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Removed debug code outputing files not removed after VM exists in ReadThreadingLikelihoodCalculationEngineUnitTest. 

Notice however that this should not be the cause of resent problems as the code was desactivated.
This commit is contained in:
Valentin Ruano-Rubio 2014-05-28 19:03:25 -04:00
parent 938172d7f0
commit 07567fdae3
1 changed files with 1 additions and 37 deletions
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38
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
View File

@ -46,8 +46,8 @@
package org.broadinstitute.gatk.tools.walkers.haplotypecaller;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.collections.Pair;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
@ -57,18 +57,11 @@ import org.broadinstitute.gatk.utils.pairhmm.FlexibleHMM;
import org.broadinstitute.gatk.utils.pairhmm.PairHMM;
import org.broadinstitute.gatk.utils.sam.ClippedGATKSAMRecord;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import htsjdk.variant.variantcontext.Allele;
import org.testng.Assert;
import org.testng.Reporter;
import org.testng.SkipException;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.*;
/**
@ -86,29 +79,6 @@ public class ReadThreadingLikelihoodCalculationEngineUnitTest extends ActiveRegi
private static FlexibleHMM hmm = new FastLoglessPairHMM((byte)10);
// for debugging purposes:
private static final boolean DUMP_LIKELIHOODS = false;
private PrintWriter likelihoodDumpWriter = null;
private File likelihoodDumpFile = null;
@BeforeClass
private void setUp() throws IOException {
if (DUMP_LIKELIHOODS) {
likelihoodDumpFile = File.createTempFile("rtlce-test", ".txt");
Reporter.log("Dumping Likelihoods in file '" + likelihoodDumpFile + "'",true);
likelihoodDumpWriter = new PrintWriter(likelihoodDumpFile);//new FileWriter(f));
}
}
@AfterClass
private void tearDown() throws IOException {
if (DUMP_LIKELIHOODS) {
likelihoodDumpWriter.close();
Reporter.log("Dumped Likelihoods in file '" + likelihoodDumpFile + "'", true);
}
}
@Test(dataProvider="activeRegionTestDataSets",enabled=false)
public void testActiveRegionsDataSet(final ActiveRegionTestDataSet as, final int kmerSize, final int readLength, final String variation, final int readCount, final int regionSize, final byte bq, final byte iq, final byte dq) {
super.testActiveRegionsDataSet(as,kmerSize,readLength,variation,readCount,regionSize,bq,iq,dq);
@ -156,7 +126,6 @@ public class ReadThreadingLikelihoodCalculationEngineUnitTest extends ActiveRegi
final double loglessDiff = loglessA1Lk - loglessA2Lk;
final double graphDiff = graphA1Lk - graphA2Lk;
final double epsilon = calculateEpsilon(graphDiff,loglessDiff);
dumpLikelihoods(read,loglessA1Lk,loglessA2Lk,graphA1Lk,graphA2Lk,read.getReadString() + " " + a1.getBaseString() + " " + a2.getBaseString());
Assert.assertEquals(graphDiff,loglessDiff,epsilon,String.format("Delta(%f,%f) = %f > %f",graphDiff,loglessDiff,Math.abs(graphDiff - loglessDiff),epsilon));
}
@ -252,11 +221,6 @@ public class ReadThreadingLikelihoodCalculationEngineUnitTest extends ActiveRegi
return false;
}
private void dumpLikelihoods(final GATKSAMRecord read, final Double loglessA1lk, final Double loglessA2lk, final Double a1lk, final Double a2lk, final String hapString) {
if (!DUMP_LIKELIHOODS) return;
likelihoodDumpWriter.println(Utils.join("\t","" + loglessA1lk,"" + loglessA2lk,"" + a1lk,"" + a2lk,read.getReadName(),read.getReadString(),hapString));
likelihoodDumpWriter.flush();
}
@DataProvider(name="readLikekihoodRatioTestData")
public Iterator<Object[]> readLikelihoodRatioTestDataSets() {