From 7598809577ab725268f20c92dcc691e4a3d3229c Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 11 Jul 2017 14:57:49 -0400 Subject: [PATCH] r171: reduced log gap cost at chaining The cost is so large that it discards too many valid seeds without HPC k-mers. This change may introduce false long gaps to reference mapping. We have another mechanism mm_filter_bad_seeds() to protect against this. In addition, minimap2 is not that bad to have long gaps. Some other aligners are worse. Still need tuning in future. --- chain.c | 2 +- main.c | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/chain.c b/chain.c index 586fc95..3887053 100644 --- a/chain.c +++ b/chain.c @@ -51,7 +51,7 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int if (dd > bw) continue; min_d = dq < dr? dq : dr; sc = min_d > q_span? q_span : dq < dr? dq : dr; - sc -= dd? ilog2_32(dd) * 4 : 0; + sc -= dd? ilog2_32(dd) * 2 : 0; if (min_d > q_span) sc -= ilog2_32(min_d) / 2; sc += f[j]; if (sc > max_f) max_f = sc, max_j = j; diff --git a/main.c b/main.c index c27d6e9..9a504a2 100644 --- a/main.c +++ b/main.c @@ -10,7 +10,7 @@ #include "minimap.h" #include "mmpriv.h" -#define MM_VERSION "2.0-r170-pre" +#define MM_VERSION "2.0-r171-pre" void liftrlimit() {