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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-11-09 22:37:36 -05:00
parent 6313aae2c4 74a18d3de8
commit 315ac68b0b
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -619,10 +619,10 @@ public class PairHMMIndelErrorModel {
return 0; // sanity check return 0; // sanity check
for (int i=0; i < b1.length; i++ ){ for (int i=0; i < b1.length; i++ ){
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) {
@ -630,10 +630,10 @@ public class PairHMMIndelErrorModel {
return 0; // sanity check return 0; // sanity check
for (int i=0; i < b1.length; i++ ){ for (int i=0; i < b1.length; i++ ){
if ( b1[i]!= b2[i]) if ( MathUtils.compareDoubles(b1[i], b2[i]) != 0 )
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[][]) {