diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java index e51871498..1436465ad 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java @@ -254,27 +254,7 @@ public class RefMetaDataTracker { */ @Deprecated public List getValues(final String name) { - return (List)(List)getValues(name, Feature.class); - } - - /** - * get all the reference meta data associated with a track name. - * @param name the name of the track we're looking for - * @param clazz the expected class of the elements bound to rod name - * @return a list of objects, representing the underlying objects that the tracks produce. I.e. for a - * dbSNP RMD this will be a RodDbSNP, etc. - * - * Important: The list returned by this function is guaranteed not to be null, but may be empty! - */ - @Deprecated - public List getValues(final String name, final Class clazz) { - RODRecordList list = getTrackDataByName(name); - - if (list.isEmpty()) - return Collections.emptyList(); - else { - return addValues(name, clazz, new ArrayList(), list, list.getLocation(), false, false); - } + return (List)(List)getValues(Feature.class, name); } @@ -313,142 +293,6 @@ public class RefMetaDataTracker { // // ------------------------------------------------------------------------------------------ - /** - * Converts all possible ROD tracks to VariantContexts objects, of all types, allowing any start and any number - * of entries per ROD. - * The name of each VariantContext corresponds to the ROD name. - * - * @return variant context - */ - @Deprecated - public List getAllVariantContexts() { - return getAllVariantContexts(null, false, false); - } - - /** - * Returns all of the variant contexts that start at the current location - * - * @param curLocation - * @return - */ - @Deprecated - public List getAllVariantContexts(final GenomeLoc curLocation) { - return getAllVariantContexts(curLocation, true, false); - } - - /** - * Converts all possible ROD tracks to VariantContexts objects. If allowedTypes != null, then only - * VariantContexts in the allow set of types will be returned. If requireStartsHere is true, then curLocation - * must not be null, and only records whose start position is == to curLocation.getStart() will be returned. - * If takeFirstOnly is true, then only a single VariantContext will be converted from any individual ROD. Of course, - * this single object must pass the allowed types and start here options if provided. Note that the result - * may return multiple VariantContexts with the same name if that particular track contained multiple RODs spanning - * the current location. - * - * The name of each VariantContext corresponds to the ROD name. - * - * - * @param curLocation location - * @param requireStartHere do we require the rod to start at this location? - * @param takeFirstOnly do we take the first rod only? - * @return variant context - */ - @Deprecated - public List getAllVariantContexts(final GenomeLoc curLocation, - final boolean requireStartHere, - final boolean takeFirstOnly) { - List contexts = new ArrayList(); - - for ( RODRecordList rodList : getBoundRodTracks() ) { - addVariantContexts(contexts, rodList, curLocation, requireStartHere, takeFirstOnly); - } - - return contexts; - } - - /** - * Gets the variant contexts associated with track name name - * - * see getVariantContexts for more information. - * - * - * @param name name - * @param curLocation location - * @param requireStartHere do we require the rod to start at this location? - * @param takeFirstOnly do we take the first rod only? - * @return variant context - */ - @Deprecated - public List getVariantContexts(final String name, - final GenomeLoc curLocation, - final boolean requireStartHere, - final boolean takeFirstOnly) { - return getVariantContexts(Arrays.asList(name), curLocation, requireStartHere, takeFirstOnly); - } - - @Deprecated - public List getVariantContexts(final Collection names, - final GenomeLoc curLocation, - final boolean requireStartHere, - final boolean takeFirstOnly) { - List contexts = new ArrayList(); - - for ( String name : names ) { - RODRecordList rodList = getTrackDataByName(name); // require that the name is an exact match - addVariantContexts(contexts, rodList, curLocation, requireStartHere, takeFirstOnly ); - } - - return contexts; - } - - /** - * Gets the variant context associated with name, and assumes the system only has a single bound track at this location. Throws an exception if not. - * see getVariantContexts for more