An attempt to cleanup the Utils directory. Email to follow.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java

@@ -1,10 +1,33 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.alignment;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;

java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java

@@ -1,7 +1,30 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.alignment;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;

java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.alignment;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
@@ -5,7 +28,7 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import net.sf.samtools.SAMRecord;
 
 import java.util.*;

java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java

@@ -1,35 +1,33 @@
-package org.broadinstitute.sting.analyzecovariates;
-
-import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
-import org.broadinstitute.sting.utils.NestedHashMap;
-
-import java.util.ArrayList;
-
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
+package org.broadinstitute.sting.analyzecovariates;
+
+import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
+import org.broadinstitute.sting.utils.collections.NestedHashMap;
+
+import java.util.ArrayList;
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin

java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java

@@ -1,10 +1,33 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.analyzecovariates;
 
 import org.broadinstitute.sting.gatk.walkers.recalibration.*;
-import org.broadinstitute.sting.utils.PackageUtils;
+import org.broadinstitute.sting.utils.classloader.PackageUtils;
-import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -12,31 +35,6 @@ import java.util.Map;
 import java.util.regex.Pattern;
 import java.io.*;
 
-/*
- * 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: rpoplin
@@ -120,7 +118,7 @@ class AnalyzeCovariatesCLP extends CommandLineProgram {
         requestedCovariates = new ArrayList<Covariate>();
 
         try {
-            for ( String line : new xReadLines(new File( RECAL_FILE )) ) {
+            for ( String line : new XReadLines(new File( RECAL_FILE )) ) {
                 lineNumber++;
                 if( COMMENT_PATTERN.matcher(line).matches() || OLD_RECALIBRATOR_HEADER.matcher(line).matches())  {
                     ; // Skip over the comment lines, (which start with '#')

java/src/org/broadinstitute/sting/commandline/Argument.java

@@ -1,4 +1,27 @@
-package org.broadinstitute.sting.utils.cmdLine;
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
+package org.broadinstitute.sting.commandline;
 
 import java.lang.annotation.Documented;
 import java.lang.annotation.ElementType;

java/src/org/broadinstitute/sting/commandline/ArgumentCollection.java

@@ -0,0 +1,43 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
+package org.broadinstitute.sting.commandline;
+
+import java.lang.annotation.*;
+
+/**
+ * @author aaron
+ * @version 1.0
+ * @date May 8, 2009
+ * <p/>
+ * @interface ArgumentCollection
+ * <p/>
+ * This object represents an class, that is a collection of arguments.
+ */
+@Documented
+@Inherited
+@Retention(RetentionPolicy.RUNTIME)
+@Target({ElementType.FIELD})
+public @interface ArgumentCollection {
+
+}

java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java

@@ -1,34 +1,31 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.cmdLine;
+package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.Utils;
 
 import java.util.List;
-import java.util.Collections;
 
 /**
  * A specific argument definition.  Maps one-to-one with a field in some class.

java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java

@@ -1,4 +1,27 @@
-package org.broadinstitute.sting.utils.cmdLine;
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
+package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.StingException;
 

java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java

@@ -1,29 +1,35 @@
-package org.broadinstitute.sting.utils.cmdLine;
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
+package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Set;
 import java.util.HashSet;
 import java.util.Collection;
-import java.util.List;
-import java.util.ArrayList;
 import java.util.Iterator;
-import java.util.Collections;
 
-/**
- * Created by IntelliJ IDEA.
- * User: mhanna
- * Date: May 3, 2009
- * Time: 6:02:04 PM
- * <p/>
- * The Broad Institute
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT
- * This software and its documentation are copyright 2009 by the
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- * <p/>
- * This software is supplied without any warranty or guaranteed support whatsoever. Neither
- * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- */
 /**
  * A collection of argument definitions.
  */

java/src/org/broadinstitute/sting/commandline/ArgumentException.java

@@ -0,0 +1,36 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
+package org.broadinstitute.sting.commandline;
+
+import org.broadinstitute.sting.utils.StingException;
+
+/**
+ * Generic class for handling misc parsing exceptions.
+ */
+public class ArgumentException extends StingException {
+    public ArgumentException( String message ) {
+        super( message );
+    }
+}
+

java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java

@@ -1,21 +1,29 @@
-package org.broadinstitute.sting.utils.cmdLine;
+/*
-
+ * Copyright (c) 2010 The Broad Institute
-import java.util.*;
+ * Permission is hereby granted, free of charge, to any person
-/**
+ * obtaining a copy of this software and associated documentation
- * Created by IntelliJ IDEA.
+ * files (the ÓSoftwareÓ), to deal in the Software without
- * User: mhanna
+ * restriction, including without limitation the rights to use,
- * Date: May 3, 2009
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * Time: 6:36:43 PM
+ * copies of the Software, and to permit persons to whom the
- * <p/>
+ * Software is furnished to do so, subject to the following
- * The Broad Institute
+ * conditions:
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT
+ * The above copyright notice and this permission notice shall be
- * This software and its documentation are copyright 2009 by the
+ * included in all copies or substantial portions of the Software.
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
+ *
- * <p/>
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
- * This software is supplied without any warranty or guaranteed support whatsoever. Neither
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
+ * 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.
  */
 
