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 bac6e640f2388d541c8ed302a21470cf066fc195..3aca09cc9a484528610d3db03c1d26b934e7d039 100644 (file)
--- 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 469eda654b376b7d76411af57ca18fdc22d70441..9e93b13bf9be72a208dfda69abc8ffbb43b78f50 100644 (file)
--- 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) {