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 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.*;