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Added an option to list all available feature classes and exit. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1056 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-19 00:00:12 +00:00
parent ed7afd8b70
commit 9a0151b7e1
1 changed files with 8 additions and 1 deletions
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9
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java
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@ -27,6 +27,7 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
@Argument(fullName="features", shortName="F", doc="Feature test (optionally with arguments) to apply to genotype posteriors. Syntax: 'testname[:arguments]'") public String[] FEATURES;
@Argument(fullName="variants_out", shortName="VO", doc="File to which modified variants should be written") public File VARIANTS_OUT;
@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_features", shortName="list", doc="List the available features and exit") public Boolean LIST_FEATURES = false;
private ArrayList<Class> featureClasses;
private PrintWriter vwriter;
@ -61,11 +62,17 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
* Prepare the output file and the list of available features.
*/
public void initialize() {
featureClasses = PackageUtils.getClassesImplementingInterface(IndependentVariantFeature.class);
if (LIST_FEATURES) {
out.println("\nAvailable features: " + getAvailableFeatureClasses() + "\n");
System.exit(0);
}
try {
vwriter = new PrintWriter(VARIANTS_OUT);
vwriter.println(AlleleFrequencyEstimate.geliHeaderString());
featureClasses = PackageUtils.getClassesImplementingInterface(IndependentVariantFeature.class);
} catch (FileNotFoundException e) {
throw new StingException(String.format("Could not open file '%s' for writing", VARIANTS_OUT.getAbsolutePath()));
}