From 546623dcb4563a82b9c44a20de11c3ca9e21fa17 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 4 Oct 2021 21:24:35 -0400 Subject: [PATCH] r1109: disable chain_skip_scale by default Enabling the option slows down alignment, possibly because it fragments chains in difficult regions. --- main.c | 2 +- options.c | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/main.c b/main.c index fb8e1bc..2c85166 100644 --- a/main.c +++ b/main.c @@ -7,7 +7,7 @@ #include "mmpriv.h" #include "ketopt.h" -#define MM_VERSION "2.22-r1108-dirty" +#define MM_VERSION "2.22-r1109-dirty" #ifdef __linux__ #include diff --git a/options.c b/options.c index d4ef242..a672334 100644 --- a/options.c +++ b/options.c @@ -19,7 +19,7 @@ void mm_mapopt_init(mm_mapopt_t *opt) opt->min_mid_occ = 10; opt->max_mid_occ = 1000000; opt->sdust_thres = 0; // no SDUST masking - opt->q_occ_frac = 0.02f; + opt->q_occ_frac = 0.01f; opt->min_cnt = 3; opt->min_chain_score = 40; @@ -33,7 +33,7 @@ void mm_mapopt_init(mm_mapopt_t *opt) opt->rmq_rescue_size = 1000; opt->rmq_rescue_ratio = 0.1f; opt->chain_gap_scale = 0.8f; - opt->chain_skip_scale = 0.04f; + opt->chain_skip_scale = 0.0f; opt->max_max_occ = 4095; opt->occ_dist = 500;