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Turn off index caching. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5514 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-03-25 18:48:23 +00:00
parent 8e67c5567c
commit ac39f5532e
1 changed files with 1 additions and 28 deletions
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29
java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
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@ -73,9 +73,6 @@ public class GATKBAMIndex implements BAMIndex, BrowseableBAMIndex {
private SAMSequenceDictionary mBamDictionary = null; private SAMSequenceDictionary mBamDictionary = null;
private Integer mLastReferenceRetrieved = null;
private WeakHashMap<Integer,BAMIndexContent> mQueriesByReference = new WeakHashMap<Integer,BAMIndexContent>();
public GATKBAMIndex(final File file, final SAMSequenceDictionary dictionary) { public GATKBAMIndex(final File file, final SAMSequenceDictionary dictionary) {
mFile = file; mFile = file;
mBamDictionary = dictionary; mBamDictionary = dictionary;
@ -466,32 +463,8 @@ public class GATKBAMIndex implements BAMIndex, BrowseableBAMIndex {
* @return The index information for this reference. * @return The index information for this reference.
*/ */
protected BAMIndexContent getQueryResults(final int referenceIndex) { protected BAMIndexContent getQueryResults(final int referenceIndex) {
// WeakHashMap is a bit weird in that its lookups are done via equals() equality, but expirations must be
// handled via == equality. This implementation jumps through a few hoops to make sure that == equality still
// holds even in the context of boxing/unboxing.
// If this query is for the same reference index as the last query, return it.
if(mLastReferenceRetrieved!=null && mLastReferenceRetrieved == referenceIndex)
return mQueriesByReference.get(referenceIndex);
// If not, check to see whether it's available in the cache.
BAMIndexContent queryResults = mQueriesByReference.get(referenceIndex);
if(queryResults != null) {
mLastReferenceRetrieved = referenceIndex;
mQueriesByReference.put(referenceIndex,queryResults);
return queryResults;
}
// If not in the cache, attempt to load it from disk. // If not in the cache, attempt to load it from disk.
queryResults = query(referenceIndex,1,-1); return query(referenceIndex,1,-1);
if(queryResults != null) {
mLastReferenceRetrieved = referenceIndex;
mQueriesByReference.put(referenceIndex,queryResults);
return queryResults;
}
// Not even available on disk.
return null;
} }
/** /**