+package org.broadinstitute.sting.commandline;
+
+import java.util.*;
 /**
  * Represents a list of potential matches between the arguments defined
  * by the argument sources and the arguments passed in via the command line.

java/src/org/broadinstitute/sting/commandline/ArgumentSource.java

@@ -1,29 +1,27 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.cmdLine;
+package org.broadinstitute.sting.commandline;
 
 import java.lang.reflect.Field;
 import java.util.Collection;

java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java

@@ -1,34 +1,31 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.cmdLine;
+package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.StingException;
 import org.apache.log4j.Logger;
 
-import java.lang.annotation.Annotation;
 import java.lang.reflect.*;
 import java.util.*;
 

java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java

@@ -1,4 +1,27 @@
-package org.broadinstitute.sting.utils.cmdLine;
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
+package org.broadinstitute.sting.commandline;
 
 import org.apache.log4j.*;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
@@ -12,23 +35,6 @@ import java.util.Collections;
 import java.util.EnumSet;
 import java.util.Enumeration;
 
-/**
- * User: aaron
- * Date: Mar 19, 2009
- * Time: 3:54:56 PM
- * <p/>
- * The Broad Institute
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT
- * This software and its documentation are copyright 2009 by the
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- * <p/>
- * This software is supplied without any warranty or guaranteed support whatsoever. Neither
- * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- * <p/>
- * <p/>
- * This class is our implementation of the command line parser, similar to Pickard's.  We instead
- * support GNU style command line arguments, and use this class to setup the global parser.
- */
 public abstract class CommandLineProgram {
 
     /** The command-line program and the arguments it returned. */

java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java

@@ -1,12 +1,34 @@
-package org.broadinstitute.sting.utils.cmdLine;
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
 
-import org.broadinstitute.sting.utils.JVMUtils;
+package org.broadinstitute.sting.commandline;
+
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
 
 import java.util.Map;
 import java.util.List;
 import java.util.LinkedHashMap;
 import java.util.Collection;
-import java.lang.reflect.Field;
 
 /**
  * Static utility methods for working with command-line arguments.

java/src/org/broadinstitute/sting/commandline/EnumerationArgumentDefault.java

@@ -0,0 +1,63 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
+package org.broadinstitute.sting.commandline;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * @author aaron
+ * <p/>
+ * Annotation EnumerationArgumentDefault
+ * <p/>
+ * Allows the default argument value to be set for an enum; this allows us to treat enums as
+ * booleans on the command line. I.e.
+ *
+ * if we're using an enum Shape,
+ *
+ * enum shape {
+ *  SQUARE,
+ *  CIRCLE,
+ *  @EnumerationArgumentDefault
+ *  TRIANGLE
+ * }
+ *
+ * and a command line option -shape, the EnumerationArgumentDefault would allow you to say:
+ * -shape
+ * or
+ * -shape TRIANGLE
+ *
+ * would get -shape set to TRIANGLE, where:
+ *
+ * -shape SQUARE
+ *
+ * would set shape to SQUARE
+ *
+ */
+@Retention(RetentionPolicy.RUNTIME)
+@Target(ElementType.FIELD)
+public @interface EnumerationArgumentDefault {
+}

java/src/org/broadinstitute/sting/commandline/ParsingEngine.java

@@ -1,8 +1,31 @@
-package org.broadinstitute.sting.utils.cmdLine;
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
+package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.JVMUtils;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
 import org.broadinstitute.sting.utils.help.HelpFormatter;
@@ -11,20 +34,6 @@ import org.apache.log4j.Logger;
 import java.lang.reflect.*;
 import java.util.*;
 
-/**
- * Created by IntelliJ IDEA.
- * User: mhanna
- * Date: May 3, 2009
- * Time: 4:35:25 PM
- * BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
- * Software and documentation are copyright 2005 by the Broad Institute.
- * All rights are reserved.
- *
- * Users acknowledge that this software is supplied without any warranty or support.
- * The Broad Institute is not responsible for its use, misuse, or
- * functionality.
- */
-
 /**
  * A parser for Sting command-line arguments.
  */

java/src/org/broadinstitute/sting/commandline/ParsingMethod.java

@@ -1,4 +1,27 @@
-package org.broadinstitute.sting.utils.cmdLine;
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
+package org.broadinstitute.sting.commandline;
 
 import java.util.regex.Pattern;
 import java.util.regex.Matcher;

java/src/org/broadinstitute/sting/commandline/package-info.java

@@ -0,0 +1,27 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
+/**
+ * Parses a wide variety of command-line arguments in single-pass and multipass strategies.
+ */
+package org.broadinstitute.sting.commandline;

java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -1,10 +1,33 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk;
 
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
-import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentTypeDescriptor;
+import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
@@ -17,31 +40,6 @@ import java.util.*;
 
 import net.sf.picard.filter.SamRecordFilter;
 
-/*
- * 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.
- */
-
 /**
  * @author aaron
  */
@@ -164,7 +162,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
         for( File inputFile: inputFiles ) {
             if (inputFile.getName().endsWith(".list") ) {
                 try {
-                    for( String fileName : new xReadLines(inputFile) )
+                    for( String fileName : new XReadLines(inputFile) )
                         unpackedReads.add( new File(fileName) );
                 }
                 catch( FileNotFoundException ex ) {

java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -1,32 +1,38 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk;
 
