From 31ef055224fe2a23141bd82d87f30b9dd5f5b34a Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 1 Oct 2010 04:29:55 +0000 Subject: [PATCH] I am changing the gap open probability back to 0.001. It seems that being conservative here is a good thing... --- kaln.c | 2 +- misc/HmmGlocal.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/kaln.c b/kaln.c index bac6e64..3aca09c 100644 --- a/kaln.c +++ b/kaln.c @@ -379,7 +379,7 @@ static float g_qual2prob[256]; #define set_u(u, b, i, k) { int x=(i)-(b); x=x>0?x:0; (u)=((k)-x+1)*3; } -ka_probpar_t ka_probpar_def = { 1e-4, 0.1, 10 }; +ka_probpar_t ka_probpar_def = { 0.001, 0.1, 10 }; /* The topology of the profile HMM: diff --git a/misc/HmmGlocal.java b/misc/HmmGlocal.java index 469eda6..9e93b13 100644 --- a/misc/HmmGlocal.java +++ b/misc/HmmGlocal.java @@ -4,7 +4,7 @@ import java.lang.*; public class HmmGlocal { private double[] qual2prob; - private double cd, ce; // gap open probility [1e-4], gap extension probability [0.1] + private double cd, ce; // gap open probility [1e-3], gap extension probability [0.1] private int cb; // band width [7] public HmmGlocal(final double d, final double e, final int b) { -- 2.39.2