Add CorrectUmis to dagr tasks (#366)

* Add CorrectUmis to dagr tasks

tasks/src/main/scala/dagr/tasks/fgbio/CorrectUmis.scala

@@ -0,0 +1,57 @@
+/*
+ * 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.fgbio
+
+import dagr.core.tasksystem.Pipe
+import dagr.tasks.DagrDef.{FilePath, PathToBam}
+import dagr.tasks.DataTypes.SamOrBam
+
+import scala.collection.mutable.ListBuffer
+
+case class CorrectUmis(in: PathToBam,
+                       out: PathToBam,
+                       maxMismatches: Int,
+                       minDistance: Int,
+                       rejects: Option[PathToBam] = None,
+                       metrics: Option[FilePath] = None,
+                       umis: Seq[String] = Seq.empty,
+                       umiFiles: Seq[FilePath] = Seq.empty,
+                       umiTag: Option[String] = None,
+                       dontStoreOriginalUmis: Boolean = false
+                      ) extends FgBioTask with Pipe[SamOrBam, SamOrBam]{
+
+  override protected def addFgBioArgs(buffer: ListBuffer[Any]): Unit = {
+    buffer.append("-i", in)
+    buffer.append("-o", out)
+    buffer.append("-m", maxMismatches)
+    buffer.append("-d", minDistance)
+    rejects.foreach {r => buffer.append("-r", r) }
+    metrics.foreach {m => buffer.append("-M", m) }
+    if (umis.nonEmpty)     { buffer.append("-u"); buffer.append(umis: _*)     }
+    if (umiFiles.nonEmpty) { buffer.append("-U"); buffer.append(umiFiles: _*) }
+    umiTag.foreach { t => buffer.append("-t", t) }
+    buffer.append("-x", dontStoreOriginalUmis)
+  }
+}