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VariantsToVCF is up and running again; integration tests are reenabled (and added one for dbSNP).ant

This commit is contained in:
Eric Banks 2011-08-09 03:03:43 -04:00
parent cb28875c2a
commit 70b3daf689
7 changed files with 187 additions and 187 deletions
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31
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -112,7 +112,7 @@ public class VariantContextAdaptors {
alleles.add(refAllele);
// add all of the alt alleles
boolean sawNullAllele = false;
boolean sawNullAllele = refAllele.isNull();
for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) {
if ( ! Allele.acceptableAlleleBases(alt) ) {
//System.out.printf("Excluding dbsnp record %s%n", dbsnp);
@ -133,7 +133,7 @@ public class VariantContextAdaptors {
Byte refBaseForIndel = new Byte(ref.getBases()[index]);
Map<String, Genotype> genotypes = null;
VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (sawNullAllele ? 1 : 0), dbsnp.getEnd(), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes, refBaseForIndel);
VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (sawNullAllele ? 1 : 0), dbsnp.getEnd() - (refAllele.isNull() ? 1 : 0), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes, refBaseForIndel);
return vc;
} else
return null; // can't handle anything else
@ -163,16 +163,6 @@ public class VariantContextAdaptors {
@Override
public Class<? extends Feature> getAdaptableFeatureType() { return GeliTextFeature.class; }
/**
* convert to a Variant Context, given:
* @param name the name of the ROD
* @param input the Rod object, in this case a RodGeliText
* @return a VariantContext object
*/
// VariantContext convert(String name, Object input) {
// return convert(name, input, null);
// }
/**
* convert to a Variant Context, given:
* @param name the name of the ROD
@ -238,16 +228,6 @@ public class VariantContextAdaptors {
@Override
public Class<? extends Feature> getAdaptableFeatureType() { return HapMapFeature.class; }
/**
* convert to a Variant Context, given:
* @param name the name of the ROD
* @param input the Rod object, in this case a RodGeliText
* @return a VariantContext object
*/
// VariantContext convert(String name, Object input) {
// return convert(name, input, null);
// }
/**
* convert to a Variant Context, given:
* @param name the name of the ROD
@ -262,6 +242,11 @@ public class VariantContextAdaptors {
HapMapFeature hapmap = (HapMapFeature)input;
int index = hapmap.getStart() - ref.getWindow().getStart();
if ( index < 0 )
return null; // we weren't given enough reference context to create the VariantContext
Byte refBaseForIndel = new Byte(ref.getBases()[index]);
HashSet<Allele> alleles = new HashSet<Allele>();
Allele refSNPAllele = Allele.create(ref.getBase(), true);
int deletionLength = -1;
@ -320,7 +305,7 @@ public class VariantContextAdaptors {
long end = hapmap.getEnd();
if ( deletionLength > 0 )
end += deletionLength;
VariantContext vc = new VariantContext(name, hapmap.getChr(), hapmap.getStart(), end, alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attrs);
VariantContext vc = new VariantContext(name, hapmap.getChr(), hapmap.getStart(), end, alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attrs, refBaseForIndel);
return vc;
}
}

17
public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java
View File

@ -59,7 +59,7 @@ public class DbSNPHelper {
return dbsnp;
}
public static String rsIDOfFirstRealSNP(List<Feature> featureList) {
public static String rsIDOfFirstRealSNP(List<Feature> featureList, boolean deleteMe) {
if (featureList == null)
return null;
@ -81,6 +81,21 @@ public class DbSNPHelper {
return rsID;
}
public static String rsIDOfFirstRealSNP(List<VariantContext> VCs) {
if ( VCs == null )
return null;
String rsID = null;
for ( VariantContext vc : VCs ) {
if ( vc.isSNP() ) {
rsID = vc.getID();
break;
}
}
return rsID;
}
public static String rsIDOfFirstRealIndel(List<Feature> featureList) {
if (featureList == null)
return null;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -155,7 +155,7 @@ public class VariantAnnotatorEngine {
String rsID = null;
if (vc.isSNP())
rsID = DbSNPHelper.rsIDOfFirstRealSNP(tracker.getValues(Feature.class, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
rsID = DbSNPHelper.rsIDOfFirstRealSNP(tracker.getValues(Feature.class, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME), true);
else if (vc.isIndel())
rsID = DbSNPHelper.rsIDOfFirstRealIndel(tracker.getValues(Feature.class, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
infoAnnotations.put(VCFConstants.DBSNP_KEY, rsID != null );

