diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java index 2224a114d..346ff0227 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java index 9393accb7..4ba4184d0 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java b/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java index bc8e71d4a..3d0a8657b 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java b/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java index c89406fc7..d7f0e560f 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java index 072e157cd..cfc65df79 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/Argument.java b/java/src/org/broadinstitute/sting/commandline/Argument.java index c8775d933..e4f31e145 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentCollection.java b/java/src/org/broadinstitute/sting/commandline/ArgumentCollection.java index 8ed125155..d114748ff 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java index e6ee45aee..72cf400b6 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java index e8c155c2a..8b4e09456 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java index e4a29e347..6c703fd4f 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentException.java b/java/src/org/broadinstitute/sting/commandline/ArgumentException.java index 3a335fb9c..04993df7d 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java b/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java index 7776d2fc1..3ee544c5f 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java b/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java index d3ebf59c7..451a805e7 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java index 6deb8c2ab..b4005c80a 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java b/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java index 17d195a5e..8f63146e0 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java b/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java index 3755863af..17d1080f2 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/EnumerationArgumentDefault.java b/java/src/org/broadinstitute/sting/commandline/EnumerationArgumentDefault.java index ab9366daf..ebc7a3745 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java index efd87fd91..c8b7cf419 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java b/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java index 1ca0447d0..9c7e2ddd6 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/commandline/package-info.java b/java/src/org/broadinstitute/sting/commandline/package-info.java index befd8748f..40a8e621d 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java index 8d9ba831b..dfe2528b8 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index 148f2b93d..98db32ecb 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/GATKErrorReport.java b/java/src/org/broadinstitute/sting/gatk/GATKErrorReport.java index 8a3f59db1..4ea40a6ee 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 287fc0fd4..ef51a65be 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java index 1be637c5c..ab2253933 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 3e293e6f5..beb5dc49d 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java b/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java index 22f2e9abd..9c4387e58 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java b/java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java index 8c0e61a12..c8a046986 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java index 0d7fd2577..36b02466d 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java index 21f1d4f6d..79ef27e09 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java index 57dd6598c..c36b0c671 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java index a440f5fe5..be3ee7524 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java b/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java index 9fd35f6de..44f9bdf76 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java index 5f499eada..d6ebcf487 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java index f4d9f1f4c..48f12de40 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java b/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java index 1c0a264fd..f8a1c502a 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java index c6ba6582d..710699ae2 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilterHelper.java b/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilterHelper.java index a610d94f4..27ebbb623 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java index 76fac437d..59e6147a6 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java index cdca1692f..6fbfa7858 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java index 2559386f2..639ef1486 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java index 64c0723d4..97a66be22 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java index 4a0e976ee..73628b2a7 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java index 4fe703420..228fb09bc 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java index d28aec2af..a1c1ddea4 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java index 209ed66e0..682c14914 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/AnnotatorROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/AnnotatorROD.java index 0d8313b34..74bd7e5a2 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/BeagleROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/BeagleROD.java index 8ff90401f..e1bd47f00 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java index c4f10ba6f..fa53f9513 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGLF.java index f6dde9def..2d039b8ca 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java b/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java index 52ac72928..1b90b55bf 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/TabularROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/TabularROD.java index cdadd3967..43a237c53 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManager.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManager.java index eb4f83003..ba8f64253 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java index 84877d283..92244e57c 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java index fa986fb66..80e5d8f90 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java b/java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java index 3fdacf91c..e019b6cb2 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index f0937454b..d5a384949 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java index 84dbc3ccb..d68e63ee1 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java index 0c15b34c8..86c591be2 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java index 1a53c0ccf..2f686809f 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java index 341077901..e2650ecae 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java index af690a3c8..85ae80959 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index 959e3e854..5fcd979cd 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java index 4eadd5297..5e0017e73 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 679f7ec32..a15dc0001 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 563d102e5..ede54514c 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java index 968737a5b..6546dd26c 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java index 38d1339c8..ef8e55bb2 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index 20d670404..ad58553c6 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java index d040afd5c..1363c0a0a 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java index 001226302..dd2eca482 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java index 472b02a2f..9243a99c2 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index 2cd80e133..0abf8ac96 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java index 1d9ef03ad..94b2f71ea 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java index 644a6c6ac..045e5a3e7 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 4f1d7c004..bedf35ed1 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 45770f5fa..2d9e1df41 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index c76917cd5..f602a8d93 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java index 45188ca71..d628ba400 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index c15348275..4b7531401 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index eea429962..b3e7b1873 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java index c29858fbf..27a85d78c 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java index 67aa0463b..c8992f416 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java index 617291160..2a65a7d54 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java index f5cd28960..327ac693f 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java index 01b5dd7d4..304c75800 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java index aad23c492..da7cf996c 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java index 7e9089526..06619bb80 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java index 0e08901ea..8e7683580 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java index c1e1477b3..54b17e4ea 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index 88d55b46d..03dc16523 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java index f46004fe4..c55a799ff 100755 --- 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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/ClassicGenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/ClassicGenotypeLikelihoods.java index 58758a108..8209fc949 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java b/java/src/org/broadinstitute/sting/oneoffprojects/multisamplecaller/MultiSampleCaller.java index de5264ffb..5024162b4 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java index a51fefefb..283f8d9bf 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DSBWalkerV3.