From 9da5cc25adf1fa108af7128d92f7ce9b15fa7422 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 3 Dec 2009 15:40:27 +0000
Subject: [PATCH] More archiving (with permission from Andrey) plus a move to
 core.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2242 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/mendelian}/GenotypingCallStats.java  | 0
 .../sting/mendelian}/MendelianInheritanceWalker.java          | 0
 .../sting/mendelian}/TrioConcordanceRecord.java               | 0
 .../org/broadinstitute/sting/oldindels}/CountedObject.java    | 0
 .../sting/oldindels}/CountedObjectComparatorAdapter.java      | 0
 .../src/org/broadinstitute/sting/oldindels}/Interval.java     | 0
 .../org/broadinstitute/sting/oldindels}/SimpleInterval.java   | 0
 .../sting/gatk/walkers/indels/IndelGenotyperV2Walker.java     | 1 -
 .../sting/gatk/walkers/indels/IndelGenotyperWalker.java       | 1 -
 java/src/org/broadinstitute/sting/utils/AlignmentUtils.java   | 2 --
 .../sting/{playground => }/utils/CircularArray.java           | 4 +---
 11 files changed, 1 insertion(+), 7 deletions(-)
 rename {java/src/org/broadinstitute/sting/playground/utils => archive/java/src/org/broadinstitute/sting/mendelian}/GenotypingCallStats.java (100%)
 rename {java/src/org/broadinstitute/sting/playground/gatk/walkers => archive/java/src/org/broadinstitute/sting/mendelian}/MendelianInheritanceWalker.java (100%)
 rename {java/src/org/broadinstitute/sting/playground/utils => archive/java/src/org/broadinstitute/sting/mendelian}/TrioConcordanceRecord.java (100%)
 rename {java/src/org/broadinstitute/sting/playground/utils => archive/java/src/org/broadinstitute/sting/oldindels}/CountedObject.java (100%)
 rename {java/src/org/broadinstitute/sting/playground/utils => archive/java/src/org/broadinstitute/sting/oldindels}/CountedObjectComparatorAdapter.java (100%)
 rename {java/src/org/broadinstitute/sting/playground/utils => archive/java/src/org/broadinstitute/sting/oldindels}/Interval.java (100%)
 rename {java/src/org/broadinstitute/sting/playground/utils => archive/java/src/org/broadinstitute/sting/oldindels}/SimpleInterval.java (100%)
 rename java/src/org/broadinstitute/sting/{playground => }/utils/CircularArray.java (98%)

diff --git a/java/src/org/broadinstitute/sting/playground/utils/GenotypingCallStats.java b/archive/java/src/org/broadinstitute/sting/mendelian/GenotypingCallStats.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/playground/utils/GenotypingCallStats.java
rename to archive/java/src/org/broadinstitute/sting/mendelian/GenotypingCallStats.java
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java b/archive/java/src/org/broadinstitute/sting/mendelian/MendelianInheritanceWalker.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
rename to archive/java/src/org/broadinstitute/sting/mendelian/MendelianInheritanceWalker.java
diff --git a/java/src/org/broadinstitute/sting/playground/utils/TrioConcordanceRecord.java b/archive/java/src/org/broadinstitute/sting/mendelian/TrioConcordanceRecord.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/playground/utils/TrioConcordanceRecord.java
rename to archive/java/src/org/broadinstitute/sting/mendelian/TrioConcordanceRecord.java
diff --git a/java/src/org/broadinstitute/sting/playground/utils/CountedObject.java b/archive/java/src/org/broadinstitute/sting/oldindels/CountedObject.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/playground/utils/CountedObject.java
rename to archive/java/src/org/broadinstitute/sting/oldindels/CountedObject.java
diff --git a/java/src/org/broadinstitute/sting/playground/utils/CountedObjectComparatorAdapter.java b/archive/java/src/org/broadinstitute/sting/oldindels/CountedObjectComparatorAdapter.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/playground/utils/CountedObjectComparatorAdapter.java
rename to archive/java/src/org/broadinstitute/sting/oldindels/CountedObjectComparatorAdapter.java
diff --git a/java/src/org/broadinstitute/sting/playground/utils/Interval.java b/archive/java/src/org/broadinstitute/sting/oldindels/Interval.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/playground/utils/Interval.java
rename to archive/java/src/org/broadinstitute/sting/oldindels/Interval.java
diff --git a/java/src/org/broadinstitute/sting/playground/utils/SimpleInterval.java b/archive/java/src/org/broadinstitute/sting/oldindels/SimpleInterval.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/playground/utils/SimpleInterval.java
rename to archive/java/src/org/broadinstitute/sting/oldindels/SimpleInterval.java
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
index b11131bd2..221bbd086 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
@@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.playground.utils.CircularArray;
 
 import java.util.*;
 import java.io.IOException;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperWalker.java
index 39ea0118d..6f16ebc73 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperWalker.java
@@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.filters.Platform454Filter;
 import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
 import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
-import org.broadinstitute.sting.playground.utils.CircularArray;
 
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
diff --git a/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
index 18c28679c..28ee7caa4 100644
--- a/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
@@ -5,9 +5,7 @@ import net.sf.samtools.SAMRecord;
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.picard.reference.ReferenceSequence;
-import org.broadinstitute.sting.playground.utils.CountedObject;
 
-import java.util.*;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/java/src/org/broadinstitute/sting/playground/utils/CircularArray.java b/java/src/org/broadinstitute/sting/utils/CircularArray.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/playground/utils/CircularArray.java
rename to java/src/org/broadinstitute/sting/utils/CircularArray.java
index 28fc06074..2b3372657 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/CircularArray.java
+++ b/java/src/org/broadinstitute/sting/utils/CircularArray.java
@@ -1,8 +1,6 @@
-package org.broadinstitute.sting.playground.utils;
+package org.broadinstitute.sting.utils;
 
 
-import org.broadinstitute.sting.utils.StingException;
-
 /** This class, closely resembling a deque (except that it is not dynamically grown), 
  * provides an object with array-like interface and efficient 
  * implementation of shift operation. Use this class when some kind of sliding window is required: