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required RODs are now checked by annotations. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6080 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-06-25 06:38:19 +00:00
parent 3879b02cdd
commit b46279d62e
1 changed files with 3 additions and 25 deletions
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28
java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.playground.gatk.walkers.replication_validation; package org.broadinstitute.sting.playground.gatk.walkers.replication_validation;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -28,6 +30,7 @@ import java.util.*;
* *
* A reference sample name must be provided and it must be barcoded uniquely. * A reference sample name must be provided and it must be barcoded uniquely.
*/ */
@Requires(value={},referenceMetaData={@RMD(name="reference", type=VariantContext.class)})
public class ReplicationValidationWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> { public class ReplicationValidationWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
@ -57,10 +60,8 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
PrintStream out; PrintStream out;
int maxAlleleCount; int maxAlleleCount;
boolean USE_TRUTH_ROD;
final String REFERENCE_ROD_NAME = "reference"; final String REFERENCE_ROD_NAME = "reference";
final String TRUTH_ROD_NAME = "truth";
/** /**
@ -164,29 +165,6 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
// Set the max allele count (defines the size of the error model array) // Set the max allele count (defines the size of the error model array)
maxAlleleCount = (overrideMaxAlleleCount > 0) ? overrideMaxAlleleCount : nSamples*nChromosomes; maxAlleleCount = (overrideMaxAlleleCount > 0) ? overrideMaxAlleleCount : nSamples*nChromosomes;
// Look for the reference ROD and the optional truth ROD. If truth is provided, set the truth "test" mode ON.
List<ReferenceOrderedDataSource> rods = getToolkit().getRodDataSources();
if (rods.size() < 1) {
throw new IllegalArgumentException("You must provide a reference ROD.");
}
boolean foundReferenceROD = false;
boolean foundTruthROD = false;
for (ReferenceOrderedDataSource rod : rods) {
if (rod.getName().equals(REFERENCE_ROD_NAME)) {
foundReferenceROD = true;
}
if (rod.getName().equals(TRUTH_ROD_NAME)) {
foundReferenceROD = true;
}
}
if (!foundReferenceROD) {
throw new IllegalArgumentException("You haven't provided a reference ROD. Note that the reference ROD must be labeled " + REFERENCE_ROD_NAME + ".");
}
if (rods.size() > 1 && !foundTruthROD) {
throw new IllegalArgumentException("You haven't provided a truth ROD. Note that the reference ROD must be labeled " + TRUTH_ROD_NAME + ".");
}
USE_TRUTH_ROD = foundTruthROD;
} }
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {