diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java
new file mode 100644
index 000000000..4541a0537
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java
@@ -0,0 +1,82 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.examples;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
+import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+
+/**
+ * [Short one sentence description of this walker]
+ *
+ *
+ * [Functionality of this walker]
+ *
+ *
+ * Input
+ *
+ * [Input description]
+ *
+ *
+ * Output
+ *
+ * [Output description]
+ *
+ *
+ * Examples
+ *
+ * java
+ * -jar GenomeAnalysisTK.jar
+ * -T $WalkerName
+ *
+ *
+ * @author Your Name
+ * @since Date created
+ */
+public class GATKDocsExample extends RodWalker {
+ /**
+ * Put detailed documentation about the argument here. No need to duplicate the summary information
+ * in doc annotation field, as that will be added before this text in the documentation page.
+ *
+ * Notes:
+ *
+ * - This field can contain HTML as a normal javadoc
+ * - Don't include information about the default value, as gatkdocs adds this automatically
+ * - Try your best to describe in detail the behavior of the argument, as ultimately confusing
+ * docs here will just result in user posts on the forum
+ *
+ */
+ @Argument(fullName="full", shortName="short", doc="Brief summary of argument [~ 80 characters of text]", required=false)
+ private boolean myWalkerArgument = false;
+
+ public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; }
+ public Integer reduceInit() { return 0; }
+ public Integer reduce(Integer value, Integer sum) { return value + sum; }
+ public void onTraversalDone(Integer result) { }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java
index 8d32a9bf9..a2132cee5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java
@@ -39,7 +39,6 @@ import java.util.List;
* this class contains static helper methods for DbSNP
*/
public class DbSNPHelper {
- public static final String STANDARD_DBSNP_TRACK_NAME = "dbsnp";
private DbSNPHelper() {} // don't make a DbSNPHelper
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
index 8261cd588..594c1dd28 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
@@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger;
+import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -35,6 +36,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 897e1a668..41b340058 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -321,7 +321,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
haplotypeMap.clear();
if (getAlleleListFromVCF) {
- for( final VariantContext vc_input : tracker.getValues(VariantContext.class, "alleles") ) {
+ for( final VariantContext vc_input : tracker.getValues(UAC.alleles) ) {
if( vc_input != null &&
allowableTypes.contains(vc_input.getType()) &&
ref.getLocus().getStart() == vc_input.getStart()) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index 9205e33a0..477155241 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger;
+import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -57,13 +58,13 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
}
- public static VariantContext getSNPVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, boolean requireSNP, Logger logger) {
+ public static VariantContext getSNPVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, boolean requireSNP, Logger logger, final RodBinding allelesBinding) {
if ( tracker == null || ref == null || logger == null )
throw new ReviewedStingException("Bad arguments: tracker=" + tracker + " ref=" + ref + " logger=" + logger);
VariantContext vc = null;
// search for usable record
- for( final VariantContext vc_input : tracker.getValues(VariantContext.class, "alleles", ref.getLocus()) ) {
+ for( final VariantContext vc_input : tracker.getValues(allelesBinding) ) {
if ( vc_input != null && ! vc_input.isFiltered() && (! requireSNP || vc_input.isSNP() )) {
if ( vc == null ) {
vc = vc_input;
@@ -95,7 +96,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
if ( alternateAlleleToUse != null ) {
bestAlternateAllele = alternateAlleleToUse.getBases()[0];
} else if ( useAlleleFromVCF ) {
- VariantContext vc = getSNPVCFromAllelesRod(tracker, ref, true, logger);
+ VariantContext vc = getSNPVCFromAllelesRod(tracker, ref, true, logger, UAC.alleles);
// ignore places where we don't have a variant
if ( vc == null )
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 52bf3f715..1a76bfd07 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -27,6 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File;
@@ -61,6 +64,11 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "computeSLOD", shortName = "sl", doc = "If provided, we will calculate the SLOD", required = false)
public boolean COMPUTE_SLOD = false;
+ /**
+ * When the UnifiedGenotyper is put into GENOTYPE_GIVEN_ALLELES mode it will genotype the samples using only the alleles provide in this rod binding
+ */
+ @Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when in GENOTYPE_MODE = GENOTYPE_GIVEN_ALLELES", required=false)
+ public RodBinding alleles;
// control the error modes
@Hidden
@@ -168,6 +176,7 @@ public class UnifiedArgumentCollection {
uac.OUTPUT_DEBUG_INDEL_INFO = OUTPUT_DEBUG_INDEL_INFO;
uac.INDEL_HAPLOTYPE_SIZE = INDEL_HAPLOTYPE_SIZE;
uac.DO_CONTEXT_DEPENDENT_PENALTIES = DO_CONTEXT_DEPENDENT_PENALTIES;
+ uac.alleles = alleles;
uac.GET_GAP_PENALTIES_FROM_DATA = GET_GAP_PENALTIES_FROM_DATA;
uac.INDEL_RECAL_FILE = INDEL_RECAL_FILE;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 0f2d73c3a..d31bb6fb9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -25,10 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -60,14 +57,16 @@ import java.util.*;
@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
public class UnifiedGenotyper extends LocusWalker implements TreeReducible, AnnotatorCompatibleWalker {
- @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
+ @ArgumentCollection
+ private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
/**
* A dbSNP VCF file from which to annotate.
