Merge pull request #2 from bigdatagenomics/master

Merge BDG changes
bigdatagenomics · Sep 6, 2017 · 8a1c313 · 8a1c313
2 parents beb935d + 45d32cf
commit 8a1c313
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diff --git a/deca-cli/src/main/scala/org/bdgenomics/deca/cli/CNVer.scala b/deca-cli/src/main/scala/org/bdgenomics/deca/cli/CNVer.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.cli
 
 import htsjdk.samtools.ValidationStringency

diff --git a/deca-cli/src/main/scala/org/bdgenomics/deca/cli/Coverager.scala b/deca-cli/src/main/scala/org/bdgenomics/deca/cli/Coverager.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.cli
 
 import htsjdk.samtools.ValidationStringency

diff --git a/deca-cli/src/main/scala/org/bdgenomics/deca/cli/Discoverer.scala b/deca-cli/src/main/scala/org/bdgenomics/deca/cli/Discoverer.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.cli
 
 import org.apache.spark.SparkContext

diff --git a/deca-cli/src/main/scala/org/bdgenomics/deca/cli/Normalizer.scala b/deca-cli/src/main/scala/org/bdgenomics/deca/cli/Normalizer.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.cli
 
 import org.apache.spark.SparkContext

diff --git a/deca-cli/src/main/scala/org/bdgenomics/deca/cli/NormalizingDiscoverer.scala b/deca-cli/src/main/scala/org/bdgenomics/deca/cli/NormalizingDiscoverer.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.cli
 
 import org.apache.spark.SparkContext

diff --git a/deca-cli/src/main/scala/org/bdgenomics/deca/cli/util/Handler.scala b/deca-cli/src/main/scala/org/bdgenomics/deca/cli/util/Handler.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.cli.util
 
 import org.kohsuke.args4j.{ CmdLineParser, OptionDef }

diff --git a/deca-cli/src/main/scala/org/bdgenomics/deca/cli/util/IntOptionHandler.scala b/deca-cli/src/main/scala/org/bdgenomics/deca/cli/util/IntOptionHandler.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.cli.util
 
 import org.kohsuke.args4j.spi.Setter

diff --git a/deca-cli/src/main/scala/org/bdgenomics/deca/cli/util/StringOptionHandler.scala b/deca-cli/src/main/scala/org/bdgenomics/deca/cli/util/StringOptionHandler.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.cli.util
 
 import org.kohsuke.args4j.spi.Setter

diff --git a/deca-core/src/main/scala/org/bdgenomics/deca/Coverage.scala b/deca-core/src/main/scala/org/bdgenomics/deca/Coverage.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca
 
 import breeze.linalg.{ DenseVector, sum }

diff --git a/deca-core/src/main/scala/org/bdgenomics/deca/HMM.scala b/deca-core/src/main/scala/org/bdgenomics/deca/HMM.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca
 
 import org.apache.spark.SparkContext

diff --git a/deca-core/src/main/scala/org/bdgenomics/deca/Normalization.scala b/deca-core/src/main/scala/org/bdgenomics/deca/Normalization.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca
 
 import breeze.linalg.sum

diff --git a/deca-core/src/main/scala/org/bdgenomics/deca/Timers.scala b/deca-core/src/main/scala/org/bdgenomics/deca/Timers.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca
 
 import org.bdgenomics.utils.instrumentation.Metrics

diff --git a/deca-core/src/main/scala/org/bdgenomics/deca/coverage/ReadDepthMatrix.scala b/deca-core/src/main/scala/org/bdgenomics/deca/coverage/ReadDepthMatrix.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.coverage
 
 import org.apache.spark.mllib.linalg.distributed.IndexedRowMatrix
@@ -8,9 +25,12 @@ import org.bdgenomics.adam.models.ReferenceRegion
  */
 
 case class ReadDepthMatrix(depth: IndexedRowMatrix, samples: Array[String], targets: Array[ReferenceRegion]) {
-  assert(
+  require(
     depth.numRows() == samples.length && depth.numCols() == targets.length,
-    "Size of depth matrix not consistent with samples and targets")
+    "Size of depth matrix (%dx%d) not consistent with samples (%d) and targets (%d)".format(
+      depth.numRows(), depth.numCols(),
+      samples.length,
+      targets.length))
 
   def cache() = depth.rows.cache()
 

diff --git a/deca-core/src/main/scala/org/bdgenomics/deca/hmm/FixedMatrix.scala b/deca-core/src/main/scala/org/bdgenomics/deca/hmm/FixedMatrix.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.hmm
 
 /**

diff --git a/deca-core/src/main/scala/org/bdgenomics/deca/hmm/FixedVector.scala b/deca-core/src/main/scala/org/bdgenomics/deca/hmm/FixedVector.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.hmm
 
 /**

diff --git a/deca-core/src/main/scala/org/bdgenomics/deca/hmm/SampleModel.scala b/deca-core/src/main/scala/org/bdgenomics/deca/hmm/SampleModel.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.hmm
 import java.util
 

diff --git a/deca-core/src/main/scala/org/bdgenomics/deca/hmm/TransitionProbabilities.scala b/deca-core/src/main/scala/org/bdgenomics/deca/hmm/TransitionProbabilities.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.hmm
 
 import com.esotericsoftware.kryo.io.{ Input, Output }

diff --git a/deca-core/src/main/scala/org/bdgenomics/deca/serialization/DECAKryoRegistrator.scala b/deca-core/src/main/scala/org/bdgenomics/deca/serialization/DECAKryoRegistrator.scala
@@ -1,3 +1,20 @@
+/**
+ * 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.
+ */
 package org.bdgenomics.deca.serialization
 
 import com.esotericsoftware.kryo.Kryo