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
-import org.broadinstitute.sting.utils.GATKErrorReport;
+import org.broadinstitute.sting.gatk.GATKErrorReport;
-import org.broadinstitute.sting.utils.TextFormattingUtils;
+import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
-import org.broadinstitute.sting.utils.cmdLine.*;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 
 import java.io.PrintStream;
 import java.util.*;
 
-/**
- *
- * User: aaron
- * Date: May 8, 2009
- * Time: 10:50:58 AM
- *
- * The Broad Institute
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
- * This software and its documentation are copyright 2009 by the
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- *
- * This software is supplied without any warranty or guaranteed support whatsoever. Neither
- * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- *
- */
-
-
 /**
  * @author aaron
  * @version 1.0

java/src/org/broadinstitute/sting/gatk/GATKErrorReport.java

@@ -1,7 +1,31 @@
-package org.broadinstitute.sting.utils;
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
+package org.broadinstitute.sting.gatk;
 
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
+import org.broadinstitute.sting.utils.StingException;
 import org.simpleframework.xml.Element;
 import org.simpleframework. xml.ElementList;
 import org.simpleframework.xml.Serializer;

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -1,26 +1,24 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk;
@@ -50,8 +48,8 @@ import org.broadinstitute.sting.gatk.refdata.utils.RMDIntervalGenerator;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
+import org.broadinstitute.sting.commandline.ArgumentException;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentSource;
+import org.broadinstitute.sting.commandline.ArgumentSource;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 
 import java.io.File;

java/src/org/broadinstitute/sting/gatk/WalkerManager.java

@@ -1,26 +1,24 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk;
@@ -30,9 +28,9 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.PluginManager;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.TextFormattingUtils;
+import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.help.DescriptionTaglet;
 import org.broadinstitute.sting.utils.help.DisplayNameTaglet;
 import org.broadinstitute.sting.utils.help.SummaryTaglet;

java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -1,9 +1,32 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.arguments;
 
 import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.simpleframework.xml.*;
 import org.simpleframework.xml.core.Persister;
 import org.simpleframework.xml.stream.Format;
@@ -17,23 +40,6 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-/**
- *
- * User: aaron
- * Date: May 7, 2009
- * Time: 11:46:21 AM
- *
- * The Broad Institute
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
- * This software and its documentation are copyright 2009 by the
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- *
- * This software is supplied without any warranty or guaranteed support whatsoever. Neither
- * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- *
- */
-
-
 /**
  * @author aaron
  * @version 1.0

java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java

@@ -1,27 +1,34 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.arguments;
 
-import org.broadinstitute.sting.utils.cmdLine.EnumerationArgumentDefault;
+import org.broadinstitute.sting.commandline.EnumerationArgumentDefault;
 
 import java.util.ArrayList;
 import java.util.List;
 
 
-/**
- * The Broad Institute
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT
- * This software and its documentation are copyright 2009 by the
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- * <p/>
- * This software is supplied without any warranty or guaranteed support whatsoever. Neither
- * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- * 
- * @author aaron 
- * 
- * Class ValidationExclusion
- *
- * a class for containing the exclusions from validation that the user
- * wants.
- */
 public class ValidationExclusion {
 
     // our validation options

java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java

@@ -1,15 +1,34 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.datasources;
 
-import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
-import java.io.IOException;
-import java.io.FileInputStream;
 import java.io.PrintStream;
-import java.nio.channels.FileChannel;
-import java.util.List;
 
 import net.sf.samtools.*;
 

java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java

@@ -1,7 +1,30 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.util.*;
 

java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 import org.broadinstitute.sting.gatk.refdata.*;
@@ -6,26 +29,13 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.MergingIterator;
+import org.broadinstitute.sting.utils.collections.MergingIterator;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.gatk.iterators.LocusOverflowTracker;
 
 import java.util.*;
 
-/**
- * User: hanna
- * Date: May 21, 2009
- * Time: 2:49:17 PM
- * BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
- * Software and documentation are copyright 2005 by the Broad Institute.
- * All rights are reserved.
- *
- * Users acknowledge that this software is supplied without any warranty or support.
- * The Broad Institute is not responsible for its use, misuse, or
- * functionality.
- */
-
 /**
  * A view into the reference-ordered data in the provider.
  */

java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java

@@ -1,6 +1,30 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.BlockDrivenSAMDataSource;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 

java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java

@@ -1,31 +1,40 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Iterator;
-/**
- * User: hanna
- * Date: May 18, 2009
- * Time: 2:27:17 PM
- * BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
- * Software and documentation are copyright 2005 by the Broad Institute.
- * All rights are reserved.
- *
- * Users acknowledge that this software is supplied without any warranty or support.
- * The Broad Institute is not responsible for its use, misuse, or
- * functionality.
- */
-
 /**
  * Manages the
  */

java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java

@@ -1,7 +1,30 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.filters;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.PluginManager;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
 
 import net.sf.picard.filter.SamRecordFilter;
 

java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java

@@ -1,32 +1,31 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.filters;
 
 import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 
 /**
  * Filter out reads with low mapping qualities.

