From 232fcf829a1625e570c467d3fd79e509363741c3 Mon Sep 17 00:00:00 2001 From: aaron Date: Tue, 2 Mar 2010 15:45:33 +0000 Subject: [PATCH] removing the unsupported VCF validator git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2909 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/qc/VCFValidator.java | 46 ------------------- 1 file changed, 46 deletions(-) delete mode 100644 java/src/org/broadinstitute/sting/gatk/walkers/qc/VCFValidator.java diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/VCFValidator.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/VCFValidator.java deleted file mode 100644 index a301abd1e..000000000 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/VCFValidator.java +++ /dev/null @@ -1,46 +0,0 @@ -package org.broadinstitute.sting.gatk.walkers.qc; - - -import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.gatk.walkers.Requires; -import org.broadinstitute.sting.gatk.walkers.RMD; -import org.broadinstitute.sting.gatk.refdata.RodVCF; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.utils.StingException; - -/** - * A light-weight validator for a VCF file. - */ -@Requires(value={},referenceMetaData=@RMD(name="vcf", type=RodVCF.class)) -public class VCFValidator extends RodWalker { - - /** - * It's about as simple as things come right now. We let the rod system process all of the - * entries in the file, and if no errors pop up in processing, then it validates! - */ - - public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if ( tracker != null ) { - RODRecordList rodlist = tracker.getTrackData("vcf", null); - if ( rodlist != null ) { - RodVCF rod = (RodVCF)rodlist.get(0); - if ( (rod.isSNP() || rod.isReference()) && Character.toUpperCase(rod.getReference().charAt(0)) != Character.toUpperCase(ref.getBase()) ) - throw new StingException("The reference base (" + ref.getBase() + ") does not match the base from the VCF record (" + rod.getReference() + ")"); - } - } - return 1; - } - - public Integer reduceInit() { return 0; } - - public Integer reduce(Integer value, Integer sum) { - return sum + value; - } - - public void onTraversalDone(Integer result) { - out.println("The input file is a valid VCF"); - } -}