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: