From: Heng Li <lh3@live.co.uk>
Date: Fri, 1 Oct 2010 04:29:55 +0000 (+0000)
Subject: I am changing the gap open probability back to 0.001. It seems that
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=31ef055224fe2a23141bd82d87f30b9dd5f5b34a;p=samtools.git

I am changing the gap open probability back to 0.001. It seems that
being conservative here is a good thing...
---

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) {