java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java

@@ -1,8 +1,31 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.filters;
 
 import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 
 /**
  * Filters out reads whose length is >= some value.

java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java

@@ -1,25 +1,24 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.filters;
@@ -27,7 +26,7 @@ package org.broadinstitute.sting.gatk.filters;
 import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 /**
  * Filter out 454 reads.
@@ -38,6 +37,6 @@ import org.broadinstitute.sting.utils.Utils;
 
 public class Platform454Filter implements SamRecordFilter {
     public boolean filterOut(SAMRecord rec) {
-        return (Utils.is454Read(rec));
+        return (ReadUtils.is454Read(rec));
     }
 }

java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java

@@ -1,25 +1,24 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.filters;
@@ -27,8 +26,8 @@ package org.broadinstitute.sting.gatk.filters;
 import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 
 /**
  * Filter out PL matching reads.
@@ -42,7 +41,7 @@ public class PlatformFilter implements SamRecordFilter {
 
     public boolean filterOut(SAMRecord rec) {
         for ( String name : PLFilterNames )
-            if ( Utils.isPlatformRead(rec, name.toUpperCase() ))
+            if ( ReadUtils.isPlatformRead(rec, name.toUpperCase() ))
                 return true;
         return false;
     }

java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilterHelper.java

@@ -1,6 +1,29 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.filters;
 
-import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
@@ -46,7 +69,7 @@ public class PlatformUnitFilterHelper {
 
          if ( f.exists() ) {
              try {
-                 xReadLines reader = new xReadLines(f);
+                 XReadLines reader = new XReadLines(f);
                  for ( String line : reader ) {
                      if ( EMPTYLINE_PATTERN.matcher(line).matches() ) continue; // skip empty lines
                      PlatformUnitFilter.addBlackListedLane(line); // PlatformUnitFilter will trim the line as needed

java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.filters;
 
 import java.util.*;
@@ -9,7 +32,7 @@ import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.text.XReadLines;
 
 /**
  * Removes records matching the read group tag and match string.
@@ -57,7 +80,7 @@ public class ReadGroupBlackListFilter implements SamRecordFilter {
             File file = new File(filter);
             try {
                 int lineNum = 0;
-                xReadLines lines = new xReadLines(file);
+                XReadLines lines = new XReadLines(file);
                 for (String line : lines) {
                     lineNum++;
 

java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java

@@ -1,9 +1,32 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.filters;
 
 import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 
 public class SampleFilter implements SamRecordFilter {
     @Argument(fullName = "sample_to_keep", shortName = "goodSM", doc="The name of the sample to keep, filtering out all others", required=true)

java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java

@@ -1,35 +1,33 @@
-package org.broadinstitute.sting.gatk.filters;
-
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMReadGroupRecord;
-import net.sf.picard.filter.SamRecordFilter;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
-
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
+package org.broadinstitute.sting.gatk.filters;
+
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.picard.filter.SamRecordFilter;
+import org.broadinstitute.sting.commandline.Argument;
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin

java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java

@@ -1,8 +1,31 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.io;
 
-import org.broadinstitute.sting.utils.JVMUtils;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentSource;
+import org.broadinstitute.sting.commandline.ArgumentSource;
 import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@@ -17,19 +40,6 @@ import java.lang.reflect.Field;
 import java.util.Map;
 import java.util.HashMap;
 
-/**
- * User: hanna
- * Date: Apr 30, 2009
- * Time: 9:40:09 AM
- * BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
- * Software and documentation are copyright 2005 by the Broad Institute.
- * All rights are reserved.
- *
- * Users acknowledge that this software is supplied without any warranty or support.
- * The Broad Institute is not responsible for its use, misuse, or
- * functionality.
- */
-
 /**
  * Manages the output and err streams that are created specifically for walker
  * output.

java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java

@@ -1,10 +1,33 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.io.stubs;
 
-import org.broadinstitute.sting.utils.cmdLine.ArgumentTypeDescriptor;
+import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentSource;
+import org.broadinstitute.sting.commandline.ArgumentSource;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentMatches;
+import org.broadinstitute.sting.commandline.ArgumentMatches;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentDefinition;
+import org.broadinstitute.sting.commandline.ArgumentDefinition;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
 import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
@@ -14,8 +37,6 @@ import java.io.File;
 import java.util.List;
 import java.util.Arrays;
 
-import net.sf.samtools.SAMFileReader;
-
 /**
  * Injects new command-line arguments into the system providing support for the genotype writer.
  *

java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java

@@ -1,31 +1,29 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
-import org.broadinstitute.sting.utils.cmdLine.*;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 

java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java

@@ -1,33 +1,31 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
-import org.broadinstitute.sting.utils.cmdLine.ArgumentTypeDescriptor;
+import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentSource;
+import org.broadinstitute.sting.commandline.ArgumentSource;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentMatches;
+import org.broadinstitute.sting.commandline.ArgumentMatches;
 import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;

java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java

@@ -1,31 +1,29 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
-import org.broadinstitute.sting.utils.cmdLine.*;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;

java/src/org/broadinstitute/sting/gatk/refdata/AnnotatorROD.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.refdata;
 
 import java.io.File;
@@ -8,7 +31,7 @@ import java.util.Arrays;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.text.XReadLines;
 