*
* rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate.
*/
- @ArgumentCollection protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
+ @ArgumentCollection
+ protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
public RodBinding getDbsnpRodBinding() { return dbsnp.dbsnp; }
public RodBinding getSnpEffRodBinding() { return null; }
public List> getCompRodBindings() { return Collections.emptyList(); }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 77f1c5e25..dc728ff6b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -58,6 +58,7 @@ public class UnifiedGenotyperEngine {
// the unified argument collection
private final UnifiedArgumentCollection UAC;
+ public UnifiedArgumentCollection getUAC() { return UAC; }
// the annotation engine
private final VariantAnnotatorEngine annotationEngine;
@@ -232,7 +233,7 @@ public class UnifiedGenotyperEngine {
private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map stratifiedContexts, AlignmentContext rawContext) {
VariantContext vc;
if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
- VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger);
+ VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger, UAC.alleles);
if ( vcInput == null )
return null;
vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles());
@@ -630,7 +631,7 @@ public class UnifiedGenotyperEngine {
// no extended event pileup
// if we're genotyping given alleles and we have a requested SNP at this position, do SNP
if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
- VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, refContext, false, logger);
+ VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, refContext, false, logger, UAC.alleles);
if (vcInput == null)
return null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index f61fc901b..a044abecb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -29,10 +29,8 @@ import net.sf.samtools.*;
import net.sf.samtools.util.SequenceUtil;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
@@ -155,17 +153,6 @@ public class TableRecalibrationWalker extends ReadWalker implements Tr
@Output
protected PrintStream out;
+ @Input(fullName="eval", shortName = "eval", doc="Input evaluation file(s)", required=true)
+ public List> evals;
+
+ @Input(fullName="comp", shortName = "comp", doc="Input comparison file(s)", required=false)
+ public List> compsProvided = Collections.emptyList();
+ private List> comps = new ArrayList>();
+
+ @ArgumentCollection
+ protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
+
// Help arguments
@Argument(fullName="list", shortName="ls", doc="List the available eval modules and exit")
protected Boolean LIST = false;
@@ -61,7 +68,7 @@ public class VariantEvalWalker extends RodWalker implements Tr
protected Set SAMPLE_EXPRESSIONS;
@Argument(shortName="knownName", doc="Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets", required=false)
- protected String[] KNOWN_NAMES = {DbSNPHelper.STANDARD_DBSNP_TRACK_NAME};
+ protected String[] KNOWN_NAMES = {};
// Stratification arguments
@Argument(fullName="stratificationModule", shortName="ST", doc="One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)", required=false)
@@ -115,6 +122,10 @@ public class VariantEvalWalker extends RodWalker implements Tr
// The set of all possible evaluation contexts
private HashMap evaluationContexts = null;
+ // important stratifications
+ private boolean byFilterIsEnabled = false;
+ private boolean perSampleIsEnabled = false;
+
// Output report
private GATKReport report = null;
@@ -134,28 +145,25 @@ public class VariantEvalWalker extends RodWalker implements Tr
// Just list the modules, and exit quickly.
if (LIST) { variantEvalUtils.listModulesAndExit(); }
- // Categorize each rod as an eval or a comp rod.
- for ( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) {
- if ( d.getName().startsWith("eval") ) {
- evalNames.add(d.getName());
- } else if ( d.getName().startsWith("comp") || d.getName().startsWith(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
- compNames.add(d.getName());
- } else {
- logger.info(String.format("Not evaluating ROD binding '%s' because the name did not start with %s, comp, or eval", d.getName(), Utils.join(", ", KNOWN_NAMES)));
- }
- }
-
- // Barf if we don't have any eval tracks.
- if (evalNames.size() == 0) {
- throw new UserException("No evaluation tracks were specified. Please bind one or more callsets to evaluate using the -B argument with a trackname that starts with the word 'eval'.");
+ // maintain the full list of comps
+ comps.addAll(compsProvided);
+ if ( dbsnp.dbsnp.isBound() ) {
+ comps.add(dbsnp.dbsnp);
+ knownNames.add(dbsnp.dbsnp.getName());
}
// Add a dummy comp track if none exists
- if (compNames.size() == 0) {
- compNames.add("none");
- }
+ if ( comps.size() == 0 )
+ comps.add(new RodBinding(VariantContext.class, "none", "UNBOUND", "", new Tags()));
- // Set up set of known names
+ // Cache the rod names
+ for ( RodBinding compRod : comps )
+ compNames.add(compRod.getName());
+
+ for ( RodBinding evalRod : evals )
+ evalNames.add(evalRod.getName());
+
+ // Set up set of additional known names
knownNames.addAll(Arrays.asList(KNOWN_NAMES));
// Now that we have all the rods categorized, determine the sample list from the eval rods.
