From 3d129be642d5d99b03fecc115e506f9c4bab15c4 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 22 Oct 2014 12:42:58 -0400 Subject: [PATCH] r943: change the default -y to 20, but ... for GRCh38 ALT, this is not enough. We need -y at least 40 to get high accuracy because a locus at chr19 has 35 copies. --- bwamem.c | 2 +- main.c | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bwamem.c b/bwamem.c index a7e7150..b32c166 100644 --- a/bwamem.c +++ b/bwamem.c @@ -59,7 +59,7 @@ mem_opt_t *mem_opt_init() o->pen_unpaired = 17; o->pen_clip5 = o->pen_clip3 = 5; - o->max_mem_intv = 10; + o->max_mem_intv = 20; o->min_seed_len = 19; o->split_width = 10; diff --git a/main.c b/main.c index a7ad841..7591875 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.10-r942-dirty" +#define PACKAGE_VERSION "0.7.10-r943-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);