From 51cfb60520c971e0a63d517bfb20b030c3a4a7bb Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 2 Jul 2017 22:51:45 -0400 Subject: [PATCH] r145: changed default -p from 2 to 0.8 For long reads, secondary alignments can be very information. --- main.c | 3 ++- map.c | 2 +- minimap2.1 | 10 +++++++--- 3 files changed, 10 insertions(+), 5 deletions(-) diff --git a/main.c b/main.c index 749b5f7..bf2dd6f 100644 --- a/main.c +++ b/main.c @@ -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"); diff --git a/map.c b/map.c index bb6a2c9..d363288 100644 --- a/map.c +++ b/map.c @@ -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; diff --git a/minimap2.1 b/minimap2.1 index 0afa761..545d2e2 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -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