Removed experimental tool MarkDuplicatesGATK in favor of MarkDuplicat…

…esSpark (#5166)
broadinstitute · Sep 10, 2018 · 2386612 · 2386612
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commit 2386612
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Showing 22 changed files with 256 additions and 2,314 deletions.
diff --git a/...dinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSparkUtils.java b/...dinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSparkUtils.java
@@ -22,6 +22,7 @@
 import org.broadinstitute.hellbender.utils.read.markduplicates.*;
 import org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.*;
 import picard.sam.markduplicates.util.OpticalDuplicateFinder;
+import picard.sam.markduplicates.util.ReadEnds;
 import scala.Tuple2;
 
 import java.io.Serializable;

diff --git a/...broadinstitute/hellbender/tools/walkers/markduplicates/EstimateLibraryComplexityGATK.java b/...broadinstitute/hellbender/tools/walkers/markduplicates/EstimateLibraryComplexityGATK.java
diff --git a/...n/java/org/broadinstitute/hellbender/tools/walkers/markduplicates/MarkDuplicatesGATK.java b/...n/java/org/broadinstitute/hellbender/tools/walkers/markduplicates/MarkDuplicatesGATK.java
diff --git a/...titute/hellbender/utils/read/markduplicates/AbstractMarkDuplicatesCommandLineProgram.java b/...titute/hellbender/utils/read/markduplicates/AbstractMarkDuplicatesCommandLineProgram.java
diff --git a/...ellbender/utils/read/markduplicates/AbstractOpticalDuplicateFinderCommandLineProgram.java b/...ellbender/utils/read/markduplicates/AbstractOpticalDuplicateFinderCommandLineProgram.java