diagonal minimizer hits will also be suppressed.
.TP .TP
.BI -p \ FLOAT .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 Between two chains overlaping over half of the shorter chain (controled by
.BR --mask-level ), .BR --mask-level ),
the chain with a lower score is secondary to the chain with a higher score. the chain with a lower score is secondary to the chain with a higher score.
If the ratio of the scores is below If the ratio of the scores is below
.IR FLOAT , .IR FLOAT ,
the secondary chain will not be outputted or extended with DP alignment later. 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 .TP
.BI -D \ FLOAT .BI -D \ FLOAT
Discard a chain if the fraction of matching bases over the length of Discard a chain if the fraction of matching bases over the length of