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DSBWalkerV3.java index 3d32f566e..bbd169424 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IOCrusherWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IOCrusherWalker.java index baa84c7be..d83457c23 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelErrorRateWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelErrorRateWalker.java index 6b8464f87..e413b66d6 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/PairedQualityScoreCountsWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/PairedQualityScoreCountsWalker.java index c437d247a..660f6433d 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java index d65a8a1cc..01dfcfeb1 100644 --- 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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java index 2abf11746..002d2ce12 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadErrorRateWalker.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadQualityScoreWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadQualityScoreWalker.java index 53a6e5353..bdf2c5218 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadQualityScoreWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadQualityScoreWalker.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReplaceQuals.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReplaceQuals.java index de361aaf5..09bcc5603 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReplaceQuals.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReplaceQuals.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java index 284137cc5..1c8aacd63 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java index 52b611764..96778c1c5 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ValidateDbSNPConversion.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ValidateDbSNPConversion.java index e03c5fba7..a2d178f57 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ValidateDbSNPConversion.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/ValidateDbSNPConversion.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java index 2100a08e7..0f17db4a0 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java index 4b7c397e9..518650632 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java index f83fd4780..6fb0635e7 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java index 4b2d9da7f..2e6276ee7 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/multisample/MultiSampleConcordanceWalker.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BeagleTrioToVCFWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BeagleTrioToVCFWalker.java index c0b4eb49e..7fb0a4c0d 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BeagleTrioToVCFWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/BeagleTrioToVCFWalker.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/SimpleVCFIntersectWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/SimpleVCFIntersectWalker.java index 00de5613e..9a777e413 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/SimpleVCFIntersectWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/SimpleVCFIntersectWalker.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 diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/VCFToBeagleWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/VCFToBeagleWalker.java index 18dad83ac..e4435380f 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/VCFToBeagleWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/vcftools/VCFToBeagleWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java b/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java index 7671bb5b7..a384c9084 100644 --- a/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java +++ b/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.java index b7b511f62..2e3df0dc0 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java index e5259572d..17c6f72ef 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculatePhaseLikelihoodsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculatePhaseLikelihoodsWalker.java index 0b1fd1ac1..860ff7840 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculatePhaseLikelihoodsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculatePhaseLikelihoodsWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java index 54fcc6e68..693398a50 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java index 043de686f..c39041941 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java index d5f6a76bd..5f45cf504 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java index 2d6eb1311..c16080332 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java index 3eef65888..8e81422ea 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java index d6686f418..15dd0a02d 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java index 5f86c0381..16624069c 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java index ba7197f3a..489d5022b 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java index 961d3ba9a..e3cbb163b 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java index 5653aceff..4572db0e5 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CombineDuplicatesWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CombineDuplicatesWalker.java index 73c210b67..72e225b8c 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CombineDuplicatesWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CombineDuplicatesWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CountDuplicatesWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CountDuplicatesWalker.java index c36df2e9d..d95aaffa8 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CountDuplicatesWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CountDuplicatesWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceAssessor.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceAssessor.java index 03182946d..01c4f95e1 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceAssessor.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceAssessor.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java index 79e6f5e9a..9d2308603 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java index 5521457a9..f8046ce37 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java index b24d89166..b5777634e 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java index ec4533cdd..7839f644d 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerBelowFrequencyWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerBelowFrequencyWalker.java index 94efd3866..823274537 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerBelowFrequencyWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerBelowFrequencyWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/Quad.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/Quad.java index 2c5158a16..d258c18c5 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/Quad.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/Quad.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/ReadOffsetQuad.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/ReadOffsetQuad.java index aa921d243..87820f82b 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/ReadOffsetQuad.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/ReadOffsetQuad.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/SQuad.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/SQuad.java index 112fab200..6dc0183a0 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/SQuad.