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In preparation for move 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2344 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-12-13 18:28:06 +00:00
parent 56467df49a
commit 92307361a4
2 changed files with 6 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/CountRodByRefWalker.java
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@ -11,7 +11,8 @@ import java.util.ArrayList;
import java.util.List; import java.util.List;
/** /**
* Same as CountRod but this one is a reference walker * A very simple walker that prints out counts of the number of reference ordered data objects are
* each locus. For debugging RefWalkers.
*/ */
public class CountRodByRefWalker extends RefWalker<CountRodWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> { public class CountRodByRefWalker extends RefWalker<CountRodWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> {
@Argument(fullName = "verbose", shortName = "v", doc="If true, Countrod will print out detailed information about the rods it finds and locations", required = false) @Argument(fullName = "verbose", shortName = "v", doc="If true, Countrod will print out detailed information about the rods it finds and locations", required = false)

4
java/src/org/broadinstitute/sting/gatk/walkers/CountRodWalker.java
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@ -13,6 +13,10 @@ import java.util.List;
import java.util.Collection; import java.util.Collection;
import java.util.LinkedList; import java.util.LinkedList;
/**
* A very simple walker that prints out counts of the number of reference ordered data objects are
* each locus. For debugging RodWalkers.
*/
public class CountRodWalker extends RodWalker<CountRodWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> { public class CountRodWalker extends RodWalker<CountRodWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> {
@Argument(fullName = "verbose", shortName = "v", doc="If true, Countrod will print out detailed information about the rods it finds and locations", required = false) @Argument(fullName = "verbose", shortName = "v", doc="If true, Countrod will print out detailed information about the rods it finds and locations", required = false)
public boolean verbose = false; public boolean verbose = false;