 /**
  * <pre>
@@ -71,7 +94,7 @@ public class AnnotatorROD extends TabularROD {
      */
     public static ArrayList<String> readHeader(final File source) throws FileNotFoundException {
         ArrayList<String> header = null;
-        xReadLines reader = new xReadLines(source);
+        XReadLines reader = new XReadLines(source);
 
         //find the 1st line that's non-empty and not a comment
         for ( String line : reader ) {

java/src/org/broadinstitute/sting/gatk/refdata/BeagleROD.java

@@ -1,8 +1,31 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.text.XReadLines;
 
 import java.util.*;
 import java.util.regex.Matcher;
@@ -39,7 +62,7 @@ public class BeagleROD extends BasicReferenceOrderedDatum {
     }
 
     public Object initialize(final File source) throws FileNotFoundException {
-        String firstLine = new xReadLines(source).next();
+        String firstLine = new XReadLines(source).next();
         String[] parts = firstLine.split(" ");
         if ( parts[0].equals("I") ) {
             // I id NA12891 NA12891 NA12892 NA12892

java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java

@@ -1,8 +1,30 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.refdata;
 
-import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.MalformedGenomeLocException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 
@@ -10,7 +32,6 @@ import java.util.Iterator;
 import java.util.regex.Pattern;
 import java.io.FileNotFoundException;
 import java.io.File;
-import java.io.IOException;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Constructor;
 
@@ -89,7 +110,7 @@ public class RODRecordIterator<ROD extends ReferenceOrderedDatum> implements Ite
 
     public RODRecordIterator(File file, String name, Class<ROD> type) {
         try {
-            reader = new PushbackIterator<String>(new xReadLines(file));
+            reader = new PushbackIterator<String>(new XReadLines(file));
         } catch (FileNotFoundException e) {
             Utils.scareUser("Couldn't open file: " + file);
         }

java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java

@@ -1,9 +1,29 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.refdata;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
 import org.broadinstitute.sting.utils.genotype.glf.GLFReader;
 import org.broadinstitute.sting.utils.genotype.glf.GLFRecord;
@@ -208,7 +228,7 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
      * @return a GENOTYPE object representing the nth best genotype
      */
     public LikelihoodObject.GENOTYPE getBestGenotype(int nthBest) {
-        Integer[] sorted = Utils.SortPermutation(((GLFSingleCall) mRecord).getLikelihoods());
+        Integer[] sorted = MathUtils.sortPermutation(((GLFSingleCall) mRecord).getLikelihoods());
         return LikelihoodObject.GENOTYPE.values()[sorted[nthBest - 1]];
     }
 
@@ -221,7 +241,7 @@ public class RodGLF implements VariationRod, Iterator<RodGLF> {
      * @return a GENOTYPE object representing the nth best genotype
      */
     public double getBestGenotypeValue(int nthBest) {
-        Integer[] sorted = Utils.SortPermutation(((GLFSingleCall) mRecord).getLikelihoods());
+        Integer[] sorted = MathUtils.sortPermutation(((GLFSingleCall) mRecord).getLikelihoods());
         return (((GLFSingleCall) mRecord).getLikelihoods())[sorted[nthBest - 1]];
     }
 

java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.refdata;
 
 
@@ -7,6 +30,7 @@ import java.util.regex.Pattern;
 import java.util.regex.Matcher;
 
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.text.XReadLines;
 
 import net.sf.picard.reference.ReferenceSequenceFileWalker;
 import net.sf.samtools.util.StringUtil;
@@ -567,7 +591,7 @@ public class SAMPileupRecord {
 	protected static class pileupFileIterator implements Iterator<SAMPileupRecord> {
 //		private String fieldDelimiter = new String("\t");
 		private String rodName = null;
-		private xReadLines parser = null;
+		private XReadLines parser = null;
 		private String lastProcessedLine = null;
 		
 //		private long z = 0;
@@ -575,7 +599,7 @@ public class SAMPileupRecord {
 		
 		pileupFileIterator(String name, java.io.File f) {
 			try {
-				parser = new xReadLines(f);
+				parser = new XReadLines(f);
 			} catch ( FileNotFoundException e ) {
 				Utils.scareUser("Couldn't open file: " + f);
 			}

java/src/org/broadinstitute/sting/gatk/refdata/TabularROD.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.refdata;
 
 import java.util.*;
@@ -9,7 +32,7 @@ import java.io.IOException;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.apache.log4j.Logger;
 
@@ -176,7 +199,7 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
     public static ArrayList<String> readHeader(final File source) throws FileNotFoundException {
         ArrayList<String> header = null;
         int linesLookedAt = 0;
-        xReadLines reader = new xReadLines(source);
+        XReadLines reader = new XReadLines(source);
 
         for ( String line : reader ) {
             Matcher m = HEADER_PATTERN.matcher(line);
@@ -198,7 +221,7 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
             logger.debug("USING INDEXES FOR ROD HEADER");
             // reset if necessary
             if ( !reader.hasNext() )
-                reader = new xReadLines(source);
+                reader = new XReadLines(source);
             header = new ArrayList<String>();
             int tokens = reader.next().split(DELIMITER_REGEX).length;
             for ( int i = 0; i < tokens; i++)

java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManager.java

@@ -1,31 +1,31 @@
 /*
- * Copyright (c) 2010.  The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ *
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.refdata.tracks;
 
