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Speeds up MarkDuplicates on queryname input by using the in memory read-ends map. #1411

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Oct 22, 2019
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Speeds up MarkDuplicates on queryname input by using the in memory read-ends map. #1411

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3 changes: 2 additions & 1 deletion src/main/java/picard/sam/markduplicates/MarkDuplicates.java
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Expand Up @@ -533,7 +533,8 @@ private void buildSortedReadEndLists(final boolean useBarcodes) {
final SamHeaderAndIterator headerAndIterator = openInputs(true);
final SAMFileHeader.SortOrder assumedSortOrder = headerAndIterator.header.getSortOrder();
final SAMFileHeader header = headerAndIterator.header;
final ReadEndsForMarkDuplicatesMap tmp = new DiskBasedReadEndsForMarkDuplicatesMap(MAX_FILE_HANDLES_FOR_READ_ENDS_MAP, diskCodec);
final ReadEndsForMarkDuplicatesMap tmp = assumedSortOrder == SAMFileHeader.SortOrder.queryname ?
new MemoryBasedReadEndsForMarkDuplicatesMap() : new DiskBasedReadEndsForMarkDuplicatesMap(MAX_FILE_HANDLES_FOR_READ_ENDS_MAP, diskCodec);
long index = 0;
final ProgressLogger progress = new ProgressLogger(log, (int) 1e6, "Read");
final CloseableIterator<SAMRecord> iterator = headerAndIterator.iterator;
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2 changes: 1 addition & 1 deletion src/main/java/picard/sam/markduplicates/util/MemoryBasedReadEndsForMarkDuplicatesMap.java
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Expand Up @@ -33,7 +33,7 @@
*
* @author alecw@broadinstitute.org
*/
class MemoryBasedReadEndsForMarkDuplicatesMap implements ReadEndsForMarkDuplicatesMap {
public class MemoryBasedReadEndsForMarkDuplicatesMap implements ReadEndsForMarkDuplicatesMap {

/**
* Index of this list is sequence index. Value is map from String {read group id:read name} to ReadEnds.
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