From a3343c75dbd653ddff74233e0f928889f20aeb23 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 2 Dec 2009 20:11:22 +0000
Subject: [PATCH] Move and rename a hybrid-selection-specific coverage
 calculation to hybridselection/

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2225 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../CoverageAcrossBaitsWalker.java}                           | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)
 rename java/src/org/broadinstitute/sting/playground/gatk/walkers/{CoverageAcrossIntervalsWalker.java => hybridselection/CoverageAcrossBaitsWalker.java} (97%)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageAcrossIntervalsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageAcrossIntervalsWalker.java
rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java
index 6df20a9b8..d58632400 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageAcrossIntervalsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.playground.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers.hybridselection;
 
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -24,7 +24,7 @@ import java.util.Arrays;
  */
 
 @By(DataSource.REFERENCE)
-public class CoverageAcrossIntervalsWalker extends LocusWalker<Pair<Integer, Integer>, CoverageAcrossIntervalsWalker.Coverage> {
+public class CoverageAcrossBaitsWalker extends LocusWalker<Pair<Integer, Integer>, CoverageAcrossBaitsWalker.Coverage> {
     /* Accumulates coverage across hybrid selection bait intervals to assess effect of bait adjacency.
      Requires input bait intervals that have an overhang beyond the actual bait interval to capture coverage data at these points.
      Outputs R parseable file that has all data in lists and then does some basic plotting.