VariantEval now uses the "standard" modules only by default. You can add other modules with the -E argument and not use all of the standard ones with -noStandard (they can be added back individually with -E).
Generalized some of the packaging code from VariantAnnotator. Matt might want to take a look to make this nicer...? git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3925 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
a7ff9caf54
commit
2307bed742
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@ -63,7 +63,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
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protected String[] annotationsToUse = {};
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@Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
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protected String[] annotationClassesToUse = { };
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protected String[] annotationGroupsToUse = {};
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@Argument(fullName="useAllAnnotations", shortName="all", doc="Use all possible annotations (not for the faint of heart)", required=false)
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protected Boolean USE_ALL_ANNOTATIONS = false;
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@ -131,7 +131,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
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if ( USE_ALL_ANNOTATIONS )
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engine = new VariantAnnotatorEngine(getToolkit());
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else
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engine = new VariantAnnotatorEngine(getToolkit(), annotationClassesToUse, annotationsToUse);
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engine = new VariantAnnotatorEngine(getToolkit(), annotationGroupsToUse, annotationsToUse);
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// setup the header fields
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Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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@ -60,8 +60,8 @@ public class VariantAnnotatorEngine {
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public static final String dbPrefix = "comp";
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private ArrayList<InfoFieldAnnotation> requestedInfoAnnotations;
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private ArrayList<GenotypeAnnotation> requestedGenotypeAnnotations;
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private List<InfoFieldAnnotation> requestedInfoAnnotations;
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private List<GenotypeAnnotation> requestedGenotypeAnnotations;
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private HashMap<String, String> dbAnnotations = new HashMap<String, String>();
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@ -82,16 +82,14 @@ public class VariantAnnotatorEngine {
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// use this constructor if you want all possible annotations
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public VariantAnnotatorEngine(GenomeAnalysisEngine engine) {
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List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = PackageUtils.getClassesImplementingInterface(InfoFieldAnnotation.class);
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requestedInfoAnnotations = getInstances(infoAnnotationClasses);
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List<Class<? extends GenotypeAnnotation>> genotypeAnnotationClasses = PackageUtils.getClassesImplementingInterface(GenotypeAnnotation.class);
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requestedGenotypeAnnotations = getInstances(genotypeAnnotationClasses);
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requestedInfoAnnotations = PackageUtils.getInstancesOfClassesImplementingInterface(InfoFieldAnnotation.class);
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requestedGenotypeAnnotations = PackageUtils.getInstancesOfClassesImplementingInterface(GenotypeAnnotation.class);
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initialize(engine);
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}
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// use this constructor if you want to select specific annotations (and/or interfaces)
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public VariantAnnotatorEngine(GenomeAnalysisEngine engine, String[] annotationClassesToUse, String[] annotationsToUse) {
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public VariantAnnotatorEngine(GenomeAnalysisEngine engine, String[] annotationGroupsToUse, String[] annotationsToUse) {
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// create a map for all annotation classes which implement our top-level interfaces
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HashMap<String, Class> classMap = new HashMap<String, Class>();
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for ( Class c : PackageUtils.getClassesImplementingInterface(InfoFieldAnnotation.class) )
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@ -103,7 +101,7 @@ public class VariantAnnotatorEngine {
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HashSet<Class> classes = new HashSet<Class>();
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// get the classes from the provided groups (interfaces)
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for ( String group : annotationClassesToUse ) {
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for ( String group : annotationGroupsToUse ) {
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Class interfaceClass = classMap.get(group);
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if ( interfaceClass == null )
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interfaceClass = classMap.get(group + "Annotation");
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@ -128,31 +126,14 @@ public class VariantAnnotatorEngine {
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for ( Class c : classes ) {
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// note that technically an annotation can work on both the INFO and FORMAT fields
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if ( InfoFieldAnnotation.class.isAssignableFrom(c) )
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requestedInfoAnnotations.add((InfoFieldAnnotation)getInstance(c));
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requestedInfoAnnotations.add((InfoFieldAnnotation)PackageUtils.getSimpleInstance(c));
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if ( GenotypeAnnotation.class.isAssignableFrom(c) )
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requestedGenotypeAnnotations.add((GenotypeAnnotation)getInstance(c));
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requestedGenotypeAnnotations.add((GenotypeAnnotation)PackageUtils.getSimpleInstance(c));
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}
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initialize(engine);
