Update Picard metrics parsing to better handle nonexistent files

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

@@ -63,18 +63,18 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
 
   def summaryFiles: Map[String, File] = Map()
 
-  def summaryStats: Map[String, Any] = {
-    val (header, content) = Picard.getMetrics(output)
-
-    (for (category <- 0 until content.size) yield {
-      content(category)(0) -> (
-        for (
-          i <- 1 until header.size if i < content(category).size
-        ) yield {
-          header(i).toLowerCase -> content(category)(i)
-        }).toMap
-    }
-    ).toMap
+  def summaryStats: Map[String, Any] = Picard.getMetrics(output) match {
+    case None => Map()
+    case Some((header, content)) =>
+      (for (category <- 0 until content.size) yield {
+        content(category)(0) -> (
+          for (
+            i <- 1 until header.size if i < content(category).size
+          ) yield {
+            header(i).toLowerCase -> content(category)(i)
+          }).toMap
+      }
+      ).toMap
   }
 }
 

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

@@ -74,11 +74,13 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
 
   def summaryFiles: Map[String, File] = Map("output_histogram" -> outputHistogram)
 
-  def summaryStats: Map[String, Any] = {
-    val (header, content) = Picard.getMetrics(output)
-    (for (i <- 0 to header.size if i < content.head.size)
-      yield (header(i).toLowerCase -> content.head(i))).toMap
+  def summaryStats: Map[String, Any] = Picard.getMetrics(output) match {
+    case None => Map()
+    case Some((header, content)) =>
+      (for (i <- 0 to header.size if i < content.head.size)
+        yield header(i).toLowerCase -> content.head(i)).toMap
   }
+
 }
 
 object CollectInsertSizeMetrics {

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

@@ -77,13 +77,13 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
     //"output_chart" -> chartOutput
     ).collect { case (key, Some(value)) => key -> value }
 
-  def summaryStats: Map[String, Any] = {
-    val (header, content) = Picard.getMetrics(output)
-
-    header
-      .zip(content)
-      .map { case (h, c) => h.toLowerCase -> c.head }
-      .toMap
+  def summaryStats: Map[String, Any] = Picard.getMetrics(output) match {
+    case None => Map()
+    case Some((header, content)) =>
+      header
+        .zip(content)
+        .map { case (h, c) => h.toLowerCase -> c.head }
+        .toMap
   }
 
   override def commandLine = super.commandLine +

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

@@ -95,18 +95,18 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
 
   def summaryFiles: Map[String, File] = Map()
 
-  def summaryStats: Map[String, Any] = {
-    val (header, content) = Picard.getMetrics(outputMetrics)
-
-    (for (category <- 0 until content.size) yield {
-      content(category)(0) -> (
-        for (
-          i <- 1 until header.size if i < content(category).size
-        ) yield {
-          header(i).toLowerCase -> content(category)(i)
-        }).toMap
-    }
-    ).toMap
+  def summaryStats: Map[String, Any] = Picard.getMetrics(outputMetrics) match {
+    case None => Map()
+    case Some((header, content)) =>
+      (for (category <- 0 until content.size) yield {
+        content(category)(0) -> (
+          for (
+            i <- 1 until header.size if i < content(category).size
+          ) yield {
+            header(i).toLowerCase -> content(category)(i)
+          }).toMap
+      }
+      ).toMap
   }
 }
 object MarkDuplicates {

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

@@ -66,15 +66,20 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
 }
 
 object Picard {
-  def getMetrics(file: File) = {
-    val lines = Source.fromFile(file).getLines().toArray
+  def getMetrics(file: File): Option[(