From 7a991421f784910809e310753be2f70dc10ee5a1 Mon Sep 17 00:00:00 2001 From: asivache Date: Fri, 15 Jan 2010 21:11:14 +0000 Subject: [PATCH] -erw argument, begone! Rod traversals are now enabled. current tests pass, more tests for RODWalkers are welcome ;) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2601 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/arguments/GATKArgumentCollection.java | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 6b6766aac..fcdd71592 100755 --- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -142,9 +142,9 @@ public class GATKArgumentCollection { public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL; /** Should we enable rodWalkers? This is currently unsafe */ - @Element(required = false) - @Argument(fullName = "enableRodWalkers", shortName = "erw", doc = "Enable experimental rodWalker support. TEMPORARY HACK TO ALLOW EXPERIMENTATION WITH ROD WALKERS. [default is false]}.", required = false) - public boolean enableRodWalkers = false; +// @Element(required = false) +// @Argument(fullName = "enableRodWalkers", shortName = "erw", doc = "Enable experimental rodWalker support. TEMPORARY HACK TO ALLOW EXPERIMENTATION WITH ROD WALKERS. [default is false]}.", required = false) +// public boolean enableRodWalkers = false; @Element(required = false) @Argument(fullName = "experimental_sharding",shortName="es", doc="Use the experimental sharding strategy. Will not work for all traversal types.", required = false) @@ -303,9 +303,9 @@ public class GATKArgumentCollection { if (other.intervalMerging != this.intervalMerging) { return false; } - if (other.enableRodWalkers != this.enableRodWalkers) { - return false; - } +// if (other.enableRodWalkers != this.enableRodWalkers) { +// return false; +// } return true; }