Some changes involving output of marginal calls to different, per-filter files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1191 348d0f76-0448-11de-a6fe-93d51630548a
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kiran
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commit
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@ -27,15 +27,16 @@ import java.util.HashSet;
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*/
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@Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=rodVariants.class))
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public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
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@Argument(fullName="features", shortName="F", doc="Feature test (optionally with arguments) to apply to genotype posteriors. Syntax: 'testname[:arguments]'") public String[] FEATURES;
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@Argument(fullName="exclusion_criterion", shortName="X", doc="Exclusion test (optionally with arguments) to apply to variant call. Syntax: 'testname[:arguments]'") public String[] EXCLUSIONS;
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@Argument(fullName="variants_out", shortName="VO", doc="File to which modified variants should be written") public File VARIANTS_OUT;
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@Argument(fullName="variants_out_head", shortName="VOH", doc="File to which modified variants should be written") public String VARIANTS_OUT_HEAD;
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@Argument(fullName="features", shortName="F", doc="Feature test (optionally with arguments) to apply to genotype posteriors. Syntax: 'testname[:arguments]'", required=false) public String[] FEATURES;
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@Argument(fullName="exclusion_criterion", shortName="X", doc="Exclusion test (optionally with arguments) to apply to variant call. Syntax: 'testname[:arguments]'", required=false) public String[] EXCLUSIONS;
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@Argument(fullName="verbose", shortName="V", doc="Show how the variant likelihoods are changing with the application of each feature") public Boolean VERBOSE = false;
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@Argument(fullName="list", shortName="ls", doc="List the available features and exclusion criteria and exit") public Boolean LIST = false;
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private ArrayList<Class> featureClasses;
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private ArrayList<Class> exclusionClasses;
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private PrintWriter vwriter;
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private HashMap<String, PrintWriter> ewriters;
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/**
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* Prepare the output file and the list of available features.
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@ -45,17 +46,37 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
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exclusionClasses = PackageUtils.getClassesImplementingInterface(VariantExclusionCriterion.class);
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if (LIST) {
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out.println("\nAvailable features: " + getAvailableClasses(featureClasses) + "\n");
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out.println("\nAvailable exclusion criteria: " + getAvailableClasses(exclusionClasses) + "\n");
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out.println("\nAvailable features: " + getAvailableClasses(featureClasses));
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out.println("Available exclusion criteria: " + getAvailableClasses(exclusionClasses) + "\n");
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System.exit(0);
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}
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try {
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vwriter = new PrintWriter(VARIANTS_OUT);
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vwriter = new PrintWriter(VARIANTS_OUT_HEAD + ".included.geli.calls");
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vwriter.println(AlleleFrequencyEstimate.geliHeaderString());
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ewriters = new HashMap<String, PrintWriter>();
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if (EXCLUSIONS != null) {
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for (String requestedExclusionString : EXCLUSIONS) {
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String[] requestedExclusionPieces = requestedExclusionString.split(":");
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String requestedExclusionName = requestedExclusionPieces[0];
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for ( Class exclusionClass : exclusionClasses ) {
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String exclusionClassName = rationalizeClassName(exclusionClass);
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if (requestedExclusionName.equalsIgnoreCase(exclusionClassName)) {
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PrintWriter writer = new PrintWriter(VARIANTS_OUT_HEAD + ".excluded." + exclusionClassName + ".geli.calls");
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writer.println(AlleleFrequencyEstimate.geliHeaderString());
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ewriters.put(exclusionClassName, writer);
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}
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}
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}
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}
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} catch (FileNotFoundException e) {
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throw new StingException(String.format("Could not open file '%s' for writing", VARIANTS_OUT.getAbsolutePath()));
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//throw new StingException(String.format("Could not open file '%s' for writing", VARIANTS_OUT.getAbsolutePath()));
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throw new StingException(String.format("Could not open file(s) for writing"));
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}
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}
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@ -111,82 +132,91 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
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if (VERBOSE) { out.println("Original:\n " + variant); }
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// Apply features that modify the likelihoods and LOD scores
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for (String requestedFeatureString : FEATURES) {
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String[] requestedFeaturePieces = requestedFeatureString.split(":");
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String requestedFeatureName = requestedFeaturePieces[0];
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String requestedFeatureArgs = (requestedFeaturePieces.length == 2) ? requestedFeaturePieces[1] : "";
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if (FEATURES != null) {
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for (String requestedFeatureString : FEATURES) {
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String[] requestedFeaturePieces = requestedFeatureString.split(":");
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String requestedFeatureName = requestedFeaturePieces[0];
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String requestedFeatureArgs = (requestedFeaturePieces.length == 2) ? requestedFeaturePieces[1] : "";
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int notYetSeenFeature = 0;
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for ( Class featureClass : featureClasses ) {
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String featureClassName = rationalizeClassName(featureClass);
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int notYetSeenFeature = 0;
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for ( Class featureClass : featureClasses ) {
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String featureClassName = rationalizeClassName(featureClass);
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if (requestedFeatureName.equalsIgnoreCase(featureClassName)) {
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try {
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IndependentVariantFeature ivf = (IndependentVariantFeature) featureClass.newInstance();
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ivf.initialize(requestedFeatureArgs);
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if (requestedFeatureName.equalsIgnoreCase(featureClassName)) {
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try {
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IndependentVariantFeature ivf = (IndependentVariantFeature) featureClass.newInstance();
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ivf.initialize(requestedFeatureArgs);
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variant.adjustLikelihoods(ivf.compute(ref, context));
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variant.adjustLikelihoods(ivf.compute(ref, context));
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if (VERBOSE) { out.println(featureClassName + ":\n " + variant); }
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} catch (InstantiationException e) {
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throw new StingException(String.format("Cannot instantiate feature class '%s': must be concrete class", featureClass.getSimpleName()));
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} catch (IllegalAccessException e) {
