Add Picard's BaitDesigner and ExtractSequences tasks

tasks/src/main/scala/dagr/tasks/picard/BaitDesigner.scala

@@ -0,0 +1,71 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2019 Fulcrum Genomics LLC
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+package dagr.tasks.picard
+
+import dagr.tasks.DagrDef.{DirPath, PathToFasta, PathToIntervals}
+import picard.util.BaitDesigner.DesignStrategy
+
+import scala.collection.mutable.ListBuffer
+
+/** Task to run Picard's BaitDesigner. */
+class BaitDesigner(
+  val targets: PathToIntervals,
+  val designName: String,
+  val ref: PathToFasta,
+  val outputDirectory: DirPath,
+  val leftPrimer: Option[String] = None,
+  val rightPrimer: Option[String] = None,
+  val designStrategy: Option[DesignStrategy] = None,
+  val baitSize: Option[Int] = None,
+  val minimumBaitsPerTarget: Option[Int] = None,
+  val baitOffset: Option[Int] = None,
+  val padding: Option[Int] = None,
+  val repeatTolerance: Option[Int] = None,
+  val poolSize: Option[Int] = None,
+  val fillPools: Option[Boolean] = None,
+  val designOnTargetStrand: Option[Boolean] = None,
+  val mergeNearbyTargets: Option[Boolean] = None,
+  val outputAgilentFiles: Option[Boolean] = None
+  ) extends PicardTask {
+
+  override protected def addPicardArgs(buffer: ListBuffer[Any]): Unit = {
+    buffer.append("TARGETS=" + targets)
+    buffer.append("DESIGN_NAME=" + designName)
+    buffer.append("REFERENCE_SEQUENCE=" + ref)
+    buffer.append("OUTPUT_DIRECTORY=" + outputDirectory)
+    leftPrimer.foreach(primer           => buffer.append("LEFT_PRIMER=" + primer))
+    rightPrimer.foreach(primer          => buffer.append("RIGHT_PRIMER=" + primer))
+    designStrategy.foreach(strategy     => buffer.append("DESIGN_STRATEGY=" + strategy))
+    baitSize.foreach(size               => buffer.append("BAIT_SIZE=" + size))
+    minimumBaitsPerTarget.foreach(min   => buffer.append("MINIMUM_BAITS_PER_TARGET=" + min))
+    baitOffset.foreach(offset           => buffer.append("BAIT_OFFSET=" + offset))
+    padding.foreach(pad                 => buffer.append("PADDING=" + pad))
+    repeatTolerance.foreach(tol         => buffer.append("REPEAT_TOLERANCE=" + tol))
+    poolSize.foreach(pool               => buffer.append("POOL_SIZE=" + pool))
+    fillPools.foreach(fill              => buffer.append("FILL_POOLS=" + fill))
+    designOnTargetStrand.foreach(target => buffer.append("DESIGN_ON_TARGET_STRAND=" + target))
+    mergeNearbyTargets.foreach(merge    => buffer.append("MERGE_NEARBY_TARGETS=" + merge))
+    outputAgilentFiles.foreach(agilent  => buffer.append("OUTPUT_AGILENT_FILES=" + agilent))
+  }
+}

tasks/src/main/scala/dagr/tasks/picard/ExtractSequences.scala

@@ -0,0 +1,44 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2019 Fulcrum Genomics LLC
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+package dagr.tasks.picard
+
+import dagr.tasks.DagrDef.{PathToFasta, PathToIntervals}
+
+import scala.collection.mutable.ListBuffer
+
+/** Task to run Picard's ExtractSequences. */
+class ExtractSequences(
+  val intervals: PathToIntervals,
+  val output: PathToFasta,
+  val ref: PathToFasta,
+  val lineLength: Option[Int] = None
+  ) extends PicardTask {
+
+  override protected def addPicardArgs(buffer: ListBuffer[Any]): Unit = {
+    buffer.append("INTERVAL_LIST=" + intervals)
+    buffer.append("REFERENCE_SEQUENCE=" + ref)
+    buffer.append("OUTPUT=" + output)
+    lineLength.foreach(length => buffer.append("LINE_LENGTH=" + length))
+  }
+}