@@ -190,6 +198,12 @@ public class VariantEvalWalker extends RodWalker implements Tr
// Initialize the set of stratifications and evaluations to use
stratificationObjects = variantEvalUtils.initializeStratificationObjects(this, NO_STANDARD_STRATIFICATIONS, STRATIFICATIONS_TO_USE);
Set> evaluationObjects = variantEvalUtils.initializeEvaluationObjects(NO_STANDARD_MODULES, MODULES_TO_USE);
+ for ( VariantStratifier vs : getStratificationObjects() ) {
+ if ( vs.getClass().getSimpleName().equals("Filter") )
+ byFilterIsEnabled = true;
+ else if ( vs.getClass().getSimpleName().equals("Sample") )
+ perSampleIsEnabled = true;
+ }
// Initialize the evaluation contexts
evaluationContexts = variantEvalUtils.initializeEvaluationContexts(stratificationObjects, evaluationObjects, null, null);
@@ -221,61 +235,66 @@ public class VariantEvalWalker extends RodWalker implements Tr
if (tracker != null) {
String aastr = (ancestralAlignments == null) ? null : new String(ancestralAlignments.getSubsequenceAt(ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStop()).getBases());
- // track sample vc
- HashMap> vcs = variantEvalUtils.getVariantContexts(tracker, ref, compNames, evalNames, typesToUse != null);
+ // --------- track --------- sample - VariantContexts -
+ HashMap, HashMap>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled);
+ HashMap, HashMap>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false);
- for ( String compName : compNames ) {
- VariantContext comp = vcs.containsKey(compName) && vcs.get(compName) != null && vcs.get(compName).containsKey(ALL_SAMPLE_NAME) ? vcs.get(compName).get(ALL_SAMPLE_NAME) : null;
+ // for each eval track
+ for ( final RodBinding evalRod : evals ) {
+ final HashMap> evalSet = evalVCs.containsKey(evalRod) ? evalVCs.get(evalRod) : new HashMap>(0);
- for ( String evalName : evalNames ) {
- for ( String sampleName : sampleNamesForStratification ) {
- VariantContext eval = vcs.containsKey(evalName) && vcs.get(evalName) != null ? vcs.get(evalName).get(sampleName) : null;
+ // for each sample stratifier
+ for ( final String sampleName : sampleNamesForStratification ) {
+ Set evalSetBySample = evalSet.get(sampleName);
+ if ( evalSetBySample == null ) {
+ evalSetBySample = new HashSet(1);
+ evalSetBySample.add(null);
+ }
- // todo: Eric, this is really the problem. We select single eval and comp VCs independently
- // todo: discarding multiple eval tracks at the sites and not providing matched comps
- // todo: where appropriate. Really this loop should look like:
- // todo: for each eval track:
- // todo: for each eval in track:
- // todo: for each compTrack:
- // todo: comp = findMatchingComp(eval, compTrack) // find the matching comp in compTrack
- // todo: call evalModule(eval, comp)
- // todo: // may return null if no such comp exists, but proceed as eval modules may need to see eval / null pair
- // todo: for each comp not matched by an eval in compTrack:
- // todo: call evalModule(null, comp)
- // todo: // need to call with null comp, as module
- // todo: note that the reason Kiran pre-computed the possible VCs is to apply the modifiers
- // todo: like subset to sample, etc. So you probably will want a master map that maps
- // todo: from special eval bindings to the digested VC for efficiency.
-
- if ( typesToUse != null ) {
- if ( eval != null && ! typesToUse.contains(eval.getType()) ) eval = null;
- if ( comp != null && ! typesToUse.contains(comp.getType()) ) comp = null;
-// if ( eval != null ) logger.info("Keeping " + eval);
- }
-
- if (eval != null && aastr != null) {
+ // for each eval in the track
+ for ( VariantContext eval : evalSetBySample ) {
+ // deal with ancestral alleles if requested
+ if ( eval != null && aastr != null ) {
HashMap newAts = new HashMap(eval.getAttributes());
newAts.put("ANCESTRALALLELE", aastr);
-
eval = VariantContext.modifyAttributes(eval, newAts);
}
- HashMap> stateMap = new HashMap>();
- for ( VariantStratifier vs : stratificationObjects ) {
- ArrayList states = vs.getRelevantStates(ref, tracker, comp, compName, eval, evalName, sampleName);
- stateMap.put(vs, states);
- }
+ // for each comp track
+ for ( final RodBinding compRod : comps ) {
+ // no sample stratification for comps
+ final Set compSet = compVCs.get(compRod) == null ? new HashSet(0) : compVCs.get(compRod).values().iterator().next();
- ArrayList stateKeys = new ArrayList();
- variantEvalUtils.initializeStateKeys(stateMap, null, null, stateKeys);
+ // find the comp
+ final VariantContext comp = findMatchingComp(eval, compSet);
- HashSet stateKeysHash = new HashSet(stateKeys);
+ HashMap> stateMap = new HashMap>();
+ for ( VariantStratifier vs : stratificationObjects ) {
+ ArrayList states = vs.getRelevantStates(ref, tracker, comp, compRod.getName(), eval, evalRod.getName(), sampleName);
+ stateMap.put(vs, states);
+ }
- for ( StateKey stateKey : stateKeysHash ) {
- NewEvaluationContext nec = evaluationContexts.get(stateKey);
+ ArrayList stateKeys = new ArrayList();
+ variantEvalUtils.initializeStateKeys(stateMap, null, null, stateKeys);
- synchronized (nec) {
- nec.apply(tracker, ref, context, comp, eval);
+ HashSet stateKeysHash = new HashSet(stateKeys);
+
+ for ( StateKey stateKey : stateKeysHash ) {
+ NewEvaluationContext nec = evaluationContexts.get(stateKey);
+
+ // eval against the comp
+ synchronized (nec) {
+ nec.apply(tracker, ref, context, comp, eval);
+ }
+
+ // eval=null against all comps of different type
+ for ( VariantContext otherComp : compSet ) {
+ if ( otherComp != comp ) {
+ synchronized (nec) {
+ nec.apply(tracker, ref, context, otherComp, null);
+ }
+ }
+ }
}
}
}
@@ -286,6 +305,38 @@ public class VariantEvalWalker extends RodWalker implements Tr
return null;
}
+ private VariantContext findMatchingComp(final VariantContext eval, final Set comps) {
+ // if no comps, return null
+ if ( comps == null || comps.isEmpty() )
+ return null;
+
+ // if no eval, return any comp
+ if ( eval == null )
+ return comps.iterator().next();
+
+ // find all of the matching comps
+ List matchingComps = new ArrayList(comps.size());
+ for ( VariantContext comp : comps ) {
+ if ( comp.getType() == eval.getType() )
+ matchingComps.add(comp);
+ }
+
+ // if no matching comp, return null
+ if ( matchingComps.size() == 0 )
+ return null;
+
+ // find the comp which matches the alternate allele from eval
+ Allele altEval = eval.getAlternateAlleles().size() == 0 ? null : eval.getAlternateAllele(0);
+ for ( VariantContext comp : matchingComps ) {
+ Allele altComp = comp.getAlternateAlleles().size() == 0 ? null : comp.getAlternateAllele(0);
+ if ( (altEval == null && altComp == null) || (altEval != null && altEval.equals(altComp)) )
+ return comp;
+ }
+
+ // if none match, just return the first one
+ return matchingComps.get(0);
+ }
+
public Integer treeReduce(Integer lhs, Integer rhs) { return null; }
@Override
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index 8c281b2f8..87b8bac1d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -93,28 +93,35 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
nCalledLoci++;
- if (vc1.isVariant()) nVariantLoci++;
- switch (vc1.getType()) {
- case NO_VARIATION:
- nRefLoci++;
- break;
- case SNP:
- nSNPs++;
- if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
- break;
- case MNP:
- nMNPs++;
- if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
- break;
- case INDEL:
- if (vc1.isInsertion()) nInsertions++;
- else nDeletions++;
- break;
- case MIXED:
- nComplex++;
- break;
- default:
- throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
+ // Note from Eric:
+ // This is really not correct. What we really want here is a polymorphic vs. monomorphic count (i.e. on the Genotypes).
+ // So in order to maintain consistency with the previous implementation (and the intention of the original author), I've
+ // added in a proxy check for monomorphic status here.
