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Merging bug fixes

This commit is contained in:
Guillermo del Angel 2012-04-19 12:49:30 -04:00
parent a530127956 02ff930f6a
commit 0e6e0cb907
2 changed files with 8 additions and 2 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -402,6 +402,12 @@ public class PairHMMIndelErrorModel {
contextLogGapOpenProbabilities, contextLogGapOpenProbabilities, contextLogGapContinuationProbabilities,
startIndexInHaplotype, matchMetricArray, XMetricArray, YMetricArray);
previousHaplotypeSeen = haplotypeBases.clone();
/* double l2 = computeReadLikehoodGivenHaplotype(haplotypeBases, readBases, readQuals, contextLogGapOpenProbabilities,
contextLogGapContinuationProbabilities, bandedLikelihoods);
*/
if (DEBUG) {
System.out.println("H:"+new String(haplotypeBases));
System.out.println("R:"+new String(readBases));

4
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -62,7 +62,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl -NO_HEADER -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + validationDataLocation + "multiallelic.snps.bam -o %s -L " + validationDataLocation + "multiallelic.snps.intervals", 1,
Arrays.asList("c956f0ea0e5f002288a09f4bc4af1319"));
Arrays.asList("e948543b83bfd0640fcb994d72f8e234"));
executeTest("test Multiple SNP alleles", spec);
}
@ -325,7 +325,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("0240f34e71f137518be233c9890a5349"));
Arrays.asList("537dd9b4174dc356fb13d8d3098ad602"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}