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}
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private static <T> ArrayList<T> getInstances(List<Class<? extends T>> classes) {
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ArrayList<T> objects = new ArrayList<T>();
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for ( Class c : classes )
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objects.add((T)getInstance(c));
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return objects;
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}
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private static <T> T getInstance(Class<T> c) {
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try {
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return c.newInstance();
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} catch (InstantiationException e) {
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throw new StingException(String.format("Cannot instantiate annotation class '%s': must be concrete class", c.getSimpleName()));
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} catch (IllegalAccessException e) {
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throw new StingException(String.format("Cannot instantiate annotation class '%s': must have no-arg constructor", c.getSimpleName()));
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}
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}
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private void initialize(GenomeAnalysisEngine engine) {
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// check to see whether comp rods were included
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@ -181,15 +162,8 @@ public class VariantAnnotatorEngine {
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return descriptions;
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}
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/**
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* A slightly simplified interface for when you don't have any reads, so the stratifiedContexts aren't necessary, and
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* you only permit a single return value
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*
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* @param tracker
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* @param ref
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* @param vc
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* @return
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*/
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// A slightly simplified interface for when you don't have any reads, so the stratifiedContexts aren't necessary, and
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// you only permit a single return value
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public VariantContext annotateContext(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc) {
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Collection<VariantContext> results = this.annotateContext(tracker, ref, EMPTY_STRATIFIED_ALIGNMENT_CONTEXT, vc);
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@ -278,13 +252,7 @@ public class VariantAnnotatorEngine {
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return returnValue;
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}
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/**
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* Finish processing data from GenomicAnnotation.
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*
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* @param infoAnnotationOutputsList
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* @param annotationsForCurrentLocusFromAllAnnotatorInputTables
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* @return
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*/
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// Finish processing data from GenomicAnnotation.
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private List<Map<String, Object>> processGenomicAnnotation( List<Map<String, Object>> infoAnnotationOutputsList, Map<String, Object> annotationsForCurrentLocusFromAllAnnotatorInputTables)
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{
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@ -330,15 +298,8 @@ public class VariantAnnotatorEngine {
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return infoAnnotationOutputsList;
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}
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/**
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* Performs a join between the an info field record represented by outputRecordInfoField and the infoAnnotationOutputsList.
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*
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* @param infoAnnotationOutputsList
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* @param outputRecordInfoField
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* @param joinTable
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* @return
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*/
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private List<Map<String, Object>> performJoin( List<Map<String, Object>> infoAnnotationOutputsList, Map<String, Object> outputRecordInfoField, JoinTable joinTable)
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// Performs a join between the an info field record represented by outputRecordInfoField and the infoAnnotationOutputsList.
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private List<Map<String, Object>> performJoin( List<Map<String, Object>> infoAnnotationOutputsList, Map<String, Object> outputRecordInfoField, JoinTable joinTable)
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{
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//System.err.println("Looking at: " + joinTable.getLocalBindingName()+ "- join to " + joinTable.getExternalBindingName() + "." + joinTable.getExternalColumnName() );
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//for the current joinTable, for each output line, find the externalJoinColumnValue and see if it matches the joinColumnValue of any record(s) in this joinTable.
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@ -413,16 +374,10 @@ public class VariantAnnotatorEngine {
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}
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/**
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* Implements not-oneToMany mode, where the output lines have a one-to-one relationship
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* with the input variants, and all multiple-match records are collapsed into the single info field.
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* The collapsing is done by appending an _i to each key name (where 'i' is a record counter), as well
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* as a special bindingName.numMatchingRecords=n key-value pair which specifies the upper limit of the counter.
