[ADAM-793] adding command to convert ADAM nucleotide contig fragments…

… to FASTA files, fixes #793

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fasta.scala

@@ -0,0 +1,61 @@
+/**
+ * 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.{ Logging, SparkContext }
+import org.apache.spark.rdd.RDD
+import org.bdgenomics.adam.projections.NucleotideContigFragmentField._
+import org.bdgenomics.adam.projections.Projection
+import org.bdgenomics.adam.rdd.ADAMContext._
+import org.bdgenomics.formats.avro.NucleotideContigFragment
+import org.bdgenomics.utils.cli._
+import org.kohsuke.args4j.{ Argument, Option => Args4JOption }
+
+class ADAM2FastaArgs extends ParquetLoadSaveArgs {
+  @Args4JOption(required = false, name = "-partitions", usage = "Number of partitions, default 1")
+  var partitions: Int = 1
+  @Args4JOption(required = false, name = "-shuffle", usage = "Shuffle while partitioning, default false")
+  var shuffle: Boolean = false
+  @Args4JOption(required = false, name = "-line-width", usage = "Hard wrap FASTA formatted sequence at line width, default 60")
+  var lineWidth: Int = 60
+}
+
+object ADAM2Fasta extends BDGCommandCompanion {
+  override val commandName = "adam2fasta"
+  override val commandDescription = "Convert ADAM nucleotide contig fragments to FASTA files"
+
+  override def apply(cmdLine: Array[String]): ADAM2Fasta =
+    new ADAM2Fasta(Args4j[ADAM2FastaArgs](cmdLine))
+}
+
+class ADAM2Fasta(val args: ADAM2FastaArgs) extends BDGSparkCommand[ADAM2FastaArgs] with Logging {
+  override val companion = ADAM2Fasta
+
+  override def run(sc: SparkContext): Unit = {
+    val proj = Projection(contig, description, fragmentNumber, numberOfFragmentsInContig, fragmentSequence)
+
+    log.info("Loading ADAM nucleotide contig fragments from disk.")
+    val contigFragments: RDD[NucleotideContigFragment] = sc.loadParquet(args.inputPath, projection = Some(proj))
+
+    log.info("Merging fragments and writing FASTA to disk.")
+    contigFragments
+      .mergeFragments()
+      .coalesce(args.partitions, args.shuffle)
+      .saveAsFasta(args.outputPath, args.lineWidth)
+  }
+}

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

@@ -50,6 +50,7 @@ object ADAMMain extends Logging {
           VcfAnnotation2ADAM,
           ADAM2Vcf,
           Fasta2ADAM,
+          ADAM2Fasta,
           Features2ADAM,
           WigFix2Bed,
           Fragments2Reads,