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-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
This commit is contained in:
asivache 2010-01-15 21:11:14 +00:00
parent c8c5c176cd
commit 7a991421f7
1 changed files with 6 additions and 6 deletions
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12
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -142,9 +142,9 @@ public class GATKArgumentCollection {
public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL; public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL;
/** Should we enable rodWalkers? This is currently unsafe */ /** Should we enable rodWalkers? This is currently unsafe */
@Element(required = 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) // @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; // public boolean enableRodWalkers = false;
@Element(required = 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) @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) { if (other.intervalMerging != this.intervalMerging) {
return false; return false;
} }
if (other.enableRodWalkers != this.enableRodWalkers) { // if (other.enableRodWalkers != this.enableRodWalkers) {
return false; // return false;
} // }
return true; return true;
} }