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*
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* @param infoAnnotationOutputsList
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* @param matchingRecords
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* @param bindingName
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*/
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// Implements not-oneToMany mode, where the output lines have a one-to-one relationship
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// with the input variants, and all multiple-match records are collapsed into the single info field.
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// The collapsing is done by appending an _i to each key name (where 'i' is a record counter), as well
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// as a special bindingName.numMatchingRecords=n key-value pair which specifies the upper limit of the counter.
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private void addToExistingAnnotationOutputs(
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final List<Map<String, Object>> infoAnnotationOutputsList,
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final List<Map<String, String>> matchingRecords,
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@ -470,19 +425,12 @@ public class VariantAnnotatorEngine {
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}
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}
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/**
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* Implements oneToMany mode. Takes the current infoAnnotationOutputsList
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* (where each element represents a line in the output VCF file), and
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* generates a new infoAnnotationOutputsList which contains one copy of the current
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* infoAnnotationOutputs for each record matchingRecords.
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* The returned list will have size:
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* infoAnnotationOutputsList.size() * matchingRecords.size()
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*
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* @param infoAnnotationOutputsList
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* @param matchingRecords
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* @param bindingName
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* @return
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*/
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// Implements oneToMany mode. Takes the current infoAnnotationOutputsList
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// (where each element represents a line in the output VCF file), and
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// generates a new infoAnnotationOutputsList which contains one copy of the current
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// infoAnnotationOutputs for each record matchingRecords.
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// The returned list will have size:
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// infoAnnotationOutputsList.size() * matchingRecords.size()
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private List<Map<String, Object>> explodeInfoAnnotationOutputsList(
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final List<Map<String, Object>> infoAnnotationOutputsList,
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final List<Map<String, String>> matchingRecords,
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@ -515,8 +463,8 @@ public class VariantAnnotatorEngine {
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* Records statistics for the explodeInfoAnnotationOutputsList(..) calculation.
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* @param bindingName The table from which annotations were gotten
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* @param numNewVCFRecordsAnnotatedWithBindingNameData The number of new output VCF records created with annotations from this table
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* @param infoAnnotationOutputsList
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* @parma matchingRecordsSize
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* @param infoAnnotationOutputsList output list
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* @param matchingRecordsSize matching records size
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*/
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private void recordStats( final String bindingName, int numNewVCFRecordsAnnotatedWithBindingNameData, final List<Map<String, Object>> infoAnnotationOutputsList, int matchingRecordsSize ) {
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@ -549,13 +497,7 @@ public class VariantAnnotatorEngine {
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}
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/**
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* Applies the -S arg to the results
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*
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* @param infoAnnotationOutputsList
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* @return The new newInfoAnnotationOutputList with -S arg applied.
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*/
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// Applies the -S arg to the results
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private List<Map<String, Object>> applySelectArg( final List<Map<String, Object>> infoAnnotationOutputsList )
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{
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final List<Map<String, Object>> newInfoAnnotationOutputList = new LinkedList<Map<String, Object>>();
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@ -614,7 +556,7 @@ public class VariantAnnotatorEngine {
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*
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* See class-level comments for more details.