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throw new StingException(String.format("Cannot instantiate feature class '%s': must have no-arg constructor", featureClass.getSimpleName()));
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if (VERBOSE) { out.println(featureClassName + ":\n " + variant); }
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} catch (InstantiationException e) {
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throw new StingException(String.format("Cannot instantiate feature class '%s': must be concrete class", featureClass.getSimpleName()));
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} catch (IllegalAccessException e) {
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throw new StingException(String.format("Cannot instantiate feature class '%s': must have no-arg constructor", featureClass.getSimpleName()));
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}
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} else {
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notYetSeenFeature++;
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}
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} else {
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notYetSeenFeature++;
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}
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}
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if (notYetSeenFeature == featureClasses.size()) {
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throw new StingException(String.format("Unknown feature '%s'. Valid features are '%s'", requestedFeatureName, getAvailableClasses(featureClasses)));
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if (notYetSeenFeature == featureClasses.size()) {
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throw new StingException(String.format("Unknown feature '%s'. Valid features are '%s'", requestedFeatureName, getAvailableClasses(featureClasses)));
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}
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}
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}
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// Apply exclusion tests that accept or reject the variant call
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ArrayList<String> exclusionResults = new ArrayList<String>();
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for (String requestedExclusionString : EXCLUSIONS) {
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String[] requestedExclusionPieces = requestedExclusionString.split(":");
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String requestedExclusionName = requestedExclusionPieces[0];
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String requestedExclusionArgs = (requestedExclusionPieces.length == 2) ? requestedExclusionPieces[1] : "";
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if (EXCLUSIONS != null) {
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for (String requestedExclusionString : EXCLUSIONS) {
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String[] requestedExclusionPieces = requestedExclusionString.split(":");
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String requestedExclusionName = requestedExclusionPieces[0];
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String requestedExclusionArgs = (requestedExclusionPieces.length == 2) ? requestedExclusionPieces[1] : "";
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int notYetSeenExclusion = 0;
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for ( Class exclusionClass : exclusionClasses ) {
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String exclusionClassName = rationalizeClassName(exclusionClass);
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int notYetSeenExclusion = 0;
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for ( Class exclusionClass : exclusionClasses ) {
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String exclusionClassName = rationalizeClassName(exclusionClass);
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if (requestedExclusionName.equalsIgnoreCase(exclusionClassName)) {
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try {
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VariantExclusionCriterion vec = (VariantExclusionCriterion) exclusionClass.newInstance();
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vec.initialize(requestedExclusionArgs);
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if (requestedExclusionName.equalsIgnoreCase(exclusionClassName)) {
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try {
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VariantExclusionCriterion vec = (VariantExclusionCriterion) exclusionClass.newInstance();
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vec.initialize(requestedExclusionArgs);
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boolean excludeResult = vec.exclude(ref, context, variant);
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boolean excludeResult = vec.exclude(ref, context, variant);
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if (excludeResult) {
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exclusionResults.add(exclusionClassName);
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if (excludeResult) {
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exclusionResults.add(exclusionClassName);
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}
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} catch (InstantiationException e) {
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throw new StingException(String.format("Cannot instantiate exclusion class '%s': must be concrete class", exclusionClass.getSimpleName()));
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} catch (IllegalAccessException e) {
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throw new StingException(String.format("Cannot instantiate exclusion class '%s': must have no-arg constructor", exclusionClass.getSimpleName()));
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}
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} catch (InstantiationException e) {
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throw new StingException(String.format("Cannot instantiate exclusion class '%s': must be concrete class", exclusionClass.getSimpleName()));
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} catch (IllegalAccessException e) {
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throw new StingException(String.format("Cannot instantiate exclusion class '%s': must have no-arg constructor", exclusionClass.getSimpleName()));
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} else {
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notYetSeenExclusion++;
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}
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} else {
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notYetSeenExclusion++;
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}
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}
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if (notYetSeenExclusion == exclusionClasses.size()) {
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throw new StingException(String.format("Unknown exclusion '%s'. Valid exclusions are '%s'", requestedExclusionName, getAvailableClasses(exclusionClasses)));
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if (notYetSeenExclusion == exclusionClasses.size()) {
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throw new StingException(String.format("Unknown exclusion '%s'. Valid exclusions are '%s'", requestedExclusionName, getAvailableClasses(exclusionClasses)));
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}
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}
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}
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if (exclusionResults.size() > 0) {
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if (VERBOSE) {
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String exclusions = "";
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for (int i = 0; i < exclusionResults.size(); i++) {
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exclusions += exclusionResults.get(i) + (i == exclusionResults.size() - 1 ? "" : ",");
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String exclusions = "";
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for (int i = 0; i < exclusionResults.size(); i++) {
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exclusions += exclusionResults.get(i) + (i == exclusionResults.size() - 1 ? "" : ",");
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PrintWriter writer = ewriters.get(exclusionResults.get(i));
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if (writer != null) {
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writer.println(variant);
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}
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}
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if (VERBOSE) {
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out.printf("Exclusions: %s\n", exclusions);
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}
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} else {
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@ -221,5 +251,9 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
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out.printf("Processed %d loci.\n", result);
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vwriter.close();
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for (PrintWriter writer : ewriters.values()) {
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writer.close();
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}
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}
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}
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