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Package updated. Copyrights added 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5926 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-06-02 21:29:27 +00:00
parent 3d628f06f0
commit ad9dca9137
9 changed files with 135 additions and 14 deletions
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29
java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/BaseCounts.java
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@ -1,8 +1,33 @@
package org.broadinstitute.sting.oneoffprojects.walkers.reducereads;
package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
import org.broadinstitute.sting.utils.BaseUtils;
import com.google.java.contract.*;
/*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
/**
* Created by IntelliJ IDEA.
* User: depristo
@ -10,7 +35,7 @@ import com.google.java.contract.*;
* Time: 2:55 PM
*/
final class BaseCounts {
private final int counts[] = new int[4]; // fixme -- include - and I events
private final int counts[] = new int[4]; // todo -- fixme -- include - and I events
public void incr(byte base) {
int baseI = BaseUtils.simpleBaseToBaseIndex(base);

27
java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusReadCompressor.java
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@ -1,8 +1,33 @@
package org.broadinstitute.sting.oneoffprojects.walkers.reducereads;
package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
import com.google.java.contract.*;
import net.sf.samtools.SAMRecord;
/*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
/**
* Created by IntelliJ IDEA.
* User: depristo

27
java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusSite.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.reducereads;
package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -13,6 +13,31 @@ import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
/*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
/**
* Created by IntelliJ IDEA.
* User: depristo

27
java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusSpan.java
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@ -1,7 +1,32 @@
package org.broadinstitute.sting.oneoffprojects.walkers.reducereads;
package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
import org.broadinstitute.sting.utils.GenomeLoc;
/*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
/**
* Created by IntelliJ IDEA.
* User: depristo

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/MultiSampleConsensusReadCompressor.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.reducereads;
package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord;
@ -10,8 +10,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.*;
//import org.broadinstitute.sting.utils.SimpleTimer;
/*
* Copyright (c) 2009 The Broad Institute
*

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsWalker.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.oneoffprojects.walkers.reducereads;
package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReducingSAMFileWriter.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.reducereads;
package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
import net.sf.picard.sam.SamPairUtil;
import net.sf.samtools.*;

27
java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/RefPileupElement.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.reducereads;
package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
import net.sf.samtools.CigarElement;
import net.sf.samtools.SAMRecord;
@ -10,6 +10,31 @@ import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
/**
* Created by IntelliJ IDEA.
* User: depristo

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/SingleSampleConsensusReadCompressor.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.oneoffprojects.walkers.reducereads;
package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
import net.sf.samtools.*;
import org.apache.log4j.Logger;
@ -17,8 +17,6 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
import java.io.PrintStream;
import java.util.*;
//import org.broadinstitute.sting.utils.SimpleTimer;
/*
* Copyright (c) 2009 The Broad Institute
*