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/SQuad.java @@ -1,3 +1,28 @@ +/* + * Copyright (c) 2010 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + package org.broadinstitute.sting.playground.gatk.walkers.poolseq; /** diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/qc/CountPairsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/qc/CountPairsWalker.java index bd246f5bf..bcee401f0 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/qc/CountPairsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/qc/CountPairsWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java index 2da0ab071..af6d69ef7 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/ApplyVariantClustersWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/ApplyVariantClustersWalker.java index 7a4aa4bc5..a3c78ab01 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/ApplyVariantClustersWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/ApplyVariantClustersWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantConcordanceROCCurveWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantConcordanceROCCurveWalker.java index 6db5b80a5..73e5edefa 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantConcordanceROCCurveWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantConcordanceROCCurveWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java index 139b96ed6..e67bc09fb 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java index 31f6fa47c..c3b27ba99 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizer.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizer.java index 68d234cae..d2efbc1bc 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizer.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizer.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFCombine.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFCombine.java index a8bbdc136..443271dbc 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFCombine.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFCombine.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSelectWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSelectWalker.java index 4889b0013..7ea122dd4 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSelectWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSelectWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java index cff983b65..55ceb8cd6 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.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 diff --git a/java/src/org/broadinstitute/sting/playground/tools/PairMaker.java b/java/src/org/broadinstitute/sting/playground/tools/PairMaker.java index 8d827aaac..b37530b8a 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/PairMaker.java +++ b/java/src/org/broadinstitute/sting/playground/tools/PairMaker.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 diff --git a/java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.java b/java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.java index 424f01731..c08b459dc 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.java +++ b/java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.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 diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/GenotypeConcordance.java index 6ba6ebeb3..536081ad1 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/GenotypeConcordance.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 diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFApplyCuts.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFApplyCuts.java index 303f77646..ce80e2e2f 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFApplyCuts.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFApplyCuts.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 diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFCallRates.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFCallRates.java index e845e435b..72909bed2 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFCallRates.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFCallRates.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 diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFHomogenizer.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFHomogenizer.java index b26d45777..6896e4231 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFHomogenizer.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFHomogenizer.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 diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java index 76dbcf670..27adad79e 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.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 diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFOptimize.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFOptimize.java index 47811020d..588598177 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFOptimize.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFOptimize.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 diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis.java index 695048a52..eb1d23017 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis.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 diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis2.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis2.java index 0f0a14e4a..118fc8cff 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis2.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis2.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 diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java index 6d56644ad..9a53f17d0 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.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 diff --git a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java index f253e8bf9..8b2b8df08 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java +++ b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.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 diff --git a/java/src/org/broadinstitute/sting/playground/utils/ParallelSAMIterator.java b/java/src/org/broadinstitute/sting/playground/utils/ParallelSAMIterator.java index acf8564eb..2433b3f65 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/ParallelSAMIterator.java +++ b/java/src/org/broadinstitute/sting/playground/utils/ParallelSAMIterator.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 diff --git a/java/src/org/broadinstitute/sting/playground/utils/PoolUtils.java b/java/src/org/broadinstitute/sting/playground/utils/PoolUtils.java index a53a832fc..1ab570fd1 100755 --- a/java/src/org/broadinstitute/sting/playground/utils/PoolUtils.java +++ b/java/src/org/broadinstitute/sting/playground/utils/PoolUtils.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 diff --git a/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java b/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java index 65a047155..c42330407 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java +++ b/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.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 diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/templates/TableFormat.java b/java/src/org/broadinstitute/sting/playground/utils/report/templates/TableFormat.java index 546ee4248..a29b32e82 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/templates/TableFormat.java +++ b/java/src/org/broadinstitute/sting/playground/utils/report/templates/TableFormat.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 diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index 8b60ac3fe..734694e89 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.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 diff --git a/java/src/org/broadinstitute/sting/utils/MathUtils.java b/java/src/org/broadinstitute/sting/utils/MathUtils.java index a8f1680b4..bd99f88ba 100755 --- a/java/src/org/broadinstitute/sting/utils/MathUtils.java +++ b/java/src/org/broadinstitute/sting/utils/MathUtils.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 diff --git a/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java b/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java index 54277023f..5c67d19e1 100755 --- a/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java +++ b/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.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 diff --git a/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/java/src/org/broadinstitute/sting/utils/SampleUtils.java index 30fd55a86..1b330476d 100755 --- a/java/src/org/broadinstitute/sting/utils/SampleUtils.java +++ b/java/src/org/broadinstitute/sting/utils/SampleUtils.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 diff --git a/java/src/org/broadinstitute/sting/utils/Utils.java b/java/src/org/broadinstitute/sting/utils/Utils.java index 56ed3d0df..72ba105fa 100755 --- a/java/src/org/broadinstitute/sting/utils/Utils.java +++ b/java/src/org/broadinstitute/sting/utils/Utils.