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
-import org.broadinstitute.sting.utils.PluginManager;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;

java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java

@@ -1,24 +1,24 @@
 /*
- * Copyright (c) 2010.  The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ *
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.refdata.tracks.builders;
@@ -31,7 +31,7 @@ import org.broad.tribble.index.LinearIndexCreator;
 import org.broadinstitute.sting.gatk.refdata.tracks.FeatureReaderTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
-import org.broadinstitute.sting.utils.PluginManager;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;

java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.*;
@@ -5,8 +28,9 @@ import net.sf.picard.reference.ReferenceSequenceFileFactory;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequence;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 
 import java.util.*;

java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers;
 
 /*  Motivation: BAM files created by samtools which are sorted often don't
@@ -14,7 +37,7 @@ package org.broadinstitute.sting.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;

java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java

@@ -1,25 +1,24 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.walkers;
@@ -30,9 +29,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 

java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java

@@ -1,35 +1,33 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
-
-/*
- * 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.
- */
 
 /**
  * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear

java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java

@@ -1,34 +1,32 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.*;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.apache.log4j.Logger;
 
 import java.util.*;
@@ -73,7 +71,7 @@ public class SplitSamFileWalker extends ReadWalker<SAMRecord, Map<String, SAMFil
         for ( SAMReadGroupRecord readGroup : this.getToolkit().getSAMFileHeader().getReadGroups()) {
             final String sample = readGroup.getSample();
             if ( ! headers.containsKey(sample) ) {
-                SAMFileHeader header = Utils.copySAMFileHeader(this.getToolkit().getSAMFileHeader());
+                SAMFileHeader header = ReadUtils.copySAMFileHeader(this.getToolkit().getSAMFileHeader());
                 logger.debug(String.format("Creating BAM header for sample %s", sample));
                 ArrayList<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>();
                 header.setReadGroups(readGroups);
@@ -91,7 +89,7 @@ public class SplitSamFileWalker extends ReadWalker<SAMRecord, Map<String, SAMFil
             final String sample = elt.getKey();
             final String filename = outputRoot + sample + ".bam";
             logger.info(String.format("Creating BAM output file %s for sample %s", filename, sample));
-            SAMFileWriter output = Utils.createSAMFileWriterWithCompression(elt.getValue(), true, filename, BAMcompression);
+            SAMFileWriter output = ReadUtils.createSAMFileWriterWithCompression(elt.getValue(), true, filename, BAMcompression);
             outputs.put(sample, output);
         }
 

java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java

@@ -1,10 +1,33 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 

java/src/org/broadinstitute/sting/gatk/walkers/Walker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers;
 
 import java.io.PrintStream;
@@ -5,7 +28,7 @@ import java.util.List;
 
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.apache.log4j.Logger;
 
 /**

java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -40,8 +63,8 @@ public class AlleleBalance implements InfoFieldAnnotation, StandardAnnotation {
             char refChr = vc.getReference().toString().charAt(0);
             char altChr = vc.getAlternateAllele(0).toString().charAt(0);
 
-            int refCount = Utils.countOccurrences(refChr, bases);
+            int refCount = MathUtils.countOccurrences(refChr, bases);
-            int altCount = Utils.countOccurrences(altChr, bases);
+            int altCount = MathUtils.countOccurrences(altChr, bases);
 
             // sanity check
             if ( refCount + altCount == 0 )

java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -7,6 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ExtendedPileupElement;

java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java

@@ -1,6 +1,29 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -12,10 +35,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.PackageUtils;
+import org.broadinstitute.sting.utils.classloader.PackageUtils;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@@ -13,7 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.playground.gatk.walkers.annotator.GenomicAnnotation;
-import org.broadinstitute.sting.utils.PackageUtils;
+import org.broadinstitute.sting.utils.classloader.PackageUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;

java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.concordance;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -6,11 +29,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.RodVCF;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.PackageUtils;
+import org.broadinstitute.sting.utils.classloader.PackageUtils;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
 import java.io.File;

java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java

@@ -1,10 +1,33 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
 import net.sf.samtools.SAMRecord;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 
 /**
  * Computes the coverage per every <granularity> bases on the reference, or on the subset of the reference

java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
 import net.sf.samtools.SAMReadGroupRecord;
@@ -17,9 +40,9 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 
 import java.io.File;
 import java.io.IOException;

java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java

@@ -1,10 +1,33 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import net.sf.samtools.SAMRecord;
 
 import java.io.*;

java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -6,7 +29,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
 
 
 /**

java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -7,8 +30,8 @@ import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 
 /**
  * Renders a new reference in FASTA format consisting of only those loci provided in the input data set.  Has optional

java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.apache.commons.jexl.Expression;
@@ -13,7 +36,7 @@ import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
 import java.util.*;

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java

@@ -1,6 +1,30 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.genotype.CalledGenotype;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.utils.Utils;
@@ -260,7 +283,7 @@ public class DiploidGenotypePriors {
         double[] priors = new double[DiploidGenotype.values().length];
 
         for ( DiploidGenotype g : DiploidGenotype.values() ) {
-            int nRefBases = Utils.countOccurrences(ref, g.toString());
+            int nRefBases = MathUtils.countOccurrences(ref, g.toString());
             double log10POfG = 0.0;
 
             switch ( nRefBases ) {

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java

@@ -1,31 +1,29 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 
 
 public class UnifiedArgumentCollection {

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -1,26 +1,24 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
@@ -31,7 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.cmdLine.*;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.utils.genotype.*;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

@@ -1,26 +1,24 @@
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
@@ -36,7 +34,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
-import org.broadinstitute.sting.utils.AlignmentUtils;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.StingException;

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.samtools.Cigar;
@@ -15,7 +38,10 @@ import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.collections.CircularArray;
+import org.broadinstitute.sting.utils.collections.PrimitivePair;
+import org.broadinstitute.sting.commandline.Argument;
 
 import java.io.IOException;
 import java.util.*;

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java

@@ -1,8 +1,30 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.samtools.*;
 import net.sf.samtools.util.StringUtil;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@@ -12,7 +34,10 @@ import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.commandline.Argument;
 
 import java.io.File;
 import java.io.FileWriter;
@@ -251,7 +276,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         if ( readLoc.getStop() == 0 )
             readLoc = GenomeLocParser.createGenomeLoc(readLoc.getContig(), readLoc.getStart(), readLoc.getStart());
 
-        if ( readLoc.isBefore(currentInterval) || Utils.is454Read(read) ) {
+        if ( readLoc.isBefore(currentInterval) || ReadUtils.is454Read(read) ) {
             // TODO -- it would be nice if we could use indels from 454 reads as alternate consenses
             emit(read);
             return 0;

java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.samtools.SAMRecord;
@@ -12,7 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;

java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java

@@ -1,14 +1,36 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
-
+import org.broadinstitute.sting.utils.collections.Pair;
-import java.util.ArrayList;
+import org.broadinstitute.sting.commandline.Argument;
-import java.util.List;
 
 /**
  * Prints out counts of the number of reference ordered data objects are

java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -6,7 +29,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.ArrayList;
 import java.util.List;

java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -8,7 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.rodSAMPileup;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.Arrays;

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -8,8 +31,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.classloader.PackageUtils;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
+import org.broadinstitute.sting.utils.collections.NestedHashMap;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -21,31 +47,6 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 
-/*
- * 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.
- */
-
 /**
  * This walker is designed to work as the first pass in a two-pass processing step.
  * It does a by-locus traversal operating only at sites that are not in dbSNP.

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java

@@ -1,38 +1,38 @@
-package org.broadinstitute.sting.gatk.walkers.recalibration;
-
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.*;
-
-import java.util.*;
-
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMReadGroupRecord;
-
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
+package org.broadinstitute.sting.gatk.walkers.recalibration;
+
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.collections.NestedHashMap;
+
+import java.util.*;
+
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMReadGroupRecord;
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java

@@ -1,32 +1,30 @@
-package org.broadinstitute.sting.gatk.walkers.recalibration;
-
-import org.broadinstitute.sting.utils.cmdLine.Argument;
-
 /*
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2010 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
+ * files (the ÓSoftwareÓ), 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,
+ * THE SOFTWARE IS PROVIDED ÓAS ISÓ, 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
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * OTHER DEALINGS IN THE SOFTWARE.
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
+package org.broadinstitute.sting.gatk.walkers.recalibration;
+
+import org.broadinstitute.sting.commandline.Argument;
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import java.io.File;
@@ -24,46 +47,21 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
-import org.broadinstitute.sting.utils.JVMUtils;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.NestedHashMap;
+import org.broadinstitute.sting.utils.classloader.PackageUtils;
-import org.broadinstitute.sting.utils.PackageUtils;
+import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.TextFormattingUtils;
+import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentDefinition;
+import org.broadinstitute.sting.commandline.ArgumentDefinition;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentSource;
+import org.broadinstitute.sting.commandline.ArgumentSource;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentTypeDescriptor;
+import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
-/*
- * 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.
- */
-
 /**
  * This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal.
 
@@ -165,7 +163,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         logger.info( "Reading in the data from input csv file..." );
 
         try {
-            for ( String line : new xReadLines(new File( RAC.RECAL_FILE )) ) {
+            for ( String line : new XReadLines(new File( RAC.RECAL_FILE )) ) {
                 lineNumber++;
                 if( COMMENT_PATTERN.matcher(line).matches() || OLD_RECALIBRATOR_HEADER.matcher(line).matches() )  {
                     ; // Skip over the comment lines, (which start with '#')

java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.sequenom;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -11,7 +34,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.Arrays;
 import java.util.Iterator;

java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.sequenom;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -11,7 +34,7 @@ import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
 import java.util.*;

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.varianteval;
 
 import org.apache.log4j.Logger;
@@ -14,12 +37,12 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.playground.utils.report.ReportMarshaller;
 import org.broadinstitute.sting.playground.utils.report.VE2ReportFactory;
 import org.broadinstitute.sting.playground.utils.report.utils.Node;
-import org.broadinstitute.sting.utils.PackageUtils;
+import org.broadinstitute.sting.utils.classloader.PackageUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.text.XReadLines;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -277,7 +300,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
 
         int n = 1;
         try {
-            for ( String line : new xReadLines(rsIDFile) ) {
+            for ( String line : new XReadLines(rsIDFile) ) {
                 String parts[] = line.split(" ");
                 if ( parts.length != 2 )
                     throw new StingException("Invalid rsID / build pair at " + n + " line = " + line );

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.gatk.walkers.varianteval;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -8,36 +31,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.utils.TableType;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.util.ArrayList;
 import java.util.HashMap;
 
-/*
- * Copyright (c) 2010 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.
- */
-
 /**
  * @author rpoplin
  * @since Apr 6, 2010

java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/ClassicGenotypeLikelihoods.java

@@ -1,6 +1,29 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.oneoffprojects.multisamplecaller;
 
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.MathUtils;
 
 import static java.lang.Math.log10;
 import static java.lang.Math.pow;
@@ -309,15 +332,15 @@ public class ClassicGenotypeLikelihoods implements Cloneable {
     }
 
     public void sort() {
-        Integer[] permutation = Utils.SortPermutation(likelihoods);
+        Integer[] permutation = MathUtils.sortPermutation(likelihoods);
 
         Integer[] reverse_permutation = new Integer[permutation.length];
         for (int i = 0; i < reverse_permutation.length; i++) {
             reverse_permutation[i] = permutation[(permutation.length - 1) - i];
         }
 
-        sorted_genotypes = Utils.PermuteArray(genotypes, reverse_permutation);
+        sorted_genotypes = MathUtils.permuteArray(genotypes, reverse_permutation);
-        sorted_likelihoods = Utils.PermuteArray(likelihoods, reverse_permutation);
+        sorted_likelihoods = MathUtils.permuteArray(likelihoods, reverse_permutation);
     }
 
     public String toString(char ref) {

java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java

@@ -1,4 +1,27 @@
 
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.oneoffprojects.multisamplecaller;
 
 import net.sf.samtools.SAMFileHeader;
@@ -10,11 +33,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.io.File;
 import java.io.FileOutputStream;
@@ -818,7 +838,7 @@ public class MultiSampleCaller extends LocusWalker<MultiSampleCaller.MultiSample
 
 	char PickAlt(char ref, double[] allele_likelihoods)
 	{
-		Integer[] perm = Utils.SortPermutation(allele_likelihoods);
+		Integer[] perm = MathUtils.sortPermutation(allele_likelihoods);
 		if (perm[3] != BaseUtils.simpleBaseToBaseIndex(ref)) { return BaseUtils.baseIndexToSimpleBase(perm[3]); }
 		else { return BaseUtils.baseIndexToSimpleBase(perm[2]); }
 	}
@@ -1005,7 +1025,7 @@ public class MultiSampleCaller extends LocusWalker<MultiSampleCaller.MultiSample
 			{
 	            List<Integer> perm = new ArrayList<Integer>(); 
 	            for (int i = 0; i < reads[j].size(); i++) { perm.add(i); }
-	            perm = Utils.RandomSubset(perm, downsample);
+	            perm = MathUtils.randomSubset(perm, downsample);
 	           
 	            ArrayList<SAMRecord> downsampled_reads = new ArrayList<SAMRecord>();
 	            ArrayList<Integer> downsampled_offsets = new ArrayList<Integer>();

java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -5,10 +28,9 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.genotype.*;
 
 import java.util.*;
 import java.io.PrintStream;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DSBWalkerV3.java

@@ -1,9 +1,33 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import net.sf.samtools.SAMRecord;
 
 import java.util.*;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IOCrusherWalker.java

@@ -1,9 +1,32 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMFileHeader;
@@ -50,7 +73,7 @@ public class IOCrusherWalker extends ReadWalker<SAMRecord, ArrayList<SAMFileWrit
         ArrayList<SAMFileWriter> outputs = new ArrayList<SAMFileWriter>(nWaysOut);
         for ( int i = 0; i < nWaysOut; i++ ) {
             SAMFileHeader header = this.getToolkit().getSAMFileHeader();
-            outputs.add(Utils.createSAMFileWriterWithCompression(header, true, outputBase + "." + i + ".bam", BAMcompression));
+            outputs.add(ReadUtils.createSAMFileWriterWithCompression(header, true, outputBase + "." + i + ".bam", BAMcompression));
         }
         return outputs;
     }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelErrorRateWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
@@ -8,13 +31,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.CircularArray;
+import org.broadinstitute.sting.utils.collections.CircularArray;
 import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
-import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 import java.util.LinkedList;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/PairedQualityScoreCountsWalker.java

@@ -1,11 +1,34 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import net.sf.samtools.SAMRecord;
 
 /**

java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java

@@ -1,3 +1,26 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the ÓSoftwareÓ), 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 ÓAS ISÓ, 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.
+ */
+
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import java.io.IOException;
@@ -5,14 +28,12 @@ import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-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 net.sf.samtools.SAMRecord;