164
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -27,15 +27,12 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
import net.sf.samtools.util.CloseableIterator;
import org.broad.tribble.Feature;
import org.broad.tribble.dbsnp.DbSNPCodec;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
@ -43,6 +40,7 @@ import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
import org.broadinstitute.sting.utils.codecs.vcf.*;
@ -52,6 +50,7 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import java.io.File;
import java.util.*;
/**
@ -63,10 +62,13 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter baseWriter = null;
private SortingVCFWriter vcfwriter; // needed because hapmap indel records move
private SortingVCFWriter vcfwriter; // needed because hapmap/dbsnp indel records move
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@Input(fullName="variant", shortName = "V", doc="Input variant file", required=true)
public RodBinding<Feature> variants;
@Input(fullName="dbsnp", shortName = "D", doc="dbSNP VCF for populating rsIDs", required=false)
public RodBinding<VariantContext> dbsnp;
@Argument(fullName="sample", shortName="sample", doc="The sample name represented by the variant rod (for data like GELI with genotypes)", required=false)
protected String sampleName = null;
@ -77,10 +79,6 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
private Set<String> allowedGenotypeFormatStrings = new HashSet<String>();
private boolean wroteHeader = false;
// Don't allow mixed types for now
private EnumSet<VariantContext.Type> ALLOWED_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP,
VariantContext.Type.NO_VARIATION, VariantContext.Type.INDEL, VariantContext.Type.MNP);
// for dealing with indels in hapmap
CloseableIterator<GATKFeature> dbsnpIterator = null;
@ -92,128 +90,108 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )
return 0;
String rsID = DbSNPHelper.rsIDOfFirstRealSNP(tracker.getValues(Feature.class, DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
String rsID = dbsnp == null ? null : DbSNPHelper.rsIDOfFirstRealSNP(tracker.getValues(dbsnp, context.getLocation()));
Collection<VariantContext> contexts = getVariantContexts(tracker, ref);
for ( VariantContext vc : contexts ) {
if ( ALLOWED_VARIANT_CONTEXT_TYPES.contains(vc.getType()) ) {
Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
if ( rsID != null && !vc.hasID() ) {
attrs.put(VariantContext.ID_KEY, rsID);
vc = VariantContext.modifyAttributes(vc, attrs);
}
// set the appropriate sample name if necessary
if ( sampleName != null && vc.hasGenotypes() && vc.hasGenotype(variants.getName()) ) {
Genotype g = Genotype.modifyName(vc.getGenotype(variants.getName()), sampleName);
Map<String, Genotype> genotypes = new HashMap<String, Genotype>();
genotypes.put(sampleName, g);
vc = VariantContext.modifyGenotypes(vc, genotypes);
}
// todo - fix me. This may not be the cleanest way to handle features what need correct indel padding
if (fixReferenceBase) {
vc = new VariantContext("Variant",vc.getChr(),vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), vc.getFilters(),vc.getAttributes(), ref.getBase());
}
writeRecord(vc, tracker, ref.getBase());
Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
if ( rsID != null && !vc.hasID() ) {
attrs.put(VariantContext.ID_KEY, rsID);
vc = VariantContext.modifyAttributes(vc, attrs);
}
// set the appropriate sample name if necessary
if ( sampleName != null && vc.hasGenotypes() && vc.hasGenotype(variants.getName()) ) {