+ if ( !vc1.isVariant() || (vc1.hasGenotypes() && vc1.getHomRefCount() == vc1.getNSamples()) ) {
+ nRefLoci++;
+ } else {
+ nVariantLoci++;
+ switch (vc1.getType()) {
+ case NO_VARIATION:
+ break;
+ case SNP:
+ nSNPs++;
+ if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
+ break;
+ case MNP:
+ nMNPs++;
+ if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
+ break;
+ case INDEL:
+ if (vc1.isInsertion()) nInsertions++;
+ else nDeletions++;
+ break;
+ case MIXED:
+ nComplex++;
+ break;
+ default:
+ throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
+ }
}
String refStr = vc1.getReference().getBaseString().toUpperCase();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index 61a959c99..33fb008ca 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.varianteval.util;
import org.apache.log4j.Logger;
+import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport;
@@ -56,8 +57,9 @@ public class VariantEvalUtils {
/**
* Initialize required, standard and user-specified stratification objects
*
- * @param noStandardStrats don't use the standard stratifications
- * @param modulesToUse the list of stratification modules to use
+ * @param variantEvalWalker the parent walker
+ * @param noStandardStrats don't use the standard stratifications
+ * @param modulesToUse the list of stratification modules to use
* @return set of stratifications to use
*/
public TreeSet initializeStratificationObjects(VariantEvalWalker variantEvalWalker, boolean noStandardStrats, String[] modulesToUse) {
@@ -256,23 +258,6 @@ public class VariantEvalUtils {
return report;
}
- /**
- * Figure out what the allowable variation types are based on the eval context
- *
- * @param tracker the reference metadata tracker
- * @param ref the reference context
- * @param compNames the comp track names
- * @param evalNames the evaluation track names
- * @return the set of allowable variation types
- */
- public EnumSet getAllowableVariationTypes(RefMetaDataTracker tracker,
- ReferenceContext ref,
- Set compNames,
- Set evalNames,
- boolean dynamicSelectTypes ) {
- return EnumSet.allOf(VariantContext.Type.class);
- }
-
/**
* Subset a VariantContext to a single sample
*
@@ -295,7 +280,7 @@ public class VariantEvalUtils {
* @return a new VariantContext with just the requested samples
*/
public VariantContext getSubsetOfVariantContext(VariantContext vc, Collection sampleNames) {
- VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values());
+ VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values(), vc.getAlleles());
HashMap newAts = new HashMap(vcsub.getAttributes());
@@ -321,78 +306,59 @@ public class VariantEvalUtils {
*
* @param tracker the metadata tracker
* @param ref the reference context
- * @param trackNames the list of track names to process
- * @param allowableTypes a set of allowable variation types
+ * @param tracks the list of tracks to process
* @param byFilter if false, only accept PASSing VariantContexts. Otherwise, accept both PASSing and filtered
* sites
* @param subsetBySample if false, do not separate the track into per-sample VCs
* @param trackPerSample if false, don't stratify per sample (and don't cut up the VariantContext like we would need
* to do this)
- * @return a mapping of track names to a list of VariantContext objects
+ *
+ * @return the mapping of track to VC list that should be populated
*/
- protected void bindVariantContexts(HashMap> bindings, RefMetaDataTracker tracker, ReferenceContext ref, Set trackNames, EnumSet allowableTypes, boolean byFilter, boolean subsetBySample, boolean trackPerSample) {
- for (String trackName : trackNames) {
- HashMap vcs = new HashMap();
+ public HashMap, HashMap>> bindVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, List> tracks, boolean byFilter, boolean subsetBySample, boolean trackPerSample) {
+ if ( tracker == null )
+ return null;
- VariantContext vc = tracker == null ? null : tracker.getFirstValue(VariantContext.class, trackName, ref.getLocus());
+ HashMap, HashMap>> bindings = new HashMap, HashMap>>();
- // First, filter the VariantContext to represent only the samples for evaluation
- if (vc != null) {
+ for ( RodBinding track : tracks ) {
+ HashMap> mapping = new HashMap>();
+
+ for ( VariantContext vc : tracker.getValues(track, ref.getLocus()) ) {
+
+ // First, filter the VariantContext to represent only the samples for evaluation
VariantContext vcsub = vc;
- if (subsetBySample && vc.hasGenotypes() && vc.hasGenotypes(variantEvalWalker.getSampleNamesForEvaluation())) {
+ if ( subsetBySample && vc.hasGenotypes() && vc.hasGenotypes(variantEvalWalker.getSampleNamesForEvaluation()) ) {
vcsub = getSubsetOfVariantContext(vc, variantEvalWalker.getSampleNamesForEvaluation());
}
- if ((byFilter || !vcsub.isFiltered())) {
- vcs.put(VariantEvalWalker.getAllSampleName(), vcsub);
+ if ( (byFilter || !vcsub.isFiltered()) ) {
+ addMapping(mapping, VariantEvalWalker.getAllSampleName(), vcsub);
}
// Now, if stratifying, split the subsetted vc per sample and add each as a new context
- if (vc.hasGenotypes() && trackPerSample) {
- for (String sampleName : variantEvalWalker.getSampleNamesForEvaluation()) {
+ if ( vc.hasGenotypes() && trackPerSample ) {
+ for ( String sampleName : variantEvalWalker.getSampleNamesForEvaluation() ) {
VariantContext samplevc = getSubsetOfVariantContext(vc, sampleName);
- if ((byFilter || !samplevc.isFiltered())) {
- vcs.put(sampleName, samplevc);
+ if ( byFilter || !samplevc.isFiltered() ) {
+ addMapping(mapping, sampleName, samplevc);
}
}
}
- bindings.put(trackName, vcs);
+ bindings.put(track, mapping);
}
}
+
+ return bindings;
}
- /**
- * Maps track names to sample name to VariantContext objects. For eval tracks, VariantContexts per specified sample
- * are also included.
- *
- * @param tracker the metadata tracker
- * @param ref the reference context
- * @param compNames the list of comp names to process
- * @param evalNames the list of eval names to process
- * @return a mapping of track names to a list of VariantContext objects
- */
- public HashMap> getVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref, Set compNames, Set evalNames, boolean dynamicSelectTypes) {
- HashMap> vcs = new HashMap>();
-
- EnumSet allowableTypes = getAllowableVariationTypes(tracker, ref, compNames, evalNames, dynamicSelectTypes);
-
- boolean byFilter = false;
- boolean perSampleIsEnabled = false;
- for (VariantStratifier vs : variantEvalWalker.getStratificationObjects()) {
- if (vs.getClass().getSimpleName().equals("Filter")) {
- byFilter = true;
- } else if (vs.getClass().getSimpleName().equals("Sample")) {
- perSampleIsEnabled = true;
- }
- }
-
- bindVariantContexts(vcs, tracker, ref, evalNames, allowableTypes, byFilter, true, perSampleIsEnabled);
- bindVariantContexts(vcs, tracker, ref, compNames, allowableTypes, byFilter, false, false);
-
- return vcs;
+ private void addMapping(HashMap> mappings, String sample, VariantContext vc) {
+ if ( !mappings.containsKey(sample) )
+ mappings.put(sample, new HashSet());
+ mappings.get(sample).add(vc);
}
/**
diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java
index 7a749c0a2..63faf1ab9 100755
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -67,6 +67,7 @@ public abstract class BaseTest {
public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf";
public static final String b37dbSNP129 = dbsnpDataLocation + "dbsnp_129_b37.vcf";
public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";
+ public static final String hg18dbSNP132 = dbsnpDataLocation + "dbsnp_132.hg18.vcf";
public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";
public static final String b37hapmapGenotypes = hapmapDataLocation + "genotypes_r27_nr.b37_fwd.vcf";
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 88c5116b1..da0c8f81f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -16,8 +16,8 @@ import java.util.Map;
public class UnifiedGenotyperIntegrationTest extends WalkerTest {
- private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH";
- private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL";
+ private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH --dbsnp " + b36dbSNP129;
+ private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b36dbSNP129;
// --------------------------------------------------------------------------------------------------------------
//
@@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
- Arrays.asList("16b0c7b47745abcd1ddaa2e261719530"));
+ Arrays.asList("149e6ad9b3fd23551254a691286a96b3"));
executeTest("test MultiSample Pilot1", spec);
}
@@ -45,7 +45,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
GenomeAnalysisEngine.resetRandomGenerator();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
- baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
+ baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
Arrays.asList(md5));
executeTest("test MultiSample Pilot2 with alleles passed in", spec2);
}
@@ -53,13 +53,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testWithAllelesPassedIn() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
- baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
- Arrays.asList("811ddc0bd8322b14f14f58df8c627aa9"));
+ baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
+ Arrays.asList("8de2602679ffc92388da0b6cb4325ef6"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
- baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
- Arrays.asList("5cf08dd7ac3d218082f7be3915ce0b15"));
+ baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
+ Arrays.asList("ec43daadfb15b00b41aeb0017a45df0b"));
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
}
@@ -67,7 +67,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
- Arrays.asList("75156264696563c2f47620fef9424f7c"));
+ Arrays.asList("82d469145c174486ccc494884852cc58"));
executeTest("test SingleSample Pilot2", spec);
}
@@ -77,7 +77,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
- private final static String COMPRESSED_OUTPUT_MD5 = "7255e03430549cb97d8fcae34cbffb02";
+ private final static String COMPRESSED_OUTPUT_MD5 = "a5a9f38c645d6004d4640765a8b77ce4";
@Test
public void testCompressedOutput() {
@@ -107,7 +107,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
- String md5 = "7912109e83fda21dae90ef8d5dd0140d";
+ String md5 = "0a45761c0e557d9c2080eb9e7f4f6c41";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@@ -138,10 +138,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testCallingParameters() {
HashMap e = new HashMap();
- e.put( "--min_base_quality_score 26", "6d3aa9f783ca63f37c952f83eeda593c" );
- e.put( "--min_mapping_quality_score 26", "51bfdf777123bf49de5d92ffde5c74e7" );
- e.put( "--p_nonref_model GRID_SEARCH", "333328ab2c8da2875fade599e80a271f" );
- e.put( "--computeSLOD", "226caa28a4fa9fe34f3beb8a23f3d53d" );
+ e.put( "--min_base_quality_score 26", "531966aee1cd5dced61c96c4fedb59a9" );
+ e.put( "--min_mapping_quality_score 26", "c71ca370947739cb7d87b59452be7a07" );
+ e.put( "--computeSLOD", "1a5648f26c18ced27df4be031b44e72d" );
for ( Map.Entry entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -154,9 +153,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameter() {
HashMap e = new HashMap();
- e.put( "-sites_only", "5f659dee408710d3709ed72005cd863a" );
- e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "55d09bf13149bddc06cc36be0801507b" );
- e.put( "--output_mode EMIT_ALL_SITES", "727f49dcb2439b18446829efc3b1561c" );
+ e.put( "-sites_only", "d40114aa201aa33ff5f174f15b6b73af" );
+ e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "3c681b053fd2280f3c42041d24243752" );
+ e.put( "--output_mode EMIT_ALL_SITES", "eafa6d71c5ecd64dfee5d7a3f60e392e" );
