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Cache header merger.

This commit is contained in:
Matt Hanna 2011-12-14 18:05:31 -05:00
parent e061e236ab
commit 6fb4be1a09
1 changed files with 6 additions and 3 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
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@ -95,6 +95,11 @@ public class SAMDataSource {
*/ */
private final Map<SAMReaderID,GATKBAMFileSpan> readerPositions = new HashMap<SAMReaderID,GATKBAMFileSpan>(); private final Map<SAMReaderID,GATKBAMFileSpan> readerPositions = new HashMap<SAMReaderID,GATKBAMFileSpan>();
/**
* Cached representation of the merged header used to generate a merging iterator.
*/
private final SamFileHeaderMerger headerMerger;
/** /**
* The merged header. * The merged header.
*/ */
@ -287,7 +292,7 @@ public class SAMDataSource {
initializeReaderPositions(readers); initializeReaderPositions(readers);
SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate,readers.headers(),true); headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate,readers.headers(),true);
mergedHeader = headerMerger.getMergedHeader(); mergedHeader = headerMerger.getMergedHeader();
hasReadGroupCollisions = headerMerger.hasReadGroupCollisions(); hasReadGroupCollisions = headerMerger.hasReadGroupCollisions();
@ -535,8 +540,6 @@ public class SAMDataSource {
* @return An iterator over the selected data. * @return An iterator over the selected data.
*/ */
private StingSAMIterator getIterator(SAMReaders readers, Shard shard, boolean enableVerification) { private StingSAMIterator getIterator(SAMReaders readers, Shard shard, boolean enableVerification) {
SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate,readers.headers(),true);
// Set up merging to dynamically merge together multiple BAMs. // Set up merging to dynamically merge together multiple BAMs.
MergingSamRecordIterator mergingIterator = new MergingSamRecordIterator(headerMerger,readers.values(),true); MergingSamRecordIterator mergingIterator = new MergingSamRecordIterator(headerMerger,readers.values(),true);