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*
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* @param oneToMany
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* @param oneToMany true if we should break out from one to many
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*/
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public void setOneToMany(boolean oneToMany) {
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this.oneToMany = oneToMany;
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@ -694,9 +636,7 @@ public class VariantAnnotatorEngine {
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}
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/**
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* Returns a map containing stats on how many output vcf records were annotated from each database
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*/
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//Returns a map containing stats on how many output vcf records were annotated from each database
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public Map<String, Integer> getInputTableHitCounter() {
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return Collections.unmodifiableMap(inputTableHitCounter);
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}
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@ -18,7 +18,7 @@ import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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@Analysis(name = "Comp Overlap", description = "the overlap between eval and comp sites")
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public class CompOverlap extends VariantEvaluator {
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public class CompOverlap extends VariantEvaluator implements StandardEval {
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@DataPoint(name = "eval sites", description = "number of eval SNP sites")
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long nEvalSNPs = 0;
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@ -11,7 +11,7 @@ import org.broadinstitute.sting.utils.StingException;
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@Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample")
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public class CountVariants extends VariantEvaluator {
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public class CountVariants extends VariantEvaluator implements StandardEval {
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// the following fields are in output order:
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@ -37,7 +37,7 @@ import java.util.*;
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*/
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@Analysis(name = "Genotype Concordance", description = "Determine the genotype concordance between the genotypes in difference tracks")
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public class GenotypeConcordance extends VariantEvaluator {
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public class GenotypeConcordance extends VariantEvaluator implements StandardEval {
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private static final boolean PRINT_INTERESTING_SITES = true;
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protected final static Logger logger = Logger.getLogger(GenotypeConcordance.class);
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@ -8,7 +8,6 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
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import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
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import org.broadinstitute.sting.playground.utils.report.utils.TableType;
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import org.broadinstitute.sting.utils.StingException;
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import org.broad.tribble.vcf.VCFGenotypeRecord;
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import java.util.ArrayList;
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@ -43,7 +42,7 @@ import java.util.ArrayList;
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*/
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@Analysis(name = "Quality Metrics by allele count", description = "Shows various stats binned by allele count")
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public class SimpleMetricsByAC extends VariantEvaluator {
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public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval {
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// a mapping from quality score histogram bin to Ti/Tv ratio
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@DataPoint(name="TiTv by AC", description = "TiTv by allele count")
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MetricsByAc metrics = null;
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@ -0,0 +1,28 @@
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/*
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* Copyright (c) 2010.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.varianteval;
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public interface StandardEval {}
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@ -8,7 +8,7 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
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import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
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@Analysis(name = "Ti/Tv Variant Evaluator", description = "Ti/Tv Variant Evaluator")
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public class TiTvVariantEvaluator extends VariantEvaluator {
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public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval {
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@DataPoint(name = "ti_count", description = "number of transition loci")