Genotype g = Genotype.modifyName(vc.getGenotype(variants.getName()), sampleName);
Map<String, Genotype> genotypes = new HashMap<String, Genotype>();
genotypes.put(sampleName, g);
vc = VariantContext.modifyGenotypes(vc, genotypes);
}
if ( fixReferenceBase ) {
vc = VariantContext.modifyReferencePadding(vc, ref.getBase());
}
writeRecord(vc, tracker, ref.getLocus());
}
return 1;
}
private Collection<VariantContext> getVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref) {
// we need to special case the HapMap format because indels aren't handled correctly
List<Feature> features = tracker.getValues(Feature.class, variants.getName());
if ( features.size() > 0 && features.get(0) instanceof HapMapFeature ) {
ArrayList<VariantContext> hapmapVCs = new ArrayList<VariantContext>(features.size());
for ( Object feature : features ) {
HapMapFeature hapmap = (HapMapFeature)feature;
Byte refBase = null;
// if it's an indel, we need to figure out the alleles
if ( hapmap.getAlleles()[0].equals("-") ) {
Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
List<Feature> features = tracker.getValues(variants, ref.getLocus());
List<VariantContext> VCs = new ArrayList<VariantContext>(features.size());
// get the dbsnp object corresponding to this record, so we can learn whether this is an insertion or deletion
DbSNPFeature dbsnp = getDbsnpFeature(hapmap.getName());
if ( dbsnp == null || dbsnp.getVariantType().equalsIgnoreCase("mixed") )
continue;
for ( Feature record : features ) {
if ( VariantContextAdaptors.canBeConvertedToVariantContext(record) ) {
// we need to special case the HapMap format because indels aren't handled correctly
if ( record instanceof HapMapFeature) {
boolean isInsertion = dbsnp.getVariantType().equalsIgnoreCase("insertion");
// is it an indel?
HapMapFeature hapmap = (HapMapFeature)record;
if ( hapmap.getAlleles()[0].equals(HapMapFeature.NULL_ALLELE_STRING) || hapmap.getAlleles()[1].equals(HapMapFeature.NULL_ALLELE_STRING) ) {
// get the dbsnp object corresponding to this record (needed to help us distinguish between insertions and deletions)
VariantContext dbsnpVC = getDbsnp(hapmap.getName());
if ( dbsnpVC == null || dbsnpVC.isMixed() )
continue;
alleleMap.put(HapMapFeature.DELETION, Allele.create(Allele.NULL_ALLELE_STRING, isInsertion));
alleleMap.put(HapMapFeature.INSERTION, Allele.create(hapmap.getAlleles()[1], !isInsertion));
hapmap.setActualAlleles(alleleMap);
Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
alleleMap.put(HapMapFeature.DELETION, Allele.create(Allele.NULL_ALLELE_STRING, dbsnpVC.isInsertion()));
alleleMap.put(HapMapFeature.INSERTION, Allele.create(((HapMapFeature)record).getAlleles()[1], !dbsnpVC.isInsertion()));
hapmap.setActualAlleles(alleleMap);
// also, use the correct positioning for insertions
if ( isInsertion )
hapmap.updatePosition(dbsnp.getStart());
else
hapmap.updatePosition(dbsnp.getStart() - 1);
// also, use the correct positioning for insertions
hapmap.updatePosition(dbsnpVC.getStart());
if ( hapmap.getStart() < ref.getWindow().getStart() ) {
logger.warn("Hapmap record at " + ref.getLocus() + " represents an indel too large to be converted; skipping...");
continue;
if ( hapmap.getStart() < ref.getWindow().getStart() ) {
logger.warn("Hapmap record at " + ref.getLocus() + " represents an indel too large to be converted; skipping...");
continue;
}
}
refBase = ref.getBases()[hapmap.getStart() - ref.getWindow().getStart()];
