Merge ef7b858 into dccc4a1

src/main/scala/org/bdgenomics/cannoli/Gmap.scala

@@ -0,0 +1,96 @@
+/**
+ * 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.cannoli
+
+import htsjdk.samtools.ValidationStringency
+import org.apache.spark.SparkContext
+import org.apache.spark.SparkContext._
+import org.apache.spark.rdd.RDD
+import org.bdgenomics.adam.rdd.ADAMContext._
+import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
+import org.bdgenomics.adam.rdd.fragment.{ FragmentRDD, InterleavedFASTQInFormatter }
+import org.bdgenomics.adam.rdd.read.{ AlignmentRecordRDD, AnySAMOutFormatter }
+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 Gmap extends BDGCommandCompanion {
+  val commandName = "gmap"
+  val commandDescription = "ADAM Pipe API wrapper for GMAP."
+
+  def apply(cmdLine: Array[String]) = {
+    new Gmap(Args4j[GmapArgs](cmdLine))
+  }
+}
+
+class GmapArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
+  @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe from, in interleaved FASTQ format.", index = 0)
+  var inputPath: String = null
+
+  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe to.", index = 1)
+  var outputPath: String = null
+
+  @Args4jOption(required = true, name = "-genome_path", usage = "Genome database path. gmap -D, --dir argument.")
+  var genomePath: String = null
+
+  @Args4jOption(required = true, name = "-genome_name", usage = "Genome database name. gmap -d, --db argument.")
+  var genomeName: String = null
+
+  @Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file.")
+  var asSingleFile: Boolean = false
+
+  @Args4jOption(required = false, name = "-defer_merging", usage = "Defers merging single file output.")
+  var deferMerging: Boolean = false
+
+  @Args4jOption(required = false, name = "-disable_fast_concat", usage = "Disables the parallel file concatenation engine.")
+  var disableFastConcat: Boolean = false
+
+  @Args4jOption(required = false, name = "-stringency", usage = "Stringency level for various checks; can be SILENT, LENIENT, or STRICT. Defaults to STRICT.")
+  var stringency: String = "STRICT"
+
+  @Args4jOption(required = false, name = "-gmap_path", usage = "Path to the GMAP executable. Defaults to gmap.")
+  var gmapPath: String = "gmap"
+
+  // must be defined due to ADAMSaveAnyArgs, but unused here
+  var sortFastqOutput: Boolean = false
+}
+
+/**
+ * Gmap.
+ */
+class Gmap(protected val args: GmapArgs) extends BDGSparkCommand[GmapArgs] with Logging {
+  val companion = Gmap
+  val stringency = ValidationStringency.valueOf(args.stringency)
+
+  def run(sc: SparkContext) {
+    val input: FragmentRDD = sc.loadFragments(args.inputPath)
+
+    implicit val tFormatter = InterleavedFASTQInFormatter
+    implicit val uFormatter = new AnySAMOutFormatter
+
+    val gmapCommand = Seq(args.gmapPath,
+      "--dir=" + args.genomePath,
+      "--db=" + args.genomeName,
+      "--format=sampe").mkString(" ")
+
+    val output: AlignmentRecordRDD = input.pipe[AlignmentRecord, AlignmentRecordRDD, InterleavedFASTQInFormatter](gmapCommand)
+
+    output.save(args)
+  }
+}

src/main/scala/org/bdgenomics/cannoli/Gsnap.scala

@@ -0,0 +1,96 @@
+/**
+ * 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.cannoli
+
+import htsjdk.samtools.ValidationStringency
+import org.apache.spark.SparkContext
+import org.apache.spark.SparkContext._
+import org.apache.spark.rdd.RDD
+import org.bdgenomics.adam.rdd.ADAMContext._
+import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
+import org.bdgenomics.adam.rdd.fragment.{ FragmentRDD, InterleavedFASTQInFormatter }
+import org.bdgenomics.adam.rdd.read.{ AlignmentRecordRDD, AnySAMOutFormatter }
+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 Gsnap extends BDGCommandCompanion {
+  val commandName = "gsnap"
+  val commandDescription = "ADAM Pipe API wrapper for GSNAP."
+
+  def apply(cmdLine: Array[String]) = {
+    new Gsnap(Args4j[GsnapArgs](cmdLine))
+  }
+}
+
+class GsnapArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
+  @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe from, in interleaved FASTQ format.", index = 0)
+  var inputPath: String = null
+
+  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe to.", index = 1)
+  var outputPath: String = null
+
+  @Args4jOption(required = true, name = "-genome_path", usage = "Genome database path.  gsnap -D, --dir argument.")
+  var genomePath: String = null
+
+  @Args4jOption(required = true, name = "-genome_name", usage = "Genome database name.  gsnap -d, --db argument.")
+  var genomeName: String = null
+
+  @Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file.")
+  var asSingleFile: Boolean = false
+
+  @Args4jOption(required = false, name = "-defer_merging", usage = "Defers merging single file output.")
+  var deferMerging: Boolean = false
+
+  @Args4jOption(required = false, name = "-disable_fast_concat", usage = "Disables the parallel file concatenation engine.")
+  var disableFastConcat: Boolean = false
+
+  @Args4jOption(required = false, name = "-stringency", usage = "Stringency level for various checks; can be SILENT, LENIENT, or STRICT. Defaults to STRICT.")
+  var stringency: String = "STRICT"
+
+  @Args4jOption(required = false, name = "-gsnap_path", usage = "Path to the GSNAP executable. Defaults to gsnap.")
+  var gsnapPath: String = "gsnap"
+
+  // must be defined due to ADAMSaveAnyArgs, but unused here
+  var sortFastqOutput: Boolean = false
+}
+
+/**
+ * Gsnap.
+ */
+class Gsnap(protected val args: GsnapArgs) extends BDGSparkCommand[GsnapArgs] with Logging {
+  val companion = Gsnap
+  val stringency = ValidationStringency.valueOf(args.stringency)
+
+  def run(sc: SparkContext) {
+    val input: FragmentRDD = sc.loadFragments(args.inputPath)
+
+    implicit val tFormatter = InterleavedFASTQInFormatter
+    implicit val uFormatter = new AnySAMOutFormatter
+
+    val gsnapCommand = Seq(args.gsnapPath,
+      "--dir=" + args.genomePath,
+      "--db=" + args.genomeName,
+      "--format=sam").mkString(" ")
+
+    val output: AlignmentRecordRDD = input.pipe[AlignmentRecord, AlignmentRecordRDD, InterleavedFASTQInFormatter](gsnapCommand)
+
+    output.save(args)
+  }
+}