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 diff --git a/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java b/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java index 5c1723f1d..314fec7e8 100755 --- a/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java +++ b/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.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 diff --git a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java index d9944b7c5..fde50238f 100755 --- a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java +++ b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.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 diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java index b745391d0..3e760ba63 100755 --- a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java +++ b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.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 diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java index 399caea44..86b431b2d 100644 --- a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java +++ b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.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 diff --git a/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java b/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java index 119aa6818..11d540c49 100644 --- a/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java +++ b/java/src/org/broadinstitute/sting/utils/collections/CircularArray.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 diff --git a/java/src/org/broadinstitute/sting/utils/collections/ExpandingArrayList.java b/java/src/org/broadinstitute/sting/utils/collections/ExpandingArrayList.java index 18222a95a..04ef8ece3 100755 --- a/java/src/org/broadinstitute/sting/utils/collections/ExpandingArrayList.java +++ b/java/src/org/broadinstitute/sting/utils/collections/ExpandingArrayList.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 diff --git a/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java b/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java index a63529bdb..1ca4593ed 100644 --- a/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java +++ b/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.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 diff --git a/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java b/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java index aa7f5a448..9b4bc1e63 100755 --- a/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java +++ b/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.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 diff --git a/java/src/org/broadinstitute/sting/utils/collections/Pair.java b/java/src/org/broadinstitute/sting/utils/collections/Pair.java index 5015dcafc..4dbe4550a 100644 --- a/java/src/org/broadinstitute/sting/utils/collections/Pair.java +++ b/java/src/org/broadinstitute/sting/utils/collections/Pair.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 diff --git a/java/src/org/broadinstitute/sting/utils/collections/PrimitivePair.java b/java/src/org/broadinstitute/sting/utils/collections/PrimitivePair.java index 29e14d184..80a0790b5 100644 --- a/java/src/org/broadinstitute/sting/utils/collections/PrimitivePair.java +++ b/java/src/org/broadinstitute/sting/utils/collections/PrimitivePair.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 diff --git a/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java b/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java index 33ea57610..09d914b3a 100644 --- a/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java +++ b/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.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 diff --git a/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java b/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java index 248e3809a..e864e813c 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.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 diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java index 1c44e000f..b43cb7a11 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.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 diff --git a/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java b/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java index 6fbc5e9c7..5f794583d 100644 --- a/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java +++ b/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.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 diff --git a/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java b/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java index f3674dafc..54572c8b8 100755 --- a/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java +++ b/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.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 diff --git a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java index 9b0925985..ec9166660 100644 --- a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java +++ b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.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 diff --git a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java index 6c15dd4fe..42605ec1d 100644 --- a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java +++ b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.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 diff --git a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index 70caa03ed..aedc84c32 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.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 diff --git a/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java b/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java index 757db4123..1d75e00b1 100755 --- a/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.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 diff --git a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index 082db293d..b78d25321 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.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 diff --git a/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java b/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java index f2de650b9..1150b170e 100644 --- a/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java +++ b/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.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 diff --git a/java/src/org/broadinstitute/sting/utils/text/XReadLines.java b/java/src/org/broadinstitute/sting/utils/text/XReadLines.java index 7414d97fc..4cf2ccf2f 100644 --- a/java/src/org/broadinstitute/sting/utils/text/XReadLines.java +++ b/java/src/org/broadinstitute/sting/utils/text/XReadLines.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 diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java index 2928f3919..a23d84bb7 100755 --- a/java/test/org/broadinstitute/sting/WalkerTest.java +++ b/java/test/org/broadinstitute/sting/WalkerTest.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 diff --git a/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java index 1a5187e7b..e5dad416b 100755 --- a/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java +++ b/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.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 diff --git a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/AlleleUnitTest.java b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/AlleleUnitTest.java index 2ac28093a..9c351fee5 100755 --- a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/AlleleUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/AlleleUnitTest.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 diff --git a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java index 4329b1a3a..79d0fe059 100644 --- a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.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 diff --git a/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java b/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java index 6490909ae..b6c5d6720 100755 --- a/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.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 diff --git a/java/test/org/broadinstitute/sting/utils/collections/ExpandingArrayListUnitTest.java b/java/test/org/broadinstitute/sting/utils/collections/ExpandingArrayListUnitTest.java index 40c482588..d84e8f504 100755 --- a/java/test/org/broadinstitute/sting/utils/collections/ExpandingArrayListUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/collections/ExpandingArrayListUnitTest.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