}
VariantContext vc = VariantContextAdaptors.toVariantContext(variants.getName(), hapmap, ref);
if ( vc != null ) {
if ( refBase != null ) {
// TODO -- fix me
//Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
//attrs.put(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY, refBase);
//vc = VariantContext.modifyAttributes(vc, attrs);
}
hapmapVCs.add(vc);
}
// ok, we might actually be able to turn this record in a variant context
VariantContext vc = VariantContextAdaptors.toVariantContext(variants.getName(), record, ref);
if ( vc != null ) // sometimes the track has odd stuff in it that can't be converted
VCs.add(vc);
}
return hapmapVCs;
}
// for everything else, we can just convert to VariantContext
return tracker.getValues(variants, ref.getLocus());
return VCs;
}
private DbSNPFeature getDbsnpFeature(String rsID) {
private VariantContext getDbsnp(String rsID) {
if ( dbsnpIterator == null ) {
ReferenceOrderedDataSource dbsnpDataSource = null;
for ( ReferenceOrderedDataSource ds : getToolkit().getRodDataSources() ) {
if ( ds.getName().equals(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
dbsnpDataSource = ds;
break;
}
}
if ( dbsnpDataSource == null )
if ( dbsnp == null )
throw new UserException.BadInput("No dbSNP rod was provided, but one is needed to decipher the correct indel alleles from the HapMap records");
RMDTrackBuilder builder = new RMDTrackBuilder(getToolkit().getReferenceDataSource().getReference().getSequenceDictionary(),getToolkit().getGenomeLocParser(),getToolkit().getArguments().unsafe);
dbsnpIterator = builder.createInstanceOfTrack(DbSNPCodec.class, dbsnpDataSource.getFile()).getIterator();
dbsnpIterator = builder.createInstanceOfTrack(VCFCodec.class, new File(dbsnp.getSource())).getIterator();
// Note that we should really use some sort of seekable iterator here so that the search doesn't take forever
// (but it's complicated because the hapmap location doesn't match the dbsnp location, so we don't know where to seek to)
}
while ( dbsnpIterator.hasNext() ) {
GATKFeature feature = dbsnpIterator.next();
DbSNPFeature dbsnp = (DbSNPFeature)feature.getUnderlyingObject();
if ( dbsnp.getRsID().equals(rsID) )
return dbsnp;
VariantContext vc = (VariantContext)feature.getUnderlyingObject();
if ( vc.hasID() && vc.getID().equals(rsID) )
return vc;
}
return null;
}
private void writeRecord(VariantContext vc, RefMetaDataTracker tracker, byte ref) {
private void writeRecord(VariantContext vc, RefMetaDataTracker tracker, GenomeLoc loc) {
if ( !wroteHeader ) {
wroteHeader = true;
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName())));
//hInfo.add(new VCFHeaderLine("source", "VariantsToVCF"));
//hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
@ -232,13 +210,13 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
if ( samples.isEmpty() ) {
List<Feature> rods = tracker.getValues(Feature.class, variants.getName());
if ( rods.size() == 0 )
throw new IllegalStateException("No rod data is present");
List<Feature> features = tracker.getValues(variants, loc);
if ( features.size() == 0 )
throw new IllegalStateException("No rod data is present, but we just created a VariantContext");
Object rod = rods.get(0);
if ( rod instanceof HapMapFeature)
samples.addAll(Arrays.asList(((HapMapFeature)rod).getSampleIDs()));
Feature f = features.get(0);
if ( f instanceof HapMapFeature )
samples.addAll(Arrays.asList(((HapMapFeature)f).getSampleIDs()));
else
samples.addAll(vc.getSampleNames());
}