information. - * - * - * @param name name - * @param curLocation location - * @param requireStartHere do we require the rod to start at this location? - * @return variant context - */ - @Deprecated - public VariantContext getVariantContext(final String name, - final GenomeLoc curLocation, - final boolean requireStartHere) { - List contexts = getVariantContexts(name, curLocation, requireStartHere, false ); - - if ( contexts.size() > 1 ) - throw new ReviewedStingException("Requested a single VariantContext object for track " + name + " but multiple variants were present at position " + curLocation); - else if ( contexts.size() == 0 ) - return null; - else - return contexts.iterator().next(); - } - - /** - * Very simple accessor that gets the first (and only!) VC associated with name at the current location, or - * null if there's no binding here. - * - * - * @param name - * @param curLocation - * @return - */ - @Deprecated - public VariantContext getVariantContext(final String name, - final GenomeLoc curLocation) { - return getVariantContext(name, curLocation, true); - } - - @Deprecated - private void addVariantContexts(final List contexts, - final RODRecordList rodList, - final GenomeLoc curLocation, - final boolean requireStartHere, - final boolean takeFirstOnly ) { - addValues("xxx", VariantContext.class, contexts, rodList, curLocation, requireStartHere, takeFirstOnly); - } - private List addValues(final Collection names, final Class type, final List values, diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 932317700..1744cc9e8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -202,7 +202,7 @@ public class VariantAnnotator extends RodWalker { if ( tracker == null ) return 0; - Collection VCs = tracker.getVariantContexts("variant", context.getLocation(), true, false); + Collection VCs = tracker.getValues(VariantContext.class, "variant", context.getLocation()); if ( VCs.size() == 0 ) return 0; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 9dc0bbfe6..583362ae4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -203,7 +203,7 @@ public class VariantAnnotatorEngine { infoAnnotations.put(VariantContext.ID_KEY, rsID); } else { boolean overlapsComp = false; - for ( VariantContext comp : tracker.getVariantContexts(dbSet.getKey(), ref.getLocus(), false, false) ) { + for ( VariantContext comp : tracker.getValues(VariantContext.class, dbSet.getKey()) ) { if ( !comp.isFiltered() ) { overlapsComp = true; break; @@ -216,7 +216,7 @@ public class VariantAnnotatorEngine { private void annotateExpressions(RefMetaDataTracker tracker, ReferenceContext ref, Map infoAnnotations) { for ( VAExpression expression : requestedExpressions ) { - Collection VCs = tracker.getVariantContexts(expression.bindingName, ref.getLocus(), false, true); + Collection VCs = tracker.getValues(VariantContext.class, expression.bindingName); if ( VCs.size() == 0 ) continue; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java index 78057849c..a82041af2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java @@ -244,7 +244,7 @@ public class GenomicAnnotator extends RodWalker implements Tre return 0; Set results = new LinkedHashSet(); - for (VariantContext vc : tracker.getVariantContexts("variant", context.getLocation(), true, false)) { + for (VariantContext vc : tracker.getValues(VariantContext.class, "variant", context.getLocation())) { if ( (vc.isFiltered() && IGNORE_FILTERED_SITES) || (vc.isVariant() && !vc.isBiallelic()) ) { results.add(vc); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java index 19eafc872..97a4b6a8f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java @@ -119,9 +119,9 @@ public class BeagleOutputToVCFWalker extends RodWalker { return 0; GenomeLoc loc = context.getLocation(); - VariantContext vc_input = tracker.getVariantContext(INPUT_ROD_NAME, loc, true); + VariantContext vc_input = tracker.getFirstValue(VariantContext.class, INPUT_ROD_NAME, loc); - VariantContext vc_comp = tracker.getVariantContext(COMP_ROD_NAME, loc, true); + VariantContext vc_comp = tracker.getFirstValue(VariantContext.class, COMP_ROD_NAME, loc); if ( vc_input == null ) return 0; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java index 353ebb82a..354b032f2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java @@ -121,8 +121,8 @@ public class ProduceBeagleInputWalker extends RodWalker { public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) { if( tracker != null ) { GenomeLoc loc = context.getLocation(); - VariantContext variant_eval = tracker.getVariantContext(ROD_NAME, loc, true); - VariantContext validation_eval = tracker.getVariantContext(VALIDATION_ROD_NAME, loc, true); + VariantContext variant_eval = tracker.getFirstValue(VariantContext.class, ROD_NAME, loc); + VariantContext validation_eval = tracker.getFirstValue(VariantContext.class, VALIDATION_ROD_NAME, loc); if ( goodSite(variant_eval,validation_eval) ) { if ( useValidation(validation_eval, ref) ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java index ee3dfb1df..b95f3097d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java @@ -102,7 +102,7 @@ public class VariantsToBeagleUnphasedWalker extends RodWalker public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) { if( tracker != null ) { GenomeLoc loc = context.getLocation(); - VariantContext vc = tracker.getVariantContext(ROD_NAME, loc, true); + VariantContext vc = tracker.getFirstValue(VariantContext.class, ROD_NAME, loc); if ( ProduceBeagleInputWalker.canBeOutputToBeagle(vc) ) { // do we want to hold back this site? diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java index 665ac539c..2865c2380 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java @@ -57,7 +57,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker { String refBase = String.valueOf((char)ref.getBase()); - Collection vcs = tracker.getAllVariantContexts(); + Collection vcs = tracker.getValues(VariantContext.class); // Check to see if we have a called snp for ( VariantContext vc : vcs ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index 61991db2d..9e89944a5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -149,7 +149,7 @@ public class VariantFiltrationWalker extends RodWalker { if ( tracker == null ) return 0; - Collection VCs = tracker.getVariantContexts(INPUT_VARIANT_ROD_BINDING_NAME, context.getLocation(), true, false); + Collection VCs = tracker.getValues(VariantContext.class, INPUT_VARIANT_ROD_BINDING_NAME, context.getLocation()); // is there a SNP mask present? boolean hasMask = tracker.getValues("mask").size() > 0; 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 54bb888c8..897e1a668 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.getVariantContexts("alleles", ref.getLocus(), false, false) ) { + for( final VariantContext vc_input : tracker.getValues(VariantContext.class, "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 4f784d37a..865bdfafe 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 @@ -63,7 +63,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC VariantContext vc = null; // search for usable record - for( final VariantContext vc_input : tracker.getVariantContexts("alleles", ref.getLocus(), true, false) ) { + for( final VariantContext vc_input : tracker.getValues(VariantContext.class, "alleles", ref.getLocus()) ) { if ( vc_input != null && ! vc_input.isFiltered() && (! requireSNP || vc_input.isSNP() )) { if ( vc == null ) { vc = vc_input; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java index 1c5d55225..0ddfe609b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java @@ -96,8 +96,8 @@ public class UGCallVariants extends RodWalker { List VCs = new ArrayList(); for ( String name : trackNames ) { - Collection vc = tracker.getVariantContexts(name, context.getLocation(), true, true); - VCs.addAll(vc); + VariantContext vc = tracker.getFirstValue(VariantContext.class, name, context.getLocation()); + VCs.add(vc); } VariantContext mergedVC = mergeVCsWithGLs(VCs); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index 38a1dcb8d..7d805f092 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java @@ -110,7 +110,7 @@ public class RealignerTargetCreator extends RodWalker { GenomeLoc curLocus = ref.getLocus(); clearOldLocusFeatures(curLocus); - boolean requireStartHere = false; // see EVERY site of the MNP - boolean takeFirstOnly = false; // take as many entries as the VCF file has - for (VariantContext vc : tracker.getVariantContexts(rodName, context.getLocation(), requireStartHere, takeFirstOnly)) { + for (VariantContext vc : tracker.getValues(VariantContext.class, rodName)) { GenomeLoc vcLoc = VariantContextUtils.getLocation(locParser, vc); boolean atStartOfVc = curLocus.getStart() == vcLoc.getStart(); boolean atEndOfVc = curLocus.getStart() == vcLoc.getStop(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java index ae7782434..315ae36d8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java @@ -44,8 +44,8 @@ public class MergeAndMatchHaplotypes extends RodWalker { @Override