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Updating busted integration tests

This commit is contained in:
Eric Banks 2011-12-14 16:24:43 -05:00
parent e90d77e531
commit 4fddac9f22
2 changed files with 7 additions and 4 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -817,7 +817,7 @@ public class UnifiedGenotyperEngine {
// create the new likelihoods array from the alleles we are allowed to use
final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
final double[] newLikelihoods;
double[] newLikelihoods;
if ( likelihoodIndexesToUse == null ) {
newLikelihoods = originalLikelihoods;
} else {
@ -825,6 +825,9 @@ public class UnifiedGenotyperEngine {
int newIndex = 0;
for ( int oldIndex : likelihoodIndexesToUse )
newLikelihoods[newIndex++] = originalLikelihoods[oldIndex];
// might need to re-normalize
newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
}
// if there is no mass on the (new) likelihoods and we actually have alternate alleles, then just no-call the sample
@ -846,7 +849,7 @@ public class UnifiedGenotyperEngine {
if ( numNewAltAlleles == 0 )
attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
else
attrs.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, newLikelihoods);
attrs.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(newLikelihoods));
calls.add(new Genotype(sample, myAlleles, qual, null, attrs, false));
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -129,8 +129,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testOutputParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-sites_only", "44f3b5b40e6ad44486cddfdb7e0bfcd8" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "94e53320f14c5ff29d62f68d36b46fcd" );
e.put( "--output_mode EMIT_ALL_SITES", "73ad1cc41786b12c5f0e6f3e9ec2b728" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "274bd9d1b9c7857690fa5f0228ffc6d7" );
e.put( "--output_mode EMIT_ALL_SITES", "594c6d3c48bbc73289de7727d768644d" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(