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Removed Nx counting of reads in metrics with -nt > 1

This commit is contained in:
Mark DePristo 2011-10-06 18:29:26 -07:00
parent d367945dec
commit d1e70d6ec2
1 changed files with 1 additions and 3 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -66,15 +66,13 @@ public class ShardTraverser implements Callable {
microScheduler.getReadIterator(shard), microScheduler.getReadIterator(shard),
shard.getGenomeLocs(), shard.getGenomeLocs(),
microScheduler.engine.getSampleDB().getSampleNames()); // todo: microScheduler.engine is protected - is it okay to user it here? microScheduler.engine.getSampleDB().getSampleNames()); // todo: microScheduler.engine is protected - is it okay to user it here?
ShardDataProvider dataProvider = null;
for(WindowMaker.WindowMakerIterator iterator: windowMaker) { for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),microScheduler.getEngine().getGenomeLocParser(),iterator.getLocus(),iterator,microScheduler.reference,microScheduler.rods); final ShardDataProvider dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),microScheduler.getEngine().getGenomeLocParser(),iterator.getLocus(),iterator,microScheduler.reference,microScheduler.rods);
accumulator = traversalEngine.traverse( walker, dataProvider, accumulator ); accumulator = traversalEngine.traverse( walker, dataProvider, accumulator );
dataProvider.close(); dataProvider.close();
} }
if (dataProvider != null) dataProvider.close();
windowMaker.close(); windowMaker.close();
outputMergeTask = outputTracker.closeStorage(); outputMergeTask = outputTracker.closeStorage();