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Throws an exception if you attempt to use a filter that doesn't exist. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1563 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-09-09 17:33:27 +00:00
parent 1060b36288
commit 06eae52292
1 changed files with 21 additions and 5 deletions
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26
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -41,6 +41,12 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
private static final int windowSize = 10; // 10 variants on either end of the current one private static final int windowSize = 10; // 10 variants on either end of the current one
private ArrayList<VariantContext> windowInitializer = new ArrayList<VariantContext>(); private ArrayList<VariantContext> windowInitializer = new ArrayList<VariantContext>();
private void listFiltersAndExit() {
out.println("\nAvailable features: " + getAvailableClasses(featureClasses));
out.println("Available exclusion criteria: " + getAvailableClasses(exclusionClasses) + "\n");
System.exit(0);
}
/** /**
* Prepare the output file and the list of available features. * Prepare the output file and the list of available features.
*/ */
@ -48,11 +54,7 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
featureClasses = PackageUtils.getClassesImplementingInterface(IndependentVariantFeature.class); featureClasses = PackageUtils.getClassesImplementingInterface(IndependentVariantFeature.class);
exclusionClasses = PackageUtils.getClassesImplementingInterface(VariantExclusionCriterion.class); exclusionClasses = PackageUtils.getClassesImplementingInterface(VariantExclusionCriterion.class);
if (LIST) { if (LIST) { listFiltersAndExit(); }
out.println("\nAvailable features: " + getAvailableClasses(featureClasses));
out.println("Available exclusion criteria: " + getAvailableClasses(exclusionClasses) + "\n");
System.exit(0);
}
try { try {
variantsWriter = new PrintWriter(VARIANTS_OUT_HEAD + ".included.geli.calls"); variantsWriter = new PrintWriter(VARIANTS_OUT_HEAD + ".included.geli.calls");
@ -71,10 +73,13 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
String requestedFeatureName = requestedFeaturePieces[0]; String requestedFeatureName = requestedFeaturePieces[0];
String requestedFeatureArgs = (requestedFeaturePieces.length == 2) ? requestedFeaturePieces[1] : ""; String requestedFeatureArgs = (requestedFeaturePieces.length == 2) ? requestedFeaturePieces[1] : "";
boolean found = false;
for ( Class featureClass : featureClasses ) { for ( Class featureClass : featureClasses ) {
String featureClassName = rationalizeClassName(featureClass); String featureClassName = rationalizeClassName(featureClass);
if (requestedFeatureName.equalsIgnoreCase(featureClassName)) { if (requestedFeatureName.equalsIgnoreCase(featureClassName)) {
found = true;
try { try {
IndependentVariantFeature ivf = (IndependentVariantFeature) featureClass.newInstance(); IndependentVariantFeature ivf = (IndependentVariantFeature) featureClass.newInstance();
ivf.initialize(requestedFeatureArgs); ivf.initialize(requestedFeatureArgs);
@ -88,6 +93,10 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
} }
} }
} }
if (!found) {
throw new StingException("Unknown feature '" + requestedFeatureString + "'. Issue the '-ls' argument to list available features.");
}
} }
} }
@ -99,10 +108,13 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
String[] requestedExclusionPieces = requestedExclusionString.split(":"); String[] requestedExclusionPieces = requestedExclusionString.split(":");
String requestedExclusionName = requestedExclusionPieces[0]; String requestedExclusionName = requestedExclusionPieces[0];
boolean found = false;
for ( Class exclusionClass : exclusionClasses ) { for ( Class exclusionClass : exclusionClasses ) {
String exclusionClassName = rationalizeClassName(exclusionClass); String exclusionClassName = rationalizeClassName(exclusionClass);
if (requestedExclusionName.equalsIgnoreCase(exclusionClassName)) { if (requestedExclusionName.equalsIgnoreCase(exclusionClassName)) {
found = true;
try { try {
HashMap<String,String> requestedArgs = new HashMap<String,String>(); HashMap<String,String> requestedArgs = new HashMap<String,String>();
if ( requestedExclusionPieces.length == 2 ) { if ( requestedExclusionPieces.length == 2 ) {
@ -130,6 +142,10 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
} }
} }
} }
if (!found) {
throw new StingException("Unknown exclusion criterion '" + requestedExclusionString + "'. Issue the '-ls' argument to list available exclusion criteria.");
}
} }
} }