for ( Map.Entry entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -170,12 +169,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
- Arrays.asList("51bfdf777123bf49de5d92ffde5c74e7"));
+ Arrays.asList("c71ca370947739cb7d87b59452be7a07"));
executeTest("test confidence 1", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
- Arrays.asList("c67c285e70fd4457c9f9ce7bd878ddca"));
+ Arrays.asList("1c0a599d475cc7d5e745df6e9b6c0d29"));
executeTest("test confidence 2", spec2);
}
@@ -187,8 +186,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity() {
HashMap e = new HashMap();
- e.put( 0.01, "7ecc564d4db97d5932cef2e558550ed2" );
- e.put( 1.0 / 1850, "aa9e101bb9f9e111fe292fec467d915a" );
+ e.put( 0.01, "af5199fbc0853cf5888acdcc88f012bc" );
+ e.put( 1.0 / 1850, "4e6938645ccde1fdf204ffbf4e88170f" );
for ( Map.Entry entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -212,7 +211,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
- Arrays.asList("2efd686186b2c5129be4cf89274a24dd"));
+ Arrays.asList("213ebaaaacf850312d885e918eb33500"));
executeTest(String.format("test multiple technologies"), spec);
}
@@ -231,7 +230,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
- Arrays.asList("2892d35331fe9fc141ba19269ec7caed"));
+ Arrays.asList("3aecba34a89f3525afa57a38dc20e6cd"));
executeTest(String.format("test calling with BAQ"), spec);
}
@@ -250,7 +249,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
- Arrays.asList("8c2afb4289ed44521933d1a74c8d6c7f"));
+ Arrays.asList("043973c719a85de29a35a33a674616fb"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@@ -265,7 +264,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
- Arrays.asList("b6fb70590a10e1c27fb611732916f27d"));
+ Arrays.asList("68d4e6c1849e892467aed61c33e7bf24"));
executeTest(String.format("test indel caller in SLX witn low min allele count"), spec);
}
@@ -278,7 +277,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
- Arrays.asList("61642502bd08cc03cdaaeb83a5426b46"));
+ Arrays.asList("f86d453c5d2d2f33fb28ae2050658a5e"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@@ -286,16 +285,16 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testWithIndelAllelesPassedIn() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
- baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
+ baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
- Arrays.asList("69b0b3f089c80b9864294d838a061336"));
+ Arrays.asList("408d3aba4d094c067fc00a43992c2292"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
- baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf "
+ baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
- Arrays.asList("c90174cfd7dd68bdef36fe2c60145e10"));
+ Arrays.asList("94977d6e42e764280e9deaf4e3ac8c80"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
}
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
index fb7e84d22..3ff453dab 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
@@ -15,7 +15,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-50,000,000" +
- " --dbsnp:VCF " + b36dbSNP129 +
+ " --dbsnp:VCF " + hg18dbSNP132 +
" -o /dev/null",
0,
new ArrayList(0));
@@ -30,7 +30,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
- " --dbsnp:vcf " + b36dbSNP129 +
+ " --dbsnp:vcf " + hg18dbSNP132 +
" -o /dev/null",
0,
new ArrayList(0));
@@ -46,7 +46,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -L chr1:1-50,000,000" +
" -nt 10" +
- " --dbsnp:vcf " + b36dbSNP129 +
+ " --dbsnp:vcf " + hg18dbSNP132 +
" -o /dev/null",
0,
new ArrayList(0));
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
index 43ea401f7..bccb95795 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
@@ -16,7 +16,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -L chr1:1-50,000,000" +
" -standard" +
" -OQ" +
- " -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
+ " -knownSites " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -recalFile /dev/null" + moreArgs,
0,
new ArrayList(0));
@@ -31,7 +31,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" -standard" +
" -OQ" +
- " -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
+ " -knownSites " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -recalFile /dev/null" + moreArgs,
0,
new ArrayList(0));
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 8fa5f0c29..1de9a72d8 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -20,8 +20,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@@ -40,8 +40,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@@ -61,8 +61,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@@ -83,8 +83,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@@ -104,8 +104,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@@ -125,8 +125,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@@ -146,8 +146,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@@ -167,8 +167,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@@ -190,8 +190,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@@ -215,7 +215,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:eval,VCF " + fundamentalTestVCF,
+ "--eval " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
@@ -232,11 +232,11 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testSelect1() {
String extraArgs = "-L 1:1-10,000,000";
String tests = cmdRoot +
- " -B:dbsnp,VCF " + b36dbSNP129 +
- " -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
- " -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
+ " --dbsnp " + b36dbSNP129 +
+ " --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
+ " --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
- 1, Arrays.asList("14054badcd89b24c2375e1d09918f681"));
+ 1, Arrays.asList("125fe0a04b5d933cc14016598b2791cd"));
executeTestParallel("testSelect1", spec);
}
@@ -244,7 +244,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testVEGenotypeConcordance() {
String vcfFile = "GenotypeConcordanceEval.vcf";
- WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF3 " + validationDataLocation + vcfFile + " -B:comp,VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
+ WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG --eval:VCF3 " + validationDataLocation + vcfFile + " --comp:VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
1,
Arrays.asList("96f27163f16bb945f19c6623cd6db34e"));
executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
@@ -252,7 +252,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompVsEvalAC() {
- String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
+ String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d1932be3748fcf6da77dc51aec323710"));
executeTestParallel("testCompVsEvalAC",spec);
}
@@ -263,14 +263,14 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testTranches() {
- String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt";
+ String extraArgs = "-T VariantEval -R "+ hg18Reference +" --eval " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("984df6e94a546294fc7e0846cbac2dfe"));
executeTestParallel("testTranches",spec);
}
@Test
public void testCompOverlap() {
- String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals -B:comphapmap,vcf " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf -B:eval,vcf " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
+ String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals --comp:comphapmap " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf --eval " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("462d4784dd55294ef9d5118217b157a5"));
executeTestParallel("testCompOverlap",spec);
}
@@ -280,10 +280,10 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String extraArgs = "-T VariantEval -R " +
b37KGReference +
" -L 20" +
- " -B:dbsnp,VCF " + b37dbSNP132 +
- " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
+ " --dbsnp " + b37dbSNP132 +
+ " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s";
- WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("0897dfba2f4a245faddce38000555cce"));
+ WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("cbea5f9f8c046d4c014d261db352c43b"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@@ -291,11 +291,11 @@ public class VariantEvalIntegrationTest extends WalkerTest {
public void testMultipleEvalTracksWithoutGenotypes() {
String extraArgs = "-T VariantEval -R " + b37KGReference +
" -L 20" +
- " -B:dbsnp,VCF " + b37dbSNP132 +
- " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
- " -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
+ " --dbsnp " + b37dbSNP132 +
+ " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
+ " --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -noST -ST Novelty -o %s";
- WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ead3602e14ec2944b5d9e4dacc08c819"));
+ WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d07a246963ae609643620c839b20cd1e"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}
@@ -305,27 +305,27 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String extraArgs = "-T VariantEval" +
" -R " + b37KGReference +
- " -B:comp,VCF " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" +
- " -B:eval,VCF " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" +
- " -B:dbsnp,VCF " + dbsnp +
+ " --comp " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" +
+ " --eval " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" +
+ " --dbsnp " + dbsnp +
" -L 20:10000000-10100000" +
" -noST -noEV -ST Novelty -EV CompOverlap" +
" -o %s";
- WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("167a347ce0729d1bc3d4fd5069ebd674"));
+ WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("a3c2177849cb00fdff99574cff7f0e4f"));
executeTestParallel("testMultipleCompTracks",spec);
}
@Test
public void testPerSampleAndSubsettedSampleHaveSameResults() {
- String md5 = "40471a84b501eb440ee2d42e3081f228";
+ String md5 = "dab415cc76846e18fcf8c78f2b2ee033";
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestSNPsVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestSNPsVCF,
"-noEV",
"-EV CompOverlap",
"-sn HG00625",
@@ -342,8 +342,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestSNPsOneSampleVCF,
"-noEV",
"-EV CompOverlap",
"-noST",
@@ -363,8 +363,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
- "-B:dbsnp,VCF " + b37dbSNP132,
- "-B:eval,VCF " + fundamentalTestSNPsVCF,
+ "--dbsnp " + b37dbSNP132,
+ "--eval " + fundamentalTestSNPsVCF,
"-noEV",
"-EV CountVariants",
"-noST",
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
index ec3d1f580..132a11273 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
@@ -93,8 +93,8 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
selectTestSpec = new WalkerTestSpec(
"-T VariantEval" +
" -R " + b36KGReference +
- " -B:eval,vcf3 " + testFile +
- " -B:comp,vcf,storage=STREAM " + tmpFifo.getAbsolutePath() +
+ " --eval,vcf3 " + testFile +
+ " --comp,vcf,storage=STREAM " + tmpFifo.getAbsolutePath() +
" -EV CompOverlap -noEV -noST" +
" -o %s",
1,
diff --git a/settings/repository/org.broad/tribble-16.xml b/settings/repository/org.broad/tribble-16.xml
deleted file mode 100644
index e23eec339..000000000
--- a/settings/repository/org.broad/tribble-16.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-
-
-
diff --git a/settings/repository/org.broad/tribble-16.jar b/settings/repository/org.broad/tribble-18.jar
similarity index 87%
rename from settings/repository/org.broad/tribble-16.jar
rename to settings/repository/org.broad/tribble-18.jar
index 331f28ec3..1ea101dd0 100644
Binary files a/settings/repository/org.broad/tribble-16.jar and b/settings/repository/org.broad/tribble-18.jar differ
diff --git a/settings/repository/org.broad/tribble-18.xml b/settings/repository/org.broad/tribble-18.xml
new file mode 100644
index 000000000..d2648ddad
--- /dev/null
+++ b/settings/repository/org.broad/tribble-18.xml
@@ -0,0 +1,3 @@
+
+
+