public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { if (tracker != null) { - Collection pbts = tracker.getVariantContexts("pbt", ref.getLocus(), true, true); - Collection rbps = tracker.getVariantContexts("rbp", ref.getLocus(), true, true); + Collection pbts = tracker.getValues(VariantContext.class, "pbt", ref.getLocus()); + Collection rbps = tracker.getValues(VariantContext.class, "rbp", ref.getLocus()); VariantContext pbt = pbts.iterator().hasNext() ? pbts.iterator().next() : null; VariantContext rbp = rbps.iterator().hasNext() ? rbps.iterator().next() : null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java index 6e328c07e..de62f9652 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java @@ -98,9 +98,7 @@ public class MergeMNPsWalker extends RodWalker { if (tracker == null) return null; - boolean requireStartHere = true; // only see each VariantContext once - boolean takeFirstOnly = false; // take as many entries as the VCF file has - for (VariantContext vc : tracker.getVariantContexts(rodName, context.getLocation(), requireStartHere, takeFirstOnly)) + for (VariantContext vc : tracker.getValues(VariantContext.class, rodName, context.getLocation())) writeVCF(vc); return 0; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java index c747e35d0..bf26b327d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java @@ -135,9 +135,7 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker { @Override public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { if (tracker != null) { - Collection vcs = tracker.getVariantContexts(ROD_NAME, context.getLocation(), true, true); + VariantContext vc = tracker.getFirstValue(VariantContext.class, ROD_NAME, context.getLocation()); - for (VariantContext vc : vcs) { - Map genotypeMap = vc.getGenotypes(); + Map genotypeMap = vc.getGenotypes(); - for (Trio trio : trios) { - Genotype mother = vc.getGenotype(trio.getMother()); - Genotype father = vc.getGenotype(trio.getFather()); - Genotype child = vc.getGenotype(trio.getChild()); + for (Trio trio : trios) { + Genotype mother = vc.getGenotype(trio.getMother()); + Genotype father = vc.getGenotype(trio.getFather()); + Genotype child = vc.getGenotype(trio.getChild()); - ArrayList trioGenotypes = phaseTrioGenotypes(vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), mother, father, child); + ArrayList trioGenotypes = phaseTrioGenotypes(vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), mother, father, child); - Genotype phasedMother = trioGenotypes.get(0); - Genotype phasedFather = trioGenotypes.get(1); - Genotype phasedChild = trioGenotypes.get(2); + Genotype phasedMother = trioGenotypes.get(0); + Genotype phasedFather = trioGenotypes.get(1); + Genotype phasedChild = trioGenotypes.get(2); - genotypeMap.put(phasedMother.getSampleName(), phasedMother); - genotypeMap.put(phasedFather.getSampleName(), phasedFather); - genotypeMap.put(phasedChild.getSampleName(), phasedChild); - } - - VariantContext newvc = VariantContext.modifyGenotypes(vc, genotypeMap); - - vcfWriter.add(newvc, ref.getBase()); + genotypeMap.put(phasedMother.getSampleName(), phasedMother); + genotypeMap.put(phasedFather.getSampleName(), phasedFather); + genotypeMap.put(phasedChild.getSampleName(), phasedChild); } + + VariantContext newvc = VariantContext.modifyGenotypes(vc, genotypeMap); + + vcfWriter.add(newvc, ref.getBase()); } return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java index 165cef477..dd7c68247 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java @@ -204,9 +204,7 @@ public class ReadBackedPhasingWalker extends RodWalker unprocessedList = new LinkedList(); - boolean requireStartHere = true; // only see each VariantContext once - boolean takeFirstOnly = false; // take as many entries as the VCF file has - for (VariantContext vc : tracker.getVariantContexts(rodName, context.getLocation(), requireStartHere, takeFirstOnly)) { + for (VariantContext vc : tracker.getValues(VariantContext.class, rodName, context.getLocation())) { if (samplesToPhase != null) vc = reduceVCToSamples(vc, samplesToPhase); if (ReadBackedPhasingWalker.processVariantInPhasing(vc)) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java index 608d5925a..22b145911 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java @@ -84,7 +84,7 @@ public class RodSystemValidationWalker extends RodWalker { // if the argument was set, check for equivalence if (allRecordsVariantContextEquivalent && tracker != null) { - Collection col = tracker.getAllVariantContexts(); + Collection