being conservative here is a good thing...
#define set_u(u, b, i, k) { int x=(i)-(b); x=x>0?x:0; (u)=((k)-x+1)*3; }
#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:
/*
The topology of the profile HMM:
public class HmmGlocal
{
private double[] qual2prob;
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) {
private int cb; // band width [7]
public HmmGlocal(final double d, final double e, final int b) {