diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/BaseCounts.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/BaseCounts.java index 687dc2c0a..d3812d678 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/BaseCounts.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/BaseCounts.java @@ -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); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusReadCompressor.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusReadCompressor.java index 74081f01d..207972283 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusReadCompressor.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusReadCompressor.java @@ -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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusSite.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusSite.java index 041826f56..3b7d239e3 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusSite.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusSite.java @@ -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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusSpan.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusSpan.java index 6f3c0edc1..dd25915c9 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusSpan.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ConsensusSpan.java @@ -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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/MultiSampleConsensusReadCompressor.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/MultiSampleConsensusReadCompressor.java index ab87290e2..a6485ccee 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/MultiSampleConsensusReadCompressor.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/MultiSampleConsensusReadCompressor.java @@ -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 * diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsWalker.java index a1610cc52..88e697e14 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsWalker.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReducingSAMFileWriter.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReducingSAMFileWriter.java index a72395bf8..6d683e642 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReducingSAMFileWriter.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReducingSAMFileWriter.java @@ -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.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/RefPileupElement.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/RefPileupElement.java index edc0ab990..302eb18e7 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/RefPileupElement.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/RefPileupElement.java @@ -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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/SingleSampleConsensusReadCompressor.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/SingleSampleConsensusReadCompressor.java index ca5b92865..ef1c912d3 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/SingleSampleConsensusReadCompressor.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/reducereads/SingleSampleConsensusReadCompressor.java @@ -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 *