From 0dc0d586f197099980ef67d7ec8565d64dc84fee Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 22 May 2011 18:51:35 +0000
Subject: [PATCH] Phasing-specific utilies are now in the Phasing walker

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5839 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../{utils => gatk/walkers/phasing}/CardinalityCounter.java     | 2 +-
 .../broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java  | 1 -
 .../walkers/phasing}/PreciseNonNegativeDouble.java              | 2 +-
 3 files changed, 2 insertions(+), 3 deletions(-)
 rename java/src/org/broadinstitute/sting/{utils => gatk/walkers/phasing}/CardinalityCounter.java (98%)
 rename java/src/org/broadinstitute/sting/{utils => gatk/walkers/phasing}/PreciseNonNegativeDouble.java (98%)

diff --git a/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/utils/CardinalityCounter.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
index 90181e37d..06f4d3ab2 100644
--- a/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
@@ -21,7 +21,7 @@
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  * OTHER DEALINGS IN THE SOFTWARE.
  */
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.gatk.walkers.phasing;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
index 343196bb2..a56c9e21e 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
@@ -24,7 +24,6 @@
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.PreciseNonNegativeDouble;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
diff --git a/java/src/org/broadinstitute/sting/utils/PreciseNonNegativeDouble.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/utils/PreciseNonNegativeDouble.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
index d8921e1d3..99446705e 100644
--- a/java/src/org/broadinstitute/sting/utils/PreciseNonNegativeDouble.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
@@ -21,7 +21,7 @@
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  * OTHER DEALINGS IN THE SOFTWARE.
  */
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.gatk.walkers.phasing;
 
 /* PreciseNonNegativeDouble permits arithmetic operations on NON-NEGATIVE double values
    with precision (prevents underflow by representing in log10 space).