col = tracker.getValues(VariantContext.class); VariantContext con = null; for (VariantContext contextInList : col) if (con == null) con = contextInList; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 3d09ef785..69bb78b1e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -138,8 +138,8 @@ public class ValidationAmplicons extends RodWalker { // step 3 (or 1 if not new): // build up the sequence - VariantContext mask = tracker.getVariantContext("MaskAlleles",ref.getLocus()); - VariantContext validate = tracker.getVariantContext("ValidateAlleles",ref.getLocus()); + VariantContext mask = tracker.getFirstValue(VariantContext.class, "MaskAlleles",ref.getLocus()); + VariantContext validate = tracker.getFirstValue(VariantContext.class, "ValidateAlleles",ref.getLocus()); if ( mask == null && validate == null ) { if ( indelCounter > 0 ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java index 5e98350ed..d2e4392a5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java @@ -25,7 +25,7 @@ public class Novelty extends VariantStratifier implements StandardStratification public ArrayList getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { if (tracker != null && eval != null) { for (final String knownName : knownNames) { - final Collection knownComps = tracker.getVariantContexts(knownName, ref.getLocus(), true, false); + final Collection knownComps = tracker.getValues(VariantContext.class, knownName, ref.getLocus()); for ( final VariantContext c : knownComps ) { // loop over sites, looking for something that matches the type eval if ( eval.getType() == c.getType() ) { 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 285e75ed8..79cd89ca3 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 @@ -336,8 +336,7 @@ public class VariantEvalUtils { for (String trackName : trackNames) { HashMap vcs = new HashMap(); - Collection contexts = tracker == null ? null : tracker.getVariantContexts(trackName, ref.getLocus(), true, true); - VariantContext vc = contexts != null && contexts.size() == 1 ? contexts.iterator().next() : null; + VariantContext vc = tracker == null ? null : tracker.getFirstValue(VariantContext.class, trackName, ref.getLocus()); // First, filter the VariantContext to represent only the samples for evaluation if (vc != null) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java index b195256d8..1415db87c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java @@ -168,7 +168,7 @@ public class ApplyRecalibration extends RodWalker { return 1; } - for( VariantContext vc : tracker.getVariantContexts(inputNames, context.getLocation(), true, false) ) { + for( VariantContext vc : tracker.getValues(VariantContext.class, inputNames, context.getLocation()) ) { if( vc != null ) { if( VariantRecalibrator.checkRecalibrationMode( vc, MODE ) && (vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters())) ) { String filterString = null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java index 7f32882f4..e7f74de0d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java @@ -258,7 +258,7 @@ public class VariantDataManager { datum.consensusCount = 0; for( final TrainingSet trainingSet : trainingSets ) { - for( final VariantContext trainVC : tracker.getVariantContexts(trainingSet.name, context.getLocation(), false, false ) ) { + for( final VariantContext trainVC : tracker.getValues(VariantContext.class, trainingSet.name) ) { if( trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() && ((evalVC.isSNP() && trainVC.isSNP()) || ((evalVC.isIndel()||evalVC.isMixed()) && (trainVC.isIndel()||trainVC.isMixed()))) && (TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphic()) ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index 497a02baf..7bd7ea46d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -163,7 +163,7 @@ public class VariantRecalibrator extends RodWalker { // get all of the vcf rods at this locus // Need to provide reference bases to simpleMerge starting at current locus - Collection vcs = tracker.getAllVariantContexts(context.getLocation(), true, false); + Collection vcs = tracker.getValues(VariantContext.class, context.getLocation()); if ( sitesOnlyVCF ) { vcs = VariantContextUtils.sitesOnlyVariantContexts(vcs); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java index a55a53ff0..2a5a4e97c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -85,7 +85,7 @@ public class FilterLiftedVariants extends RodWalker { if ( tracker == null ) return 0; - Collection VCs = tracker.getVariantContexts("variant", context.getLocation(), true, false); + Collection VCs = tracker.getValues(VariantContext.class, "variant", context.getLocation()); for ( VariantContext vc : VCs ) filterAndWrite(ref.getBases(), vc); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index 01c7ddc91..e7e21d256 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -68,7 +68,7 @@ public class LeftAlignVariants extends RodWalker { if ( tracker == null ) return 0; - Collection VCs = tracker.getVariantContexts("variant", context.getLocation(), true, false); + Collection VCs = tracker.getValues(VariantContext.class, "variant", context.getLocation()); int changedSites = 0; for ( VariantContext vc : VCs ) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index 38ac1e013..5e85d03cb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -143,7 +143,7 @@ public class LiftoverVariants extends RodWalker { if ( tracker == null ) return 0; - Collection VCs = tracker.getVariantContexts("variant", context.getLocation(), true, false); + Collection VCs = tracker.getValues(VariantContext.class, "variant", context.getLocation()); for ( VariantContext vc : VCs ) convertAndWrite(vc, ref); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java index de194e93f..b3926bc34 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java @@ -97,7 +97,7 @@ public class RandomlySplitVariants extends RodWalker { if ( tracker == null ) return 0; - Collection vcs = tracker.getVariantContexts(INPUT_VARIANT_ROD_BINDING_NAME, context.getLocation(), true, false); + Collection vcs = tracker.getValues(VariantContext.class, INPUT_VARIANT_ROD_BINDING_NAME, context.getLocation()); for ( VariantContext vc : vcs ) { int random = GenomeAnalysisEngine.getRandomGenerator().nextInt(1000); if ( random < iFraction ) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 3bc598e2d..dc24287e9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -308,7 +308,7 @@ public class SelectVariants extends RodWalker { if ( tracker == null ) return 0; - Collection vcs = tracker.getVariantContexts(variantRodName, context.getLocation(), true, false); + Collection vcs = tracker.getValues(VariantContext.class, variantRodName, context.getLocation()); if ( vcs == null || vcs.size() == 0) { return 0; @@ -336,12 +336,12 @@ public class SelectVariants extends RodWalker { break; } if (DISCORDANCE_ONLY) { - Collection compVCs = tracker.getVariantContexts(discordanceRodName, context.getLocation(), true, false); + Collection compVCs = tracker.getValues(VariantContext.class, discordanceRodName, context.getLocation()); if (!isDiscordant(vc, compVCs)) return 0; } if (CONCORDANCE_ONLY) { - Collection compVCs = tracker.getVariantContexts(concordanceRodName, context.getLocation(), true, false); + Collection compVCs = tracker.getValues(VariantContext.class, concordanceRodName, context.getLocation()); if (!isConcordant(vc, compVCs)) return 0; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index 3bf8bd9e9..6655d26dc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -86,7 +86,7 @@ public class ValidateVariants extends RodWalker { if ( tracker == null ) return 0; - Collection VCs = tracker.getVariantContexts("variant", context.getLocation(), true, false); + Collection VCs = tracker.getValues(VariantContext.class, "variant", context.getLocation()); for ( VariantContext vc : VCs ) validate(vc, tracker, ref); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index e8a012e99..245ed9edd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -93,7 +93,7 @@ public class VariantValidationAssessor extends RodWalker { return 0; if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) { - Collection vcs = tracker.getAllVariantContexts(context.getLocation()); + Collection vcs = tracker.getValues(VariantContext.class, context.getLocation()); for ( VariantContext vc : vcs) { if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) { List vals = extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index 170daf6cc..39822d7a6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -162,7 +162,7 @@ public class VariantsToVCF extends RodWalker { } // for everything else, we can just convert to VariantContext - return tracker.getVariantContexts(INPUT_ROD_NAME, ref.getLocus(), true, false); + return tracker.getValues(VariantContext.class, INPUT_ROD_NAME, ref.getLocus()); } private DbSNPFeature getDbsnpFeature(String rsID) { diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java index 129161da3..0992dbe31 