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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2012-07-17 00:32:53 -04:00
parent f657b8bda8 6c6a324583
commit d5b3a2eabf
2 changed files with 4 additions and 3 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
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@ -663,7 +663,7 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
* @return Returns true if the read is the original read that went through map(). * @return Returns true if the read is the original read that went through map().
*/ */
private boolean isOriginalRead(LinkedList<GATKSAMRecord> list, GATKSAMRecord read) { private boolean isOriginalRead(LinkedList<GATKSAMRecord> list, GATKSAMRecord read) {
return isWholeGenome() || (list.getFirst().equals(read) && ReadUtils.getReadAndIntervalOverlapType(read, intervalList.first()) == ReadUtils.ReadAndIntervalOverlap.OVERLAP_CONTAINED); return isWholeGenome() || list.getFirst().equals(read);
} }
/** /**

5
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.diffengine; package org.broadinstitute.sting.gatk.walkers.diffengine;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -144,7 +145,7 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
* files to do the comparison. Conceptually master is the original file contained the expected * files to do the comparison. Conceptually master is the original file contained the expected
* results, but this doesn't currently have an impact on the calculations, but might in the future. * results, but this doesn't currently have an impact on the calculations, but might in the future.
*/ */
@Argument(fullName="master", shortName="m", doc="Master file: expected results", required=true) @Input(fullName="master", shortName="m", doc="Master file: expected results", required=true)
File masterFile; File masterFile;
/** /**
@ -152,7 +153,7 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
* files to do the comparison. Conceptually test is the derived file from master, but this * files to do the comparison. Conceptually test is the derived file from master, but this
* doesn't currently have an impact on the calculations, but might in the future. * doesn't currently have an impact on the calculations, but might in the future.
*/ */
@Argument(fullName="test", shortName="t", doc="Test file: new results to compare to the master file", required=true) @Input(fullName="test", shortName="t", doc="Test file: new results to compare to the master file", required=true)
File testFile; File testFile;
/** /**