1
public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/HapMapFeature.java
View File

@ -37,6 +37,7 @@ import java.util.Map;
*/
public class HapMapFeature implements Feature {
public static final String NULL_ALLELE_STRING = "-";
public static final String INSERTION = "I";
public static final String DELETION = "D";

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -396,6 +396,10 @@ public class VariantContext implements Feature { // to enable tribble intergrati
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, attributes, vc.getReferenceBaseForIndel(), true);
}
public static VariantContext modifyReferencePadding(VariantContext vc, Byte b) {
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes(), b, true);
}
public static VariantContext modifyPErrorFiltersAndAttributes(VariantContext vc, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, negLog10PError, filters, attributes, vc.getReferenceBaseForIndel(), true);
}

155
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
View File

@ -15,73 +15,90 @@ import java.util.ArrayList;
* test(s) for the VariantsToVCF walker.
*/
public class VariantsToVCFIntegrationTest extends WalkerTest {
// TODO -- eric, fix me
// @Test
// public void testVariantsToVCFUsingGeliInput() {
// List<String> md5 = new ArrayList<String>();
// md5.add("4accae035d271b35ee2ec58f403c68c6");
//
// WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
// "-R " + b36KGReference +
// " -B:variant,GeliText " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
// " -T VariantsToVCF" +
// " -L 1:10,000,000-11,000,000" +
// " -sample NA123AB" +
// " -o %s" +
// " -NO_HEADER",
// 1, // just one output file
// md5);
// executeTest("testVariantsToVCFUsingGeliInput #1", spec).getFirst();
// }
//
// @Test
// public void testGenotypesToVCFUsingGeliInput() {
// List<String> md5 = new ArrayList<String>();
// md5.add("71e8c98d7c3a73b6287ecc339086fe03");
//
// WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
// "-R " + b36KGReference +
// " -B:variant,GeliText " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" +
// " -T VariantsToVCF" +
// " -L 1:10,000,000-11,000,000" +
// " -sample NA123AB" +
// " -o %s" +
// " -NO_HEADER",
// 1, // just one output file
// md5);
// executeTest("testVariantsToVCFUsingGeliInput #2", spec).getFirst();
// }
//
// @Test
// public void testGenotypesToVCFUsingHapMapInput() {
// List<String> md5 = new ArrayList<String>();
// md5.add("f343085305e80c7a2493422e4eaad983");
//
// WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
// "-R " + b36KGReference +
// " -B:variant,HapMap " + validationDataLocation + "rawHapMap.yri.chr1.txt" +
// " -T VariantsToVCF" +
// " -L 1:1-1,000,000" +
// " -o %s" +
// " -NO_HEADER",
// 1, // just one output file
// md5);
// executeTest("testVariantsToVCFUsingHapMapInput", spec).getFirst();
// }
//
// @Test
// public void testGenotypesToVCFUsingVCFInput() {
// List<String> md5 = new ArrayList<String>();
// md5.add("86f02e2e764ba35854cff2aa05a1fdd8");
//
// WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
// "-R " + b36KGReference +
// " -B:variant,VCF " + validationDataLocation + "complexExample.vcf4" +
// " -T VariantsToVCF" +
// " -o %s" +
// " -NO_HEADER",
// 1, // just one output file
// md5);
// executeTest("testVariantsToVCFUsingVCFInput", spec).getFirst();
// }
@Test
public void testVariantsToVCFUsingDbsnpInput() {
List<String> md5 = new ArrayList<String>();
md5.add("d64942fed2a5b7b407f9537dd2b4832e");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant:dbsnp " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -T VariantsToVCF" +
" -L 1:1-30,000,000" +
" -o %s" +
" -NO_HEADER",
1, // just one output file
md5);
executeTest("testVariantsToVCFUsingDbsnpInput", spec).getFirst();
}
@Test
public void testVariantsToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>();
md5.add("4accae035d271b35ee2ec58f403c68c6");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant:GeliText " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
" -T VariantsToVCF" +
" -L 1:10,000,000-11,000,000" +
" -sample NA123AB" +
" -o %s" +
" -NO_HEADER",
1, // just one output file
md5);
executeTest("testVariantsToVCFUsingGeliInput - calls", spec).getFirst();
}
@Test
public void testGenotypesToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>();
md5.add("2413f036ec4100b8d5db179946159a82");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant:GeliText " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" +
" -T VariantsToVCF" +
" -L 1:10,100,000-10,200,000" +
" -sample NA123AB" +
" -o %s" +
" -NO_HEADER",
1, // just one output file
md5);
executeTest("testVariantsToVCFUsingGeliInput - genotypes", spec).getFirst();
}
@Test
public void testGenotypesToVCFUsingHapMapInput() {
List<String> md5 = new ArrayList<String>();
md5.add("f343085305e80c7a2493422e4eaad983");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant:HapMap " + validationDataLocation + "rawHapMap.yri.chr1.txt" +
" -T VariantsToVCF" +
" -L 1:1-1,000,000" +
" -o %s" +
" -NO_HEADER",
1, // just one output file
md5);
executeTest("testVariantsToVCFUsingHapMapInput", spec).getFirst();
}
@Test
public void testGenotypesToVCFUsingVCFInput() {
List<String> md5 = new ArrayList<String>();
md5.add("86f02e2e764ba35854cff2aa05a1fdd8");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant:VCF " + validationDataLocation + "complexExample.vcf4" +
" -T VariantsToVCF" +
" -o %s" +
" -NO_HEADER",
1, // just one output file
md5);
executeTest("testVariantsToVCFUsingVCFInput", spec).getFirst();
}
}