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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
This commit is contained in:
ebanks 2009-12-03 15:40:27 +00:00
parent b3bdcd0e60
commit 9da5cc25ad
11 changed files with 1 additions and 7 deletions
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0
java/src/org/broadinstitute/sting/playground/utils/GenotypingCallStats.java → archive/java/src/org/broadinstitute/sting/mendelian/GenotypingCallStats.java
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java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java → archive/java/src/org/broadinstitute/sting/mendelian/MendelianInheritanceWalker.java
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java/src/org/broadinstitute/sting/playground/utils/TrioConcordanceRecord.java → archive/java/src/org/broadinstitute/sting/mendelian/TrioConcordanceRecord.java
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java/src/org/broadinstitute/sting/playground/utils/CountedObject.java → archive/java/src/org/broadinstitute/sting/oldindels/CountedObject.java
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java/src/org/broadinstitute/sting/playground/utils/CountedObjectComparatorAdapter.java → archive/java/src/org/broadinstitute/sting/oldindels/CountedObjectComparatorAdapter.java
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java/src/org/broadinstitute/sting/playground/utils/Interval.java → archive/java/src/org/broadinstitute/sting/oldindels/Interval.java
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java/src/org/broadinstitute/sting/playground/utils/SimpleInterval.java → archive/java/src/org/broadinstitute/sting/oldindels/SimpleInterval.java
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java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -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;

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java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -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;

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java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
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@ -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.

4
java/src/org/broadinstitute/sting/playground/utils/CircularArray.java → java/src/org/broadinstitute/sting/utils/CircularArray.java
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@ -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: