From 6bf0cc32f9eec789b73ab661623d6a5d7be78490 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 11 Jan 2013 09:16:19 -0500 Subject: [PATCH 1/2] When reducing multiple samples it is possible to try to close a region that for a given sample has no reads. Currently we'd NPE. Fixed. --- .../walkers/compression/reducereads/SingleSampleCompressor.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java index ac3388795..0edcb22e1 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java @@ -80,7 +80,7 @@ public class SingleSampleCompressor { } public Set closeVariantRegions(CompressionStash regions) { - return slidingWindow.closeVariantRegions(regions); + return slidingWindow == null ? Collections.emptySet() : slidingWindow.closeVariantRegions(regions); } } From 67fafbb6258b9c4074a66c457a629d005409db55 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 11 Jan 2013 09:19:46 -0500 Subject: [PATCH 2/2] Forgot an include --- .../walkers/compression/reducereads/SingleSampleCompressor.java | 1 + 1 file changed, 1 insertion(+) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java index 0edcb22e1..e9ad88c03 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java @@ -4,6 +4,7 @@ import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.sam.AlignmentStartWithNoTiesComparator; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import java.util.Collections; import java.util.Set; import java.util.TreeSet;