From 07822d6c0f29a54127c851dbc54315b85ba60cd9 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Mon, 16 Jul 2012 13:32:54 -0400 Subject: [PATCH 1/2] Fixed input annotations for master/test files on DiffObjectsWalker. --- .../sting/gatk/walkers/diffengine/DiffObjectsWalker.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java index 1dc28b0e7..2b7a5612b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.diffengine; import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -144,7 +145,7 @@ public class DiffObjectsWalker extends RodWalker { * 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. */ - @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; /** @@ -152,7 +153,7 @@ public class DiffObjectsWalker extends RodWalker { * 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. */ - @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; /** From 6c6a324583592b390bd04456863b52a95f8b4a01 Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Fri, 13 Jul 2012 15:24:46 -0400 Subject: [PATCH 2/2] Loosen a restriction on isOriginalRead() * no longer needs to satisfy ReadAndIntervalOverlap.OVERLAP_CONTAINED --- .../gatk/walkers/compression/reducereads/ReduceReadsWalker.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java index 095149bae..1b11cbd4e 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java @@ -663,7 +663,7 @@ public class ReduceReadsWalker extends ReadWalker, Red * @return Returns true if the read is the original read that went through map(). */ private boolean isOriginalRead(LinkedList list, GATKSAMRecord read) { - return isWholeGenome() || (list.getFirst().equals(read) && ReadUtils.getReadAndIntervalOverlapType(read, intervalList.first()) == ReadUtils.ReadAndIntervalOverlap.OVERLAP_CONTAINED); + return isWholeGenome() || list.getFirst().equals(read); } /**