First pass at a VCF validator. Will test more tonight.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4524 348d0f76-0448-11de-a6fe-93d51630548a
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/*
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* Copyright (c) 2010.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.variantutils;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.util.variantcontext.Allele;
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import org.broad.tribble.dbsnp.DbSNPFeature;
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import org.broad.tribble.TribbleException;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Hidden;
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import java.util.*;
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import java.io.File;
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/**
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* Validates a variants file.
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*/
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@Reference(window=@Window(start=0,stop=100))
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@Requires(value={},referenceMetaData=@RMD(name=ValidateVariants.TARGET_ROD_NAME, type=VariantContext.class))
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public class ValidateVariants extends RodWalker<Integer, Integer> {
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protected static final String TARGET_ROD_NAME = "variant";
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public enum ValidationType {
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ALL, REF, IDS, ALLELES, CHR_COUNTS
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}
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@Hidden
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@Argument(fullName = "validationType", shortName = "type", doc = "which validation type to run", required = false)
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protected ValidationType type = ValidationType.ALL;
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private File file = null;
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public void initialize() {
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for ( ReferenceOrderedDataSource source : getToolkit().getRodDataSources() ) {
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if ( source.getName().equals(TARGET_ROD_NAME) ) {
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file = source.getReferenceOrderedData().getFile();
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break;
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}
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}
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null )
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return 0;
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Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false);
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for ( VariantContext vc : VCs )
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validate(vc, tracker, ref);
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return VCs.size();
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}
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public Integer reduceInit() { return 0; }
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public Integer reduce(Integer value, Integer sum) { return sum+value; }
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public void onTraversalDone(Integer result) {
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System.out.println("Successfully validated the input file. Checked " + result + " records with no failures.");
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}
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private void validate(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref) {
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// get the true reference allele
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Allele reportedRefAllele = vc.getReference();
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Allele observedRefAllele;
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// insertions
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if ( reportedRefAllele.isNull() ) {
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observedRefAllele = Allele.create(Allele.NULL_ALLELE_STRING);
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}
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// SNPs
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else if ( reportedRefAllele.length() == 1 ) {
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byte[] refByte = new byte[1];
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refByte[0] = ref.getBase();
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observedRefAllele = Allele.create(refByte, true);
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}
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// deletions
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else {
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// we can't validate arbitrarily long deletions
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if ( reportedRefAllele.length() > 100 ) {
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logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", reportedRefAllele.length(), vc.getChr(), vc.getStart()));
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return;
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}
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byte[] refBytes = ref.getBases();
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byte[] trueRef = new byte[reportedRefAllele.length()];
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for (int i = 0; i < reportedRefAllele.length(); i++)
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trueRef[i] = refBytes[i+1];
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observedRefAllele = Allele.create(trueRef, true);
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}
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// get the RS IDs
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Set<String> rsIDs = null;
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if ( tracker.hasROD(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
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List<Object> dbsnpList = tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME);
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rsIDs = new HashSet<String>();
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for ( Object d : dbsnpList ) {
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if (d instanceof DbSNPFeature )
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rsIDs.add(((DbSNPFeature)d).getRsID());
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}
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}
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try {
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switch( type ) {
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case ALL:
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vc.extraStrictValidation(observedRefAllele, rsIDs);
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break;
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case REF:
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vc.validateReferenceBases(observedRefAllele);
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break;
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case IDS:
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vc.validateRSIDs(rsIDs);
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break;
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case ALLELES:
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vc.validateAlternateAlleles();
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break;
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case CHR_COUNTS:
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vc.validateChromosomeCounts();
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break;
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}
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} catch (TribbleException e) {
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throw new UserException.MalformedFile(file, e.getMessage());
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}
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}
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}
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@ -0,0 +1,116 @@
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/*
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* Copyright (c) 2010.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.variantutils;
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import org.broadinstitute.sting.WalkerTest;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.junit.Test;
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import java.util.Arrays;
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public class ValidateVariantsIntegrationTest extends WalkerTest {
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public static String baseTestString(String file, String type) {
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return "-T ValidateVariants -R " + b36KGReference + " -L 1:10001292-10001303 -B:variant,VCF " + validationDataLocation + file + " --validationType " + type;
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}
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@Test
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public void testGoodFile() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString("validationExampleGood.vcf", "ALL"),
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0,
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Arrays.asList("")
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);
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executeTest("test good file", spec);
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}
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@Test
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public void testBadRefBase1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString("validationExampleBad.vcf", "REF"),
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0,
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UserException.MalformedFile.class
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);
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executeTest("test bad ref base #1", spec);
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}
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@Test
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public void testBadRefBase2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString("validationExampleBad2.vcf", "REF"),
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0,
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UserException.MalformedFile.class
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);
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executeTest("test bad ref base #2", spec);
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}
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@Test
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public void testBadChrCount1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString("validationExampleBad.vcf", "CHR_COUNTS"),
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0,
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UserException.MalformedFile.class
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);
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executeTest("test bad chr counts #1", spec);
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}
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@Test
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public void testBadChrCount2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString("validationExampleBad2.vcf", "CHR_COUNTS"),
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0,
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UserException.MalformedFile.class
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);
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executeTest("test bad chr counts #2", spec);
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}
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@Test
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public void testBadID() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString("validationExampleBad.vcf", "IDS") + " -D " + GATKDataLocation + "dbsnp_129_b36.rod",
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0,
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UserException.MalformedFile.class
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);
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executeTest("test bad RS ID", spec);
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}
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@Test
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public void testBadAllele() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString("validationExampleBad.vcf", "ALLELES"),
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0,
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UserException.MalformedFile.class
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);
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executeTest("test bad alt allele", spec);
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}
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}
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