From b46279d62ea6efaed974c137689f84170a9be0fd Mon Sep 17 00:00:00 2001 From: carneiro Date: Sat, 25 Jun 2011 06:38:19 +0000 Subject: [PATCH] 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 --- .../ReplicationValidationWalker.java | 28 ++----------------- 1 file changed, 3 insertions(+), 25 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java index 661f746f6..8c1fca4c6 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java @@ -1,5 +1,7 @@ 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.Genotype; 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. */ +@Requires(value={},referenceMetaData={@RMD(name="reference", type=VariantContext.class)}) public class ReplicationValidationWalker extends LocusWalker implements TreeReducible { @@ -57,10 +60,8 @@ public class ReplicationValidationWalker extends LocusWalker impl PrintStream out; int maxAlleleCount; - boolean USE_TRUTH_ROD; final String REFERENCE_ROD_NAME = "reference"; - final String TRUTH_ROD_NAME = "truth"; /** @@ -164,29 +165,6 @@ public class ReplicationValidationWalker extends LocusWalker impl // Set the max allele count (defines the size of the error model array) 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 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) {