Use maven license plugin to ensure source has correct license

CONTRIBUTING.md

@@ -47,9 +47,9 @@ or "topic" branches.
 be shown in the pull request.  If your feature branch is not based off the latest master, you will be asked to rebase
 it before it is merged.
 * If your pull request fixes an issue, reference the issue so that it will [be closed when your pull request is merged](https://github.com/blog/1506-closing-issues-via-pull-requests)
-* Run Scalariform on the code by doing the following:
+* Run the ./scripts/format-source script in order to format the code and ensure correct license headers
   ```
-  $ mvn org.scalariform:scalariform-maven-plugin:format
+  $ ./scripts/format-source
   ```
 * Keep your pull requests as small as possible. Large pull requests are hard to review. Try to break up your changes
 into self-contained and incremental pull requests, if need be, and reference dependent pull requests, e.g. "This pull
@@ -60,27 +60,3 @@ optionally, any details that you want to share about the commit.
 to check every pull request and commit. Just look for files in the ADAM repo that end in "*Suite.scala", 
 e.g. ADAMContextSuite.scala, to see examples of how to write tests. You might also want to glance at the 
 `./scripts/jenkins-test` script for more end-to-end tests.
-* Make sure to add a copyright header to all new files (see below).
-
-## Copyright header and Licensing
-
-ADAM is released under the [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.html).
-Any new files added need to have a header with a license like the following, e.g.
-
-    /**
-     * Copyright (c) 2014. [insert your company or name here]
-     *
-     * Licensed under the Apache License, Version 2.0 (the "License");
-     * you may not use this file except in compliance with the License.
-     * You may obtain a copy of the License at
-     *
-     *     http://www.apache.org/licenses/LICENSE-2.0
-     *
-     * Unless required by applicable law or agreed to in writing, software
-     * distributed under the License is distributed on an "AS IS" BASIS,
-     * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-     * See the License for the specific language governing permissions and
-     * limitations under the License.
-     */
-
-

LICENSE_header.txt

@@ -0,0 +1,15 @@
+Licensed to Big Data Genomics (BDG) under one
+or more contributor license agreements.  See the NOTICE file
+distributed with this work for additional information
+regarding copyright ownership.  The BDG licenses this file
+to you under the Apache License, Version 2.0 (the
+"License"); you may not use this file except in compliance
+with the License.  You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Vcf.scala

@@ -1,9 +1,11 @@
-/*
- * Copyright (c) 2013. Regents of the University of California
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *
@@ -13,7 +15,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
 package org.bdgenomics.adam.cli
 
 import org.bdgenomics.adam.avro.ADAMGenotype

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMCommand.scala

@@ -1,9 +1,11 @@
-/*
- * Copyright (c) 2013. Regents of the University of California
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *
@@ -13,7 +15,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
 package org.bdgenomics.adam.cli
 
 import org.apache.hadoop.mapreduce.Job

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala

@@ -1,9 +1,11 @@
-/*
- * Copyright (c) 2013. Regents of the University of California
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Args4j.scala

@@ -1,9 +1,11 @@
-/*
- * Copyright (c) 2013. Regents of the University of California
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *
@@ -13,7 +15,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
 package org.bdgenomics.adam.cli
 
 import org.kohsuke.args4j.{ CmdLineException, CmdLineParser, Option }

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Bam2ADAM.scala

@@ -1,9 +1,11 @@
-/*
- * Copyright (c) 2013. Regents of the University of California
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *

adam-cli/src/main/scala/org/bdgenomics/adam/cli/BuildInformation.scala

@@ -1,9 +1,11 @@
-/*
- * Copyright (c) 2014. Sebastien Mondet <seb@mondet.org>
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *

adam-cli/src/main/scala/org/bdgenomics/adam/cli/CalculateDepth.scala

@@ -1,11 +1,13 @@
 /**
- * Copyright 2014 Genome Bridge LLC
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,

adam-cli/src/main/scala/org/bdgenomics/adam/cli/CompareADAM.scala

@@ -1,11 +1,13 @@
-/*
- * Copyright 2013, 2014 Genome Bridge LLC
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
- * http://www.apache.org/licenses/LICENSE-2.0
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ComputeVariants.scala

@@ -0,0 +1,17 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */

adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountKmers.scala

@@ -1,9 +1,11 @@
-/*
- * Copyright (c) 2014. Regents of the University of California
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *

adam-cli/src/main/scala/org/bdgenomics/adam/cli/DictionaryCommand.scala

@@ -1,9 +1,11 @@
-/*
- * Copyright (c) 2014. Mount Sinai School of Medicine
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *
@@ -13,7 +15,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
 package org.bdgenomics.adam.cli
 
 import java.io.{ FileOutputStream, File }

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fasta2ADAM.scala

@@ -1,9 +1,11 @@
-/*
- * Copyright (c) 2014. Regents of the University of California
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *

adam-cli/src/main/scala/org/bdgenomics/adam/cli/FindReads.scala

@@ -1,9 +1,11 @@
 /**
- * Copyright 2013 Genome Bridge LLC
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *

adam-cli/src/main/scala/org/bdgenomics/adam/cli/FlagStat.scala

@@ -1,9 +1,11 @@
-/*
- * Copyright (c) 2013. Regents of the University of California
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *
@@ -13,7 +15,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
 package org.bdgenomics.adam.cli
 
 import org.bdgenomics.adam.rdd.ADAMContext._

adam-cli/src/main/scala/org/bdgenomics/adam/cli/GenotypeConcordance.scala

@@ -1,9 +1,11 @@
-/*
- * Copyright (c) 2014. Mount Sinai School of Medicine
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
  *     http://www.apache.org/licenses/LICENSE-2.0
  *
@@ -13,7 +15,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
 package org.bdgenomics.adam.cli
 
 import org.apache.spark.{ SparkContext, Logging }

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ListDict.scala

@@ -1,11 +1,13 @@
 /**
- * Copyright 2013 Genome Bridge LLC
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
  *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,