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long nTi = 0;
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@ -136,11 +136,11 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
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//
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// Arguments for choosing which modules to run
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//
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@Argument(fullName="evalModule", shortName="E", doc="One or more specific eval modules to apply to the eval track(s)", required=false)
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@Argument(fullName="evalModule", shortName="E", doc="One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noStandard is specified)", required=false)
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protected String[] modulesToUse = {};
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@Argument(fullName="useNoModules", shortName="none", doc="Use no eval modules", required=false)
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protected Boolean USE_NO_MODULES = false;
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@Argument(fullName="doNotUseAllStandardModules", shortName="noStandard", doc="Do not use the standard modules by default (instead, only those that are specified with the -E option)")
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protected Boolean NO_STANDARD = false;
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@Argument(fullName="list", shortName="ls", doc="List the available eval modules and exit")
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protected Boolean LIST = false;
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@ -272,7 +272,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
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}
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// Dynamically determined variantEvaluation classes
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private List<Class<? extends VariantEvaluator>> evaluationClasses = null;
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private Set<Class<? extends VariantEvaluator>> evaluationClasses = null;
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/** output writer for interesting sites */
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private VCFWriter writer = null;
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@ -392,21 +392,23 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
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for ( Class<? extends VariantEvaluator> c : PackageUtils.getClassesImplementingInterface(VariantEvaluator.class) )
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classMap.put(c.getSimpleName(), c);
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if ( USE_NO_MODULES ) {
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evaluationClasses = new ArrayList<Class<? extends VariantEvaluator>>(0);
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} else if ( modulesToUse.length == 0 ) {
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evaluationClasses = new ArrayList<Class<? extends VariantEvaluator>>(classMap.values());
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} else {
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// get the specific classes provided
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evaluationClasses = new ArrayList<Class<? extends VariantEvaluator>>(modulesToUse.length);
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for ( String module : modulesToUse ) {
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Class<? extends VariantEvaluator> moduleClass = classMap.get(module);
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if ( moduleClass == null )
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throw new StingException("Class " + module + " is not found; please check that you have specified the class name correctly");
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evaluationClasses.add(moduleClass);
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evaluationClasses = new HashSet<Class<? extends VariantEvaluator>>();
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// by default, use standard eval modules
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if ( !NO_STANDARD ) {
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for ( Class<? extends StandardEval> myClass : PackageUtils.getClassesImplementingInterface(StandardEval.class) ) {
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if ( classMap.containsKey(myClass.getSimpleName()) )
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evaluationClasses.add(classMap.get(myClass.getSimpleName()));
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}
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}
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// get the specific classes provided
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for ( String module : modulesToUse ) {
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if ( !classMap.containsKey(module) )
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throw new StingException("Class " + module + " is not found; please check that you have specified the class name correctly");
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evaluationClasses.add(classMap.get(module));
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}
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for ( VariantEvaluator e : instantiateEvalationsSet() ) {
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// for collecting purposes
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variantEvaluationNames.add(e.getName());
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@ -28,10 +28,9 @@ package org.broadinstitute.sting.utils.classloader;
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import org.reflections.Reflections;
