From 92e3682991ec0ba500d29681dc4cc1a81d412988 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 28 Dec 2009 20:57:32 +0000
Subject: [PATCH] Moved NHashMap to sting/utils

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2452 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/analyzecovariates/AnalysisDataManager.java         | 3 ++-
 .../sting/gatk/walkers/recalibration/RecalDataManager.java   | 1 +
 .../{gatk/walkers/recalibration => utils}/NHashMap.java      | 5 +----
 3 files changed, 4 insertions(+), 5 deletions(-)
 rename java/src/org/broadinstitute/sting/{gatk/walkers/recalibration => utils}/NHashMap.java (96%)

diff --git a/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java b/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java
index 5036e3e81..58e12816b 100755
--- a/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java
+++ b/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.analyzecovariates;
 
 import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
-import org.broadinstitute.sting.gatk.walkers.recalibration.NHashMap;
+import org.broadinstitute.sting.utils.NHashMap;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -35,6 +35,7 @@ public class AnalysisDataManager {
      * Add the given mapping to all of the collapsed hash tables
      * @param key The list of comparables that is the key for this mapping
      * @param fullDatum The RecalDatum which is the data for this mapping
+     * @param IGNORE_QSCORES_LESS_THAN The threshold in report quality for adding to the aggregate collapsed table
      */
     public final void addToAllTables( final List<? extends Comparable> key, final RecalDatum fullDatum, final int IGNORE_QSCORES_LESS_THAN ) {
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index 261b3ec1f..52cb4fae9 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.NHashMap;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/NHashMap.java b/java/src/org/broadinstitute/sting/utils/NHashMap.java
similarity index 96%
rename from java/src/org/broadinstitute/sting/gatk/walkers/recalibration/NHashMap.java
rename to java/src/org/broadinstitute/sting/utils/NHashMap.java
index 7d48d90d5..17b1c4bea 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/NHashMap.java
+++ b/java/src/org/broadinstitute/sting/utils/NHashMap.java
@@ -1,7 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers.recalibration;
-
-import org.broadinstitute.sting.utils.Pair;
-import org.broadinstitute.sting.utils.StingException;
+package org.broadinstitute.sting.utils;
 
 import java.util.*;