The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had

unicode quote characters embedded in it. These characters were invisible inside IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason have a different default charset. Fixed. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:26:32 +00:00 · 2010-04-20 15:26:32 +00:00 · c1e53d407d
parent b5f6f54968
commit c1e53d407d
197 changed files with 806 additions and 391 deletions
--- a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
@ -7,7 +7,7 @@
 * 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 
+ * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
--- a/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java
+++ b/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
+++ b/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/Argument.java
+++ b/java/src/org/broadinstitute/sting/commandline/Argument.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentCollection.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentException.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentException.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
+++ b/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
+++ b/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/EnumerationArgumentDefault.java
+++ b/java/src/org/broadinstitute/sting/commandline/EnumerationArgumentDefault.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
+++ b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
+++ b/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/commandline/package-info.java
+++ b/java/src/org/broadinstitute/sting/commandline/package-info.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
+++ b/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/GATKErrorReport.java
+++ b/java/src/org/broadinstitute/sting/gatk/GATKErrorReport.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java
+++ b/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilterHelper.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilterHelper.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/refdata/AnnotatorROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/AnnotatorROD.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/refdata/BeagleROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/BeagleROD.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/refdata/TabularROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/TabularROD.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManager.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/ClassicGenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/ClassicGenotypeLikelihoods.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java
@ -1,18 +1,20 @@

 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DSBWalkerV3.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DSBWalkerV3.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IOCrusherWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IOCrusherWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelErrorRateWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelErrorRateWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/PairedQualityScoreCountsWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/PairedQualityScoreCountsWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java
@ -1,17 +1,19 @@
 /*
 * 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
+ * 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 ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
+ * 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
--- a/Show More
+++ b/Show More