Move sickle summary methods to general sickle extension

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

@@ -19,9 +19,13 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
+import scala.collection.mutable
+import scala.io.Source
+
+class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summarizable {
   @Input(doc = "R1 input")
   var input_R1: File = _
 
@@ -76,4 +80,40 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
       optional("--quiet", quiet) +
       " > " + required(output_stats)
   }
+
+  def summaryData: Map[String, Any] = {
+    val pairKept = """FastQ paired records kept: (\d*) \((\d*) pairs\)""".r
+    val singleKept = """FastQ single records kept: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)""".r
+    val pairDiscarded = """FastQ paired records discarded: (\d*) \((\d*) pairs\)""".r
+    val singleDiscarded = """FastQ single records discarded: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)""".r
+
+    var stats: mutable.Map[String, Int] = mutable.Map()
+
+    if (output_stats.exists) for (line <- Source.fromFile(output_stats).getLines) {
+      line match {
+        case pairKept(reads, pairs) => stats += ("num_paired_reads_kept" -> reads.toInt)
+        case singleKept(total, r1, r2) => {
+          stats += ("num_reads_kept_R1" -> r1.toInt)
+          stats += ("num_reads_kept_R2" -> r2.toInt)
+        }
+        case pairDiscarded(reads, pairs) => stats += ("num_paired_reads_discarded" -> reads.toInt)
+        case singleDiscarded(total, r1, r2) => {
+          stats += ("num_reads_discarded_R1" -> r1.toInt)
+          stats += ("num_reads_discarded_R2" -> r2.toInt)
+        }
+        case _ =>
+      }
+    }
+
+    stats.toMap ++ Map("version" -> getVersion)
+  }
+
+  override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
+    (v1, v2) match {
+      case (v1: Int, v2: Int) => v1 + v2
+      case _                  => v1
+    }
+  }
+
+  def summaryFiles: Map[String, File] = Map()
 }

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
 
 import nl.lumc.sasc.biopet.core.{ SampleLibraryTag, BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.{ Gzip, Pbzip2, Md5sum, Zcat, Seqstat }
+import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.tools.FastqSync
 
 class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Sickle.scala

-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.pipelines.flexiprep
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.core.config.Configurable
-
-import argonaut._, Argonaut._
-import nl.lumc.sasc.biopet.core.summary.Summarizable
-import scalaz._, Scalaz._
-
-import scala.io.Source
-import scala.collection.mutable
-
-class Sickle(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Sickle(root) with Summarizable {
-
-  def summaryData: Map[String, Any] = {
-    val pairKept = """FastQ paired records kept: (\d*) \((\d*) pairs\)""".r
-    val singleKept = """FastQ single records kept: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)""".r
-    val pairDiscarded = """FastQ paired records discarded: (\d*) \((\d*) pairs\)""".r
-    val singleDiscarded = """FastQ single records discarded: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)""".r
-
-    var stats: mutable.Map[String, Int] = mutable.Map()
-
-    if (output_stats.exists) for (line <- Source.fromFile(output_stats).getLines) {
-      line match {
-        case pairKept(reads, pairs) => stats += ("num_paired_reads_kept" -> reads.toInt)
-        case singleKept(total, r1, r2) => {
-          stats += ("num_reads_kept_R1" -> r1.toInt)
-          stats += ("num_reads_kept_R2" -> r2.toInt)
-        }
-        case pairDiscarded(reads, pairs) => stats += ("num_paired_reads_discarded" -> reads.toInt)
-        case singleDiscarded(total, r1, r2) => {
-          stats += ("num_reads_discarded_R1" -> r1.toInt)
-          stats += ("num_reads_discarded_R2" -> r2.toInt)
-        }
-        case _ =>
-      }
-    }
-
-    stats.toMap ++ Map("version" -> getVersion)
-  }
-
-  override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
-    (v1, v2) match {
-      case (v1: Int, v2: Int) => v1 + v2
-      case _                  => v1
-    }
-  }
-
-  def summaryFiles: Map[String, File] = Map()
-}