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Features and exclusion criteria are now instantiated in VariantFiltrationWalker's initialize() method, rather than in every map() call. This means the features and exclusion criteria will only ever be initialized once. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1281 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-07-20 22:47:21 +00:00
parent 54fce98056
commit f314ef8d84
1 changed files with 67 additions and 73 deletions
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140
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java
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@ -1,8 +1,7 @@
package org.broadinstitute.sting.playground.gatk.walkers.variants; package org.broadinstitute.sting.playground.gatk.walkers.variants;
import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.refdata.rodVariants;
import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.RMD;
@ -32,12 +31,16 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
@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; @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;
@Argument(fullName="verbose", shortName="V", doc="Show how the variant likelihoods are changing with the application of each feature") public Boolean VERBOSE = false; @Argument(fullName="verbose", shortName="V", doc="Show how the variant likelihoods are changing with the application of each feature") public Boolean VERBOSE = false;
@Argument(fullName="list", shortName="ls", doc="List the available features and exclusion criteria and exit") public Boolean LIST = false; @Argument(fullName="list", shortName="ls", doc="List the available features and exclusion criteria and exit") public Boolean LIST = false;
@Argument(fullName="truth", shortName="truth", doc="Operate on truth set only") public Boolean TRUTH = false;
private ArrayList<Class> featureClasses; private ArrayList<Class> featureClasses;
private ArrayList<Class> exclusionClasses; private ArrayList<Class> exclusionClasses;
private PrintWriter vwriter; private PrintWriter vwriter;
private HashMap<String, PrintWriter> ewriters; private HashMap<String, PrintWriter> ewriters;
private ArrayList<IndependentVariantFeature> requestedFeatures;
private ArrayList<VariantExclusionCriterion> requestedExclusions;
/** /**
* Prepare the output file and the list of available features. * Prepare the output file and the list of available features.
*/ */
@ -55,27 +58,68 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
vwriter = new PrintWriter(VARIANTS_OUT_HEAD + ".included.geli.calls"); vwriter = new PrintWriter(VARIANTS_OUT_HEAD + ".included.geli.calls");
vwriter.println(AlleleFrequencyEstimate.geliHeaderString()); vwriter.println(AlleleFrequencyEstimate.geliHeaderString());
requestedFeatures = new ArrayList<IndependentVariantFeature>();
requestedExclusions = new ArrayList<VariantExclusionCriterion>();
// Initialize requested features
if (FEATURES != null) {
for (String requestedFeatureString : FEATURES) {
String[] requestedFeaturePieces = requestedFeatureString.split(":");
String requestedFeatureName = requestedFeaturePieces[0];
String requestedFeatureArgs = (requestedFeaturePieces.length == 2) ? requestedFeaturePieces[1] : "";
for ( Class featureClass : featureClasses ) {
String featureClassName = rationalizeClassName(featureClass);
if (requestedFeatureName.equalsIgnoreCase(featureClassName)) {
try {
IndependentVariantFeature ivf = (IndependentVariantFeature) featureClass.newInstance();
ivf.initialize(requestedFeatureArgs);
requestedFeatures.add(ivf);
} catch (InstantiationException e) {
throw new StingException(String.format("Cannot instantiate feature class '%s': must be concrete class", featureClass.getSimpleName()));
} catch (IllegalAccessException e) {
throw new StingException(String.format("Cannot instantiate feature class '%s': must have no-arg constructor", featureClass.getSimpleName()));
}
}
}
}
}
// Initialize requested exclusion criteria
ewriters = new HashMap<String, PrintWriter>(); ewriters = new HashMap<String, PrintWriter>();
if (EXCLUSIONS != null) { if (EXCLUSIONS != null) {
for (String requestedExclusionString : EXCLUSIONS) { for (String requestedExclusionString : EXCLUSIONS) {
String[] requestedExclusionPieces = requestedExclusionString.split(":"); String[] requestedExclusionPieces = requestedExclusionString.split(":");
String requestedExclusionName = requestedExclusionPieces[0]; String requestedExclusionName = requestedExclusionPieces[0];
String requestedExclusionArgs = (requestedExclusionPieces.length == 2) ? requestedExclusionPieces[1] : "";
for ( Class exclusionClass : exclusionClasses ) { for ( Class exclusionClass : exclusionClasses ) {
String exclusionClassName = rationalizeClassName(exclusionClass); String exclusionClassName = rationalizeClassName(exclusionClass);
if (requestedExclusionName.equalsIgnoreCase(exclusionClassName)) { if (requestedExclusionName.equalsIgnoreCase(exclusionClassName)) {
PrintWriter writer = new PrintWriter(VARIANTS_OUT_HEAD + ".excluded." + exclusionClassName + ".geli.calls"); try {
writer.println(AlleleFrequencyEstimate.geliHeaderString()); VariantExclusionCriterion vec = (VariantExclusionCriterion) exclusionClass.newInstance();
vec.initialize(requestedExclusionArgs);
ewriters.put(exclusionClassName, writer); requestedExclusions.add(vec);
PrintWriter writer = new PrintWriter(VARIANTS_OUT_HEAD + ".excluded." + exclusionClassName + ".geli.calls");
writer.println(AlleleFrequencyEstimate.geliHeaderString());
ewriters.put(exclusionClassName, writer);
} catch (InstantiationException e) {
throw new StingException(String.format("Cannot instantiate exclusion class '%s': must be concrete class", exclusionClass.getSimpleName()));
} catch (IllegalAccessException e) {
throw new StingException(String.format("Cannot instantiate exclusion class '%s': must have no-arg constructor", exclusionClass.getSimpleName()));
}
} }
} }
} }
} }
} catch (FileNotFoundException e) { } catch (FileNotFoundException e) {
//throw new StingException(String.format("Could not open file '%s' for writing", VARIANTS_OUT.getAbsolutePath()));
throw new StingException(String.format("Could not open file(s) for writing")); throw new StingException(String.format("Could not open file(s) for writing"));
} }
} }
@ -126,82 +170,34 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
*/ */
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) { public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
rodVariants variant = (rodVariants) tracker.lookup("variant", null); rodVariants variant = (rodVariants) tracker.lookup("variant", null);
rodGFF hapmapSite = null;
for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {
if ( datum != null && datum instanceof rodGFF ) {
hapmapSite = (rodGFF) datum;
}
}
// Ignore places where we don't have a variant or where the reference base is ambiguous. // Ignore places where we don't have a variant or where the reference base is ambiguous.
