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Fix for HMM optimization. If the two penalty arrays match exactly the function should return the end of the array instead of 0.

This commit is contained in:
Ryan Poplin 2011-11-09 22:00:52 -05:00
parent d828eba7f4
commit 348f2db7fd
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -622,7 +622,7 @@ public class PairHMMIndelErrorModel {
if ( b1[i]!= b2[i]) if ( b1[i]!= b2[i])
return i; return i;
} }
return 0; // sanity check return b1.length;
} }
private int computeFirstDifferingPosition(double[] b1, double[] b2) { private int computeFirstDifferingPosition(double[] b1, double[] b2) {
@ -633,7 +633,7 @@ public class PairHMMIndelErrorModel {
if ( b1[i]!= b2[i]) if ( b1[i]!= b2[i])
return i; return i;
} }
return 0; // sanity check return b1.length;
} }
private final static double[] getHaplotypeLikelihoods(final int numHaplotypes, final int readCounts[], final double readLikelihoods[][]) { private final static double[] getHaplotypeLikelihoods(final int numHaplotypes, final int readCounts[], final double readLikelihoods[][]) {