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Merge pull request #1243 from broadinstitute/gvda_rodwalkers_dont_downsample_1179 

Fix bug where gatkdocs of RodWalkers reported default LocusWalker downsampling settings
This commit is contained in:
Geraldine Van der Auwera 2015-11-23 21:39:43 -05:00
parent 5a3756410c 88a0514ec7
commit 1f8e45f0ba
1 changed files with 29 additions and 7 deletions
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36
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java
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@ -228,13 +228,17 @@ public class WalkerDocumentationHandler extends GenericDocumentationHandler {
*/
private HashMap<String, Object> getDownSamplingSettings(Class myClass, HashMap<String, Object> dsSettings) {
//
// Retrieve annotation
if (myClass.isAnnotationPresent(Downsample.class)) {
final Annotation thisAnnotation = myClass.getAnnotation(Downsample.class);
if(thisAnnotation instanceof Downsample) {
final Downsample dsAnnotation = (Downsample) thisAnnotation;
dsSettings.put("by", dsAnnotation.by().toString());
dsSettings.put("to_cov", dsAnnotation.toCoverage());
// Check for RODWalker first
if (!checkForRODWalker(myClass).equals("yes")) {
//
// Retrieve annotation
if (myClass.isAnnotationPresent(Downsample.class)) {
final Annotation thisAnnotation = myClass.getAnnotation(Downsample.class);
if(thisAnnotation instanceof Downsample) {
final Downsample dsAnnotation = (Downsample) thisAnnotation;
dsSettings.put("by", dsAnnotation.by().toString());
dsSettings.put("to_cov", dsAnnotation.toCoverage());
}
}
}
return dsSettings;
@ -320,6 +324,24 @@ public class WalkerDocumentationHandler extends GenericDocumentationHandler {
return getWalkerType(mySuperClass);
}
/**
* Utility function that checks whether an instance of class c is a subclass of RODWalker.
*
* @param myClass the class to query for the annotation
* @return "yes" or "no" (can't use a Boolean because of the recursion)
*/
private String checkForRODWalker(Class myClass) {
//
// Look up superclasses recursively until we find either RODWalker or (Walker or Object)
final Class mySuperClass = myClass.getSuperclass();
if (mySuperClass.getSimpleName().equals("RodWalker")) {
return "yes";
} else if (mySuperClass.getSimpleName().equals("Object") || mySuperClass.getSimpleName().equals("Walker")) {
return "";
}
return checkForRODWalker(mySuperClass);
}
/**
* Utility function that finds the values of ReadFilters annotation applied to an instance of class c.
*