if (variant != null && BaseUtils.simpleBaseToBaseIndex(ref) != -1) { if (variant != null && (!TRUTH || hapmapSite != null) && BaseUtils.simpleBaseToBaseIndex(ref) != -1) {
if (VERBOSE) { out.println("Original:\n " + variant); } if (VERBOSE) { out.println("Original:\n " + variant); }
// Apply features that modify the likelihoods and LOD scores // Apply features that modify the likelihoods and LOD scores
if (FEATURES != null) { for ( IndependentVariantFeature ivf : requestedFeatures ) {
for (String requestedFeatureString : FEATURES) { variant.adjustLikelihoods(ivf.compute(ref, context));
String[] requestedFeaturePieces = requestedFeatureString.split(":");
String requestedFeatureName = requestedFeaturePieces[0];
String requestedFeatureArgs = (requestedFeaturePieces.length == 2) ? requestedFeaturePieces[1] : "";
int notYetSeenFeature = 0; if (VERBOSE) { out.println(rationalizeClassName(ivf.getClass()) + ":\n " + variant); }
for ( Class featureClass : featureClasses ) {
String featureClassName = rationalizeClassName(featureClass);
if (requestedFeatureName.equalsIgnoreCase(featureClassName)) {
try {
IndependentVariantFeature ivf = (IndependentVariantFeature) featureClass.newInstance();
ivf.initialize(requestedFeatureArgs);
variant.adjustLikelihoods(ivf.compute(ref, context));
if (VERBOSE) { out.println(featureClassName + ":\n " + variant); }
} catch (InstantiationException e) {
throw new StingException(String.format("Cannot instantiate feature class '%s': must be concrete class", featureClass.getSimpleName()));
} catch (IllegalAccessException e) {
throw new StingException(String.format("Cannot instantiate feature class '%s': must have no-arg constructor", featureClass.getSimpleName()));
}
} else {
notYetSeenFeature++;
}
}
if (notYetSeenFeature == featureClasses.size()) {
throw new StingException(String.format("Unknown feature '%s'. Valid features are '%s'", requestedFeatureName, getAvailableClasses(featureClasses)));
}
}
} }
// Apply exclusion tests that accept or reject the variant call // Apply exclusion tests that accept or reject the variant call
ArrayList<String> exclusionResults = new ArrayList<String>(); ArrayList<String> exclusionResults = new ArrayList<String>();
if (EXCLUSIONS != null) { for ( VariantExclusionCriterion vec : requestedExclusions ) {
for (String requestedExclusionString : EXCLUSIONS) { boolean excludeResult = vec.exclude(ref, context, variant);
String[] requestedExclusionPieces = requestedExclusionString.split(":");
String requestedExclusionName = requestedExclusionPieces[0];
String requestedExclusionArgs = (requestedExclusionPieces.length == 2) ? requestedExclusionPieces[1] : "";
int notYetSeenExclusion = 0; if (excludeResult) {
for ( Class exclusionClass : exclusionClasses ) { exclusionResults.add(rationalizeClassName(vec.getClass()));
String exclusionClassName = rationalizeClassName(exclusionClass);
if (requestedExclusionName.equalsIgnoreCase(exclusionClassName)) {
try {
VariantExclusionCriterion vec = (VariantExclusionCriterion) exclusionClass.newInstance();
vec.initialize(requestedExclusionArgs);
boolean excludeResult = vec.exclude(ref, context, variant);
if (excludeResult) {
exclusionResults.add(exclusionClassName);
}
} catch (InstantiationException e) {
throw new StingException(String.format("Cannot instantiate exclusion class '%s': must be concrete class", exclusionClass.getSimpleName()));
} catch (IllegalAccessException e) {
throw new StingException(String.format("Cannot instantiate exclusion class '%s': must have no-arg constructor", exclusionClass.getSimpleName()));
}
} else {
notYetSeenExclusion++;
}
}
if (notYetSeenExclusion == exclusionClasses.size()) {
throw new StingException(String.format("Unknown exclusion '%s'. Valid exclusions are '%s'", requestedExclusionName, getAvailableClasses(exclusionClasses)));
}
} }
} }
@ -216,9 +212,7 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
} }
} }
if (VERBOSE) { if (VERBOSE) { out.printf("Exclusions: %s\n", exclusions); }
out.printf("Exclusions: %s\n", exclusions);
}
} else { } else {
vwriter.println(variant); vwriter.println(variant);
} }