Added yaml support to tsv parser

biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala

@@ -40,7 +40,7 @@ object BiopetToolsExecutable extends BiopetExecutable {
     nl.lumc.sasc.biopet.tools.MpileupToVcf,
     nl.lumc.sasc.biopet.tools.PrefixFastq,
     nl.lumc.sasc.biopet.tools.SageCountFastq,
-    nl.lumc.sasc.biopet.tools.SamplesTsvToJson,
+    nl.lumc.sasc.biopet.tools.SamplesTsvToConfig,
     nl.lumc.sasc.biopet.tools.SeqStat,
     nl.lumc.sasc.biopet.tools.SquishBed,
     nl.lumc.sasc.biopet.tools.SummaryToTsv,

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala → biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToConfig.scala

@@ -14,18 +14,18 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{ PrintWriter, File }
+import java.io.{File, PrintWriter}
 
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
-import nl.lumc.sasc.biopet.utils.ToolCommand
-import scala.collection.mutable
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, ToolCommand}
 
+import scala.collection.mutable
 import scala.io.Source
 
 /**
  * This tool can convert a tsv to a json file
  */
-object SamplesTsvToJson extends ToolCommand {
+object SamplesTsvToConfig extends ToolCommand {
   case class Args(inputFiles: List[File] = Nil,
                   tagFiles: List[File] = Nil,
                   outputFile: Option[File] = None) extends AbstractArgs
@@ -47,14 +47,16 @@ object SamplesTsvToJson extends ToolCommand {
     val argsParser = new OptParser
     val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
-    val jsonString = stringFromInputs(cmdArgs.inputFiles, cmdArgs.tagFiles)
+    val configMap = stringFromInputs(cmdArgs.inputFiles, cmdArgs.tagFiles)
     cmdArgs.outputFile match {
+      case Some(file) if file.getName.endsWith(".yml") || file.getName.endsWith(".yaml") =>
+        ConfigUtils.mapToYamlFile(configMap, file)
       case Some(file) => {
         val writer = new PrintWriter(file)
-        writer.println(jsonString)
+        writer.println(ConfigUtils.mapToJson(configMap).spaces2)
         writer.close()
       }
-      case _ => println(jsonString)
+      case _ => println(ConfigUtils.mapToYaml(configMap))
     }
   }
 
@@ -94,11 +96,11 @@ object SamplesTsvToJson extends ToolCommand {
     librariesValues.foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
   }
 
-  def stringFromInputs(inputs: List[File], tagsInputs: List[File]): String = {
+  def stringFromInputs(inputs: List[File], tagsInputs: List[File]): Map[String, Any] = {
     val map = inputs.map(f => mapFromFile(f))
       .foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
     val tags = tagsInputs.map(f => mapFromFile(f, tags = true))
       .foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
-    mapToJson(mergeMaps(map, tags)).spaces2
+    mergeMaps(map, tags)
   }
 }

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala → biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToConfigTest.scala

@@ -25,8 +25,8 @@ import org.testng.annotations.Test
 /**
  * Created by ahbbollen on 28-8-15.
  */
-class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
-  import SamplesTsvToJson._
+class SamplesTsvToConfigTest extends TestNGSuite with MockitoSugar with Matchers {
+  import SamplesTsvToConfig._
   private def resourcePath(p: String): String = {
     Paths.get(getClass.getResource(p).toURI).toString
   }

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 import java.nio.file.Paths
 
-import nl.lumc.sasc.biopet.tools.SamplesTsvToJson._
+import nl.lumc.sasc.biopet.tools.SamplesTsvToConfig._
 import org.scalatest.Matchers
 import org.scalatest.mock.MockitoSugar
 import org.scalatest.testng.TestNGSuite

biopet-utils/pom.xml

@@ -76,7 +76,7 @@
         <dependency>
             <groupId>org.yaml</groupId>
             <artifactId>snakeyaml</artifactId>
-            <version>1.15</version>
+            <version>1.17</version>
         </dependency>
         <dependency>
             <groupId>io.argonaut</groupId>