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java @@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.util.HashMap; @@ -15,75 +16,106 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { static HashMap paramsFilesNoReadGroupTest = new HashMap(); static HashMap paramsFilesSolidIndels = new HashMap(); - @Test - public void testCountCovariates1() { - HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "7b5832d4b2a23b8ef2bb639eb59bfa88" ); - e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "9c006f8e9fb5752b1c139f5a8cc7ea88"); - e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "e6f7b4ab9aa291022e0ba8b7dbe4c77e" ); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "e6b98af01c5a08e4954b79ec42db6fc3" ); + private static final class CCTest extends TestDataProvider { + String file, md5; - for ( String parallelism : Arrays.asList("", " -nt 4")) { - for ( Map.Entry entry : e.entrySet() ) { - String bam = entry.getKey(); - String md5 = entry.getValue(); - - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + b36KGReference + - " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" + - " -T CountCovariates" + - " -I " + bam + - ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) - ? " -L 1:10,800,000-10,810,000" : " -L 1:10,000,000-10,200,000" ) + - " -cov ReadGroupCovariate" + - " -cov QualityScoreCovariate" + - " -cov CycleCovariate" + - " -cov DinucCovariate" + - " --solid_recal_mode SET_Q_ZERO" + - " -recalFile %s" + parallelism, - 1, // just one output file - Arrays.asList(md5)); - List result = executeTest("testCountCovariates1" + parallelism, spec).getFirst(); - paramsFiles.put(bam, result.get(0).getAbsolutePath()); - } + private CCTest(final String file, final String md5) { + super(CCTest.class); + this.file = file; + this.md5 = md5; } } - - @Test - public void testTableRecalibrator1() { - HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0278cce4cfdab869dc0c11d6852a984b" ); - e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "6797d7ffa4ef6c48413719ba32696ccf"); - e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "2bb3374dde131791d7638031ae3b3e10" ); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "1f9d8944b73169b367cb83b0d22e5432" ); - for ( Map.Entry entry : e.entrySet() ) { - String bam = entry.getKey(); - String md5 = entry.getValue(); - String paramsFile = paramsFiles.get(bam); - System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile); - if ( paramsFile != null ) { - WalkerTestSpec spec = new WalkerTestSpec( - "-R " + b36KGReference + - " -T TableRecalibration" + - " -I " + bam + - ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) + @DataProvider(name = "cctestdata") + public Object[][] createCCTestData() { + + new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "" ); + new CCTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", ""); + new CCTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "" ); + new CCTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "" ); + return CCTest.getTests(CCTest.class); + } + + @Test(dataProvider = "cctestdata") + public void testCountCovariates1(CCTest test) { + testCC(test, ""); + } + + @Test(dataProvider = "cctestdata") + public void testCountCovariates4(CCTest test) { + testCC(test, " -nt 4"); + } + + private final void testCC(CCTest test, String parallelism) { + String bam = test.file; + String md5 = test.md5; + + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + "-R " + b36KGReference + + " --DBSNP " + GATKDataLocation + "dbsnp_132_b37.vcf" + + " -T CountCovariates" + + " -I " + bam + + ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) + ? " -L 1:10,800,000-10,810,000" : " -L 1:10,000,000-10,200,000" ) + + " -cov ReadGroupCovariate" + + " -cov QualityScoreCovariate" + + " -cov CycleCovariate" + + " -cov DinucCovariate" + + " --solid_recal_mode SET_Q_ZERO" + + " -recalFile %s" + parallelism, + 1, // just one output file + Arrays.asList(md5)); + List result = executeTest("testCountCovariates1" + parallelism, spec).getFirst(); + paramsFiles.put(bam, result.get(0).getAbsolutePath()); + } + + + private static final class TRTest extends TestDataProvider { + String file, md5; + + private TRTest(final String file, final String md5) { + super(TRTest.class); + this.file = file; + this.md5 = md5; + } + } + + @DataProvider(name = "trtestdata") + public Object[][] createTRTestData() { + new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "" ); + new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", ""); + new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "" ); + new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "" ); + return