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import org.reflections.scanners.ResourcesScanner;
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import org.reflections.scanners.SubTypesScanner;
|
||||
import org.reflections.util.ClasspathHelper;
|
||||
import org.reflections.util.ConfigurationBuilder;
|
||||
import org.reflections.util.ManifestAwareClasspathHelper;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
|
||||
import java.net.URL;
|
||||
import java.util.Set;
|
||||
|
|
@ -81,6 +80,24 @@ public class PackageUtils {
|
|||
return concreteTypes;
|
||||
}
|
||||
|
||||
public static <T> List<T> getInstancesOfClassesImplementingInterface(Class<T> iface) {
|
||||
List<Class<? extends T>> classes = PackageUtils.getClassesImplementingInterface(iface);
|
||||
List<T> instances = new ArrayList<T>();
|
||||
for ( Class<? extends T> c : classes )
|
||||
instances.add(getSimpleInstance(c));
|
||||
return instances;
|
||||
}
|
||||
|
||||
public static <T> T getSimpleInstance(Class<T> c) {
|
||||
try {
|
||||
return c.newInstance();
|
||||
} catch (InstantiationException e) {
|
||||
throw new StingException(String.format("Cannot instantiate class '%s': must be concrete class", c.getSimpleName()));
|
||||
} catch (IllegalAccessException e) {
|
||||
throw new StingException(String.format("Cannot instantiate class '%s': must have no-arg constructor", c.getSimpleName()));
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Return the interface classes that extend the specified interface.
|
||||
*
|
||||
|
|
|
|||
|
|
@ -29,7 +29,7 @@ public class
|
|||
String extraArgs = "-L 1:1-10,000,000";
|
||||
for (String tests : testsEnumerations) {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
|
||||
1, Arrays.asList("119601d7e9e67a1053663b2e546250ed"));
|
||||
1, Arrays.asList("a12bd969ca3bc676752e078d205c730a"));
|
||||
executeTest("testSelect1", spec);
|
||||
}
|
||||
}
|
||||
|
|
@ -38,7 +38,7 @@ public class
|
|||
public void testSelect2() {
|
||||
String extraArgs = "-L 1:1-10,000,000";
|
||||
WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s",
|
||||
1, Arrays.asList("06d495ab8169a2570eebdc54ecdffe10"));
|
||||
1, Arrays.asList("2c1a99b225b55dcf605410ba5e6be789"));
|
||||
executeTest("testSelect2", spec);
|
||||
}
|
||||
|
||||
|
|
@ -46,7 +46,7 @@ public class
|
|||
public void testVEGenotypeConcordance() {
|
||||
String vcfFiles[] = {"GenotypeConcordanceEval.vcf", "GenotypeConcordanceEval.vcf.gz"};
|
||||
for (String vcfFile : vcfFiles) {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B eval,VCF," + validationDataLocation + vcfFile + " -B comp,VCF," + validationDataLocation + "GenotypeConcordanceComp.vcf -E GenotypeConcordance -reportType CSV -o %s",
|
||||
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B eval,VCF," + validationDataLocation + vcfFile + " -B comp,VCF," + validationDataLocation + "GenotypeConcordanceComp.vcf -noStandard -E GenotypeConcordance -reportType CSV -o %s",
|
||||
1,
|
||||
Arrays.asList("15d1075d384da2bb7445f7493f2b6a07"));
|
||||
executeTest("testVEGenotypeConcordance" + vcfFile, spec);
|
||||
|
|
@ -57,8 +57,8 @@ public class
|
|||
@Test
|
||||
public void testVESimple() {
|
||||
HashMap<String, String> expectations = new HashMap<String, String>();
|
||||
expectations.put("-L 1:1-10,000,000", "629b8b124306435ff56b66357354dfbc");
|
||||
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "f51c299d500b347d098c7ab25f54a436");
|
||||
expectations.put("-L 1:1-10,000,000", "a48e4ca3a019bf46eb3a178a6a80822f");
|
||||
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0 -E MendelianViolationEvaluator", "bc35dfefce72899d4c673bfc37c9a7f3");
|
||||
|
||||
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
|
||||
String extraArgs = entry.getKey();
|
||||
|
|
@ -75,15 +75,15 @@ public class
|
|||
@Test
|
||||
public void testVEComplex() {
|
||||
HashMap<String, String> expectations = new HashMap<String, String>();
|
||||
String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -MVQ 30" +
|
||||
String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -MVQ 30 -E MendelianViolationEvaluator" +
|
||||
" -B dbsnp_130,dbSNP," + GATKDataLocation + "dbsnp_130_b36.rod" +
|
||||
" -B comp_hapmap,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
|
||||
|
||||
|
||||
String matchingMD5 = "d01725ce4e46c8fea0855a923c1598fd";
|
||||
String matchingMD5 = "38c8906cc364d04ba39a437d93d752d3";
|
||||
expectations.put("", matchingMD5);
|
||||
expectations.put(" -known comp_hapmap -known dbsnp", matchingMD5);
|
||||
expectations.put(" -known comp_hapmap", "a50be9240f6c90503fb6333d8a78b974");
|
||||
expectations.put(" -known comp_hapmap", "b839c8e9f26b01281899f86362b5323c");
|
||||
for (String tests : testsEnumerations) {
|
||||
for (Map.Entry<String, String> entry : expectations.entrySet()) {
|
||||
String extraArgs2 = entry.getKey();
|
||||
|
|
@ -103,7 +103,7 @@ public class
|
|||
"-R " + oneKGLocation + "reference/human_b36_both.fasta " +
|
||||
"-L 21 " +
|
||||
"-D " + GATKDataLocation + "dbsnp_129_b36.rod " +
|
||||
"-E CountFunctionalClasses " +
|
||||
"-E CountFunctionalClasses -noStandard " +
|
||||
"-B eval,VCF," + validationDataLocation + "test.filtered.maf_annotated.vcf " +
|
||||
"-o %s";
|
||||
String md5 = "d41d8cd98f00b204e9800998ecf8427e";
|
||||
|
|
@ -114,11 +114,11 @@ public class
|
|||
|
||||
@Test
|
||||
public void testVEWriteVCF() {
|
||||
String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30";
|
||||
String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30 -E MendelianViolationEvaluator";
|
||||
for (String tests : testsEnumerations) {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s",
|
||||
2,
|
||||
Arrays.asList("483f821ce96f4cf571e9bba356c9f325", "989bc30dea6c8a4cf771cd1b9fdab488"));
|
||||
Arrays.asList("8059c6b53ba15598bf89d65c79742566", "989bc30dea6c8a4cf771cd1b9fdab488"));
|
||||
executeTest("testVEWriteVCF", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue