Package updated. Copyrights added

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5926 348d0f76-0448-11de-a6fe-93d51630548a

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);

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

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

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

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
  *

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;

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.*;

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

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
  *