TRTest.getTests(TRTest.class); + } + + @Test(dataProvider = "trtestdata", dependsOnMethods = "testCountCovariates1") + public void testTableRecalibrator1(TRTest test) { + String bam = test.file; + String md5 = test.md5; + String paramsFile = paramsFiles.get(bam); + System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile); + if ( paramsFile != null ) { + WalkerTestSpec spec = new WalkerTestSpec( + "-R " + b36KGReference + + " -T TableRecalibration" + + " -I " + bam + + ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) ? " -L 1:10,800,000-10,810,000" : " -L 1:10,100,000-10,300,000" ) + - " -o %s" + - " --no_pg_tag" + - " --solid_recal_mode SET_Q_ZERO" + - " -recalFile " + paramsFile, - 1, // just one output file - Arrays.asList(md5)); - executeTest("testTableRecalibrator1", spec); - } + " -o %s" + + " --no_pg_tag" + + " --solid_recal_mode SET_Q_ZERO" + + " -recalFile " + paramsFile, + 1, // just one output file + Arrays.asList(md5)); + executeTest("testTableRecalibrator1", spec); } } @Test public void testCountCovariatesUseOriginalQuals() { HashMap e = new HashMap(); - e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "3404965ec4fa99873fe6a44521944fd5"); + e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", ""); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -97,7 +129,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { " -standard" + " -OQ" + " -recalFile %s" + - " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod", + " --DBSNP " + GATKDataLocation + "dbsnp_132_b37.vcf", 1, // just one output file Arrays.asList(md5)); executeTest("testCountCovariatesUseOriginalQuals", spec); @@ -107,7 +139,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorMaxQ70() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0278cce4cfdab869dc0c11d6852a984b" ); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -136,7 +168,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesSolidIndelsRemoveRefBias() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "c9ea5f995e1e2b7a5688533e678dcedc" ); + e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -144,7 +176,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" + + " --DBSNP " + GATKDataLocation + "dbsnp_132_b37.vcf" + " -T CountCovariates" + " -I " + bam + " -standard" + @@ -162,7 +194,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorSolidIndelsRemoveRefBias() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "993fae4270e7e1e15986f270acf247af" ); + e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -190,7 +222,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesVCF() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "170f0c3cc4b8d72c539136effeec9a16"); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", ""); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -214,7 +246,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesBED() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "b460478d9683e827784e42bc352db8bb"); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", ""); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -238,7 +270,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesVCFPlusDBsnp() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "a3d892bd60d8f679affda3c1e3af96c1"); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", ""); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -249,7 +281,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { " -B:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" + " -T CountCovariates" + " -I " + bam + - " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" + + " --DBSNP " + GATKDataLocation + "dbsnp_132_b37.vcf" + " -L 1:10,000,000-10,200,000" + " -cov ReadGroupCovariate" + " -cov QualityScoreCovariate" + @@ -266,7 +298,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesNoIndex() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "284ccac1f8fe485e52c86333cac7c2d4" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -274,7 +306,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" + + " --DBSNP " + GATKDataLocation + "dbsnp_132_b37.vcf" + " -T CountCovariates" + " -I " + bam + " -cov ReadGroupCovariate" + @@ -292,7 +324,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorNoIndex() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "c167799c2d9cab815d7c9b23337f162e" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey();