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Removed dysfunctional tranches support from VariantEval

This commit is contained in:
Mark DePristo 2011-09-07 16:09:24 -04:00
parent aa9e32f2f1
commit 2ded027762
2 changed files with 1 additions and 19 deletions
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18
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -149,9 +149,6 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
@Argument(shortName="mvq", fullName="mendelianViolationQualThreshold", doc="Minimum genotype QUAL score for each trio member required to accept a site as a violation", required=false)
protected double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 50;
@Argument(fullName="tranchesFile", shortName="tf", doc="The input tranches file describing where to cut the data", required=false)
private String TRANCHE_FILENAME = null;
@Argument(fullName="ancestralAlignments", shortName="aa", doc="Fasta file with ancestral alleles", required=false)
private File ancestralAlignmentsFile = null;
@ -226,16 +223,6 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
}
sampleNamesForStratification.add(ALL_SAMPLE_NAME);
// Add select expressions for anything in the tranches file
if ( TRANCHE_FILENAME != null ) {
// we are going to build a few select names automatically from the tranches file
for ( Tranche t : Tranche.readTranches(new File(TRANCHE_FILENAME)) ) {
logger.info("Adding select for all variant above the pCut of : " + t);
SELECT_EXPS.add(String.format(VariantRecalibrator.VQS_LOD_KEY + " >= %.2f", t.minVQSLod));
SELECT_NAMES.add(String.format("TS-%.2f", t.ts));
}
}
// Initialize select expressions
for (VariantContextUtils.JexlVCMatchExp jexl : VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS)) {
SortableJexlVCMatchExp sjexl = new SortableJexlVCMatchExp(jexl.name, jexl.exp);
@ -245,18 +232,13 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
// Initialize the set of stratifications and evaluations to use
stratificationObjects = variantEvalUtils.initializeStratificationObjects(this, NO_STANDARD_STRATIFICATIONS, STRATIFICATIONS_TO_USE);
Set<Class<? extends VariantEvaluator>> evaluationObjects = variantEvalUtils.initializeEvaluationObjects(NO_STANDARD_MODULES, MODULES_TO_USE);
boolean usingJEXL = false;
for ( VariantStratifier vs : getStratificationObjects() ) {
if ( vs.getClass().getSimpleName().equals("Filter") )
byFilterIsEnabled = true;
else if ( vs.getClass().getSimpleName().equals("Sample") )
perSampleIsEnabled = true;
usingJEXL = usingJEXL || vs.getClass().equals(JexlExpression.class);
}
if ( TRANCHE_FILENAME != null && ! usingJEXL )
throw new UserException.BadArgumentValue("tf", "Requires the JexlExpression ST to enabled");
// Initialize the evaluation contexts
evaluationContexts = variantEvalUtils.initializeEvaluationContexts(stratificationObjects, evaluationObjects, null, null);

2
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -261,7 +261,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
return String.format("%s -select '%s' -selectName %s", cmd, select, name);
}
@Test
@Test(enabled = false) // no longer supported in the GATK
public void testTranches() {
String extraArgs = "-T VariantEval -R "+ hg18Reference +" --eval " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("6af2b9959aa1778a5b712536de453952"));