Merge 0ab45cd into 5f0ef28

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Vcf2HBase.scala

@@ -0,0 +1,82 @@
+/**
+ * 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.adam.cli
+
+import org.apache.spark.SparkContext
+import org.bdgenomics.adam.hbase.HBaseFunctions
+import org.bdgenomics.adam.instrumentation.Timers._
+import org.bdgenomics.adam.models.{ RecordGroupDictionary, SequenceDictionary, SnpTable }
+import org.bdgenomics.adam.projections.{ AlignmentRecordField, Filter }
+import org.bdgenomics.adam.rdd.ADAMContext._
+import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
+import org.bdgenomics.adam.rdd.read.{ AlignedReadRDD, AlignmentRecordRDD, MDTagging }
+import org.bdgenomics.adam.rich.RichVariant
+import org.bdgenomics.formats.avro.AlignmentRecord
+import org.bdgenomics.utils.cli._
+import org.bdgenomics.utils.misc.Logging
+import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
+
+object Vcf2HBase extends BDGCommandCompanion {
+  val commandName = "Vcf2HBase"
+  val commandDescription = "Write a VCF file to HBase"
+
+  def apply(cmdLine: Array[String]) = {
+    new Vcf2HBase(Args4j[Vcf2HBaseArgs](cmdLine))
+  }
+}
+
+class Vcf2HBaseArgs extends Args4jBase {
+
+  @Argument(required = true, metaVar = "VCF", usage = "The VCF file to convert", index = 0)
+  var vcfPath: String = _
+
+  @Argument(required = true, metaVar = "HBASE_TABLE", usage = "HBase table name in which to load VCF file")
+  var hbaseTable: String = null
+
+  @Args4jOption(required = true, name = "-seq_dict_id", usage = "User defined name to apply to the sequence dictionary create from this VCF, or name of existing sequence dictionary to be used")
+  var seqDictId: String = null
+
+  @Args4jOption(required = false, name = "-use_existing_seqdict", usage = "Use an existing sequence dictionary, don't write a new one")
+  var useExistingSeqDict: Boolean = false
+
+  @Args4jOption(required = false, name = "-repartition", usage = "Repartition into N partitions prior to writing to HBase")
+  var repartitionNum: Int = 0
+
+  @Argument(required = true, metaVar = "STAGING_FOLDER", usage = "Location for temporary files during bulk load")
+  var stagingFolder: String = null
+}
+
+class Vcf2HBase(protected val args: Vcf2HBaseArgs) extends BDGSparkCommand[Vcf2HBaseArgs] with Logging {
+  val companion = Vcf2HBase
+
+  def run(sc: SparkContext) {
+
+    val vcRdd = sc.loadVcf(args.vcfPath)
+
+    val hbaseConnection = new HBaseFunctions.HBaseDataAccessObject(sc)
+    HBaseFunctions.saveVariantContextRDDToHBaseBulk(hbaseConnection,
+      vcRdd,
+      args.hbaseTable,
+      args.seqDictId,
+      args.stagingFolder,
+      args.useExistingSeqDict,
+      Some(args.repartitionNum))
+
+  }
+
+}

adam-core/pom.xml

@@ -136,6 +136,10 @@
       <groupId>org.apache.spark</groupId>
       <artifactId>spark-core_${scala.version.prefix}</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.apache.spark</groupId>
+      <artifactId>spark-streaming_${scala.version.prefix}</artifactId>
+    </dependency>
     <dependency>
       <groupId>it.unimi.dsi</groupId>
       <artifactId>fastutil</artifactId>
@@ -185,5 +189,25 @@
       <groupId>com.google.guava</groupId>
       <artifactId>guava</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.apache.hbase</groupId>
+      <artifactId>hbase-hadoop2-compat</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.hbase</groupId>
+      <artifactId>hbase-server</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.hbase</groupId>
+      <artifactId>hbase-it</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.hbase</groupId>
+      <artifactId>hbase-client</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.hbase</groupId>
+      <artifactId>hbase-spark</artifactId>
+    </dependency>
   </dependencies>
 </project>