zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Allow walkers to enforce the ordering in which ReadFilters are applied (so that they're now done in the order specified in the walker). Useful if you have a computationally expensive filter (like adaptor clipping) that should only be applied to reads passing all other filters. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5600 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-08 03:34:50 +00:00
parent 53db7b8faa
commit 4f17004590
1 changed files with 7 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
java/src/org/broadinstitute/sting/gatk/WalkerManager.java
View File

@ -445,10 +445,14 @@ public class WalkerManager extends PluginManager<Walker> {
* @return An array of types extending from SamRecordFilter. Will never be null. * @return An array of types extending from SamRecordFilter. Will never be null.
*/ */
public static Collection<Class<? extends SamRecordFilter>> getReadFilterTypes(Class<?> walkerClass) { public static Collection<Class<? extends SamRecordFilter>> getReadFilterTypes(Class<?> walkerClass) {
Set<Class<? extends SamRecordFilter>> filterTypes = new HashSet<Class<? extends SamRecordFilter>>(); List<Class<? extends SamRecordFilter>> filterTypes = new ArrayList<Class<? extends SamRecordFilter>>();
while(walkerClass != null) { while(walkerClass != null) {
if(walkerClass.isAnnotationPresent(ReadFilters.class)) if(walkerClass.isAnnotationPresent(ReadFilters.class)) {
filterTypes.addAll(Arrays.asList(walkerClass.getAnnotation(ReadFilters.class).value())); for ( Class c : walkerClass.getAnnotation(ReadFilters.class).value() ) {
if( !filterTypes.contains(c) )
filterTypes.add(c);
}
}
walkerClass = walkerClass.getSuperclass(); walkerClass = walkerClass.getSuperclass();
} }
return filterTypes; return filterTypes;