Updating licenses for all scala files

GSATDG-5

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/CNV/xhmmCNVpipeline.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.qscripts.CNV
 
 import org.broadinstitute.sting.queue.extensions.gatk._

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.qscripts
 
 import org.broadinstitute.sting.queue.QScript

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/DevNullOutput.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.qscripts.examples
 

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.qscripts.examples
 
 import org.broadinstitute.sting.queue.QScript

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.qscripts.examples
 
 import org.broadinstitute.sting.queue.QScript

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.qscripts.examples
 
 import org.broadinstitute.sting.queue.QScript

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.qscripts.examples
 

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala

@@ -1,26 +1,23 @@
-import org.broadinstitute.sting.queue.function.RetryMemoryLimit
+/*
-import org.broadinstitute.sting.queue.QScript
+* Copyright (c) 2012 The Broad Institute
-import org.broadinstitute.sting.queue.extensions.gatk._
+* 
-
+* Permission is hereby granted, free of charge, to any person
-class ExampleRetryMemoryLimit extends QScript {
+* obtaining a copy of this software and associated documentation
-  @Input(doc="The reference file for the bam files.", shortName="R")
+* files (the "Software"), to deal in the Software without
-  var referenceFile: File = _
+* restriction, including without limitation the rights to use,
-
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
-  @Input(doc="Bam file to genotype.", shortName="I")
+* copies of the Software, and to permit persons to whom the
-  var bamFile: File = _
+* Software is furnished to do so, subject to the following
-
+* conditions:
-  def script() {
+* 
-    for (scatterCount <- 1 to 2) {
+* The above copyright notice and this permission notice shall be
-      val ug = new UnifiedGenotyper with RetryMemoryLimit
+* included in all copies or substantial portions of the Software.
-      // First run with 1m
+* 
-      ug.memoryLimit = .001
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-      // On retry run with 1g
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-      ug.retryMemoryFunction = (d => d * 1000)
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-      ug.reference_sequence = referenceFile
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-      ug.input_file = Seq(bamFile)
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-      ug.out = swapExt(bamFile, ".bam", ".scattered_%d.vcf".format(scatterCount))
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-      ug.scatterCount = scatterCount
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-      add(ug)
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-    }
-  }
-}

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.qscripts.examples
 
 import org.broadinstitute.sting.queue.QScript

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.qscripts.examples
 
 import org.broadinstitute.sting.queue.QScript

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/ChunkVCF.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.qscripts.lib
 
 import org.broadinstitute.sting.queue.QScript

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/VcfToPed.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.qscripts.lib
 
 import org.broadinstitute.sting.queue.QScript

public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue
 

public/scala/src/org/broadinstitute/sting/queue/QCommandPlugin.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue
 
 import engine.QStatusMessenger

public/scala/src/org/broadinstitute/sting/queue/QException.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue
 
 import org.broadinstitute.sting.utils.exceptions.StingException

public/scala/src/org/broadinstitute/sting/queue/QScript.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue
 

public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue
 
 import scala.tools.nsc.{Global, Settings}

public/scala/src/org/broadinstitute/sting/queue/QSettings.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue
 

public/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobManager.scala

@@ -1,6 +1,6 @@
 /*
-* Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 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
@@ -9,17 +9,18 @@
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
-*
+* 
 * 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
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
-* OTHER DEALINGS IN THE SOFTWARE.
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
 package org.broadinstitute.sting.queue.engine

public/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine
 

public/scala/src/org/broadinstitute/sting/queue/engine/CommandLinePluginManager.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine
 

public/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine
 

public/scala/src/org/broadinstitute/sting/queue/engine/InProcessJobManager.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.engine
 
 import org.broadinstitute.sting.queue.function.InProcessFunction

public/scala/src/org/broadinstitute/sting/queue/engine/InProcessRunner.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.engine
 
 import org.broadinstitute.sting.queue.function.InProcessFunction

public/scala/src/org/broadinstitute/sting/queue/engine/JobManager.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine
 

public/scala/src/org/broadinstitute/sting/queue/engine/JobRunInfo.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine
 

public/scala/src/org/broadinstitute/sting/queue/engine/JobRunner.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine
 

public/scala/src/org/broadinstitute/sting/queue/engine/MappingEdge.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine
 

public/scala/src/org/broadinstitute/sting/queue/engine/QEdge.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine
 

public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine
 

public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine
 

public/scala/src/org/broadinstitute/sting/queue/engine/QNode.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine
 

public/scala/src/org/broadinstitute/sting/queue/engine/QStatusMessenger.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.engine
 
 import org.broadinstitute.sting.queue.util.RemoteFile

public/scala/src/org/broadinstitute/sting/queue/engine/RunnerStatus.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.engine
 
 object RunnerStatus extends Enumeration {

public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobManager.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute 
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person 
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation 
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without 
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use, 
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell 
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the 
+* 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: 
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be 
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software. 
+* 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 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT 
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, 
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine.drmaa
 

public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine.drmaa
 

public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobManager.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine.gridengine
 

public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine.gridengine
 

public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobManager.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine.lsf
 

public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine.lsf
 

public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobManager.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine.shell
 

public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.engine.shell
 

public/scala/src/org/broadinstitute/sting/queue/extensions/cancer/MuTect.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.extensions.cancer
 
 import java.io.File

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.gatk
 

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.extensions.gatk
 
 import org.broadinstitute.sting.queue.function.{RetryMemoryLimit, JavaCommandLineFunction}

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.gatk
 

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.gatk
 

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.gatk
 

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.gatk
 

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.gatk
 

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.gatk
 

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ReadScatterFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.gatk
 

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.extensions.gatk
 
 import java.io.File

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.gatk
 

public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.gatk
 

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.picard
 

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.extensions.picard
 
 import org.broadinstitute.sting.commandline.{Argument, Output, Input}

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.extensions.picard
 
 import org.broadinstitute.sting.commandline.{Argument, Output, Input}

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.extensions.picard
 
 import org.broadinstitute.sting.commandline.{Argument, Output, Input}

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.picard
 

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.picard
 

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.picard
 

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.picard
 

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.picard
 

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.picard
 

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.picard
 

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.picard
 

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.picard
 

public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.samtools
 

public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.samtools
 

public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.samtools
 

public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.extensions.snpeff
 

public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function
 

public/scala/src/org/broadinstitute/sting/queue/function/InProcessFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function
 

public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function
 

public/scala/src/org/broadinstitute/sting/queue/function/ListWriterFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function
 

public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function
 

public/scala/src/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function
 

public/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function.scattergather
 

public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ConcatenateLogsFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function.scattergather
 

public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function.scattergather
 

public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function.scattergather
 

public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function.scattergather
 

public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.function.scattergather
 

public/scala/src/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.function.scattergather
 
 import org.broadinstitute.sting.queue.function.InProcessFunction

public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.library.clf.vcf
 
 import java.io.File

public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.library.clf.vcf
 
 import java.io.File

public/scala/src/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.library.ipf
 
 import collection.JavaConversions._

public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.library.ipf.vcf
 
 import collection.JavaConversions._

public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.library.ipf.vcf
 
 import org.broadinstitute.sting.queue.function.InProcessFunction

public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.library.ipf.vcf
 
 import collection.JavaConversions._

public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.library.ipf.vcf
 
 import collection.JavaConversions._

public/scala/src/org/broadinstitute/sting/queue/util/ClassFieldCache.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.util
 
 import org.broadinstitute.sting.commandline._

public/scala/src/org/broadinstitute/sting/queue/util/CollectionUtils.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.util
 
 /**

public/scala/src/org/broadinstitute/sting/queue/util/DoC/package.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.util
 
 import java.io.File
@@ -8,6 +33,10 @@ import org.broadinstitute.sting.commandline.{Input, Gather, Output}
 import org.broadinstitute.sting.queue.function.CommandLineFunction
 import org.broadinstitute.sting.gatk.walkers.coverage.CoverageUtils
 
+*/
+
+*/
+
 package object DoC {
   class DoC(val bams: List[File], val DoC_output: File, val countType: CoverageUtils.CountPileupType, val MAX_DEPTH: Int, val minMappingQuality: Int, val minBaseQuality: Int, val scatterCountInput: Int, val START_BIN: Int, val NUM_BINS: Int, val minCoverageCalcs: Seq[Int]) extends CommandLineGATK with ScatterGatherableFunction {
     val DOC_OUTPUT_SUFFIX: String = ".sample_interval_summary"

public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.util
 

public/scala/src/org/broadinstitute/sting/queue/util/EmailSettings.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.util
 

public/scala/src/org/broadinstitute/sting/queue/util/Logging.scala

@@ -1,3 +1,28 @@
+/*
+* Copyright (c) 2012 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.queue.util
 
 import org.apache.log4j._

public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.util
 

public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala

@@ -1,26 +1,27 @@
 /*
- * Copyright (c) 2012, The Broad Institute
+* Copyright (c) 2012 The Broad Institute
- *
+* 
- * Permission is hereby granted, free of charge, to any person
+* Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
+* obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
+* files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
+* restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
+* 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:
+* conditions:
- *
+* 
- * The above copyright notice and this permission notice shall be
+* The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
+* 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
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * OTHER DEALINGS IN THE SOFTWARE.
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- */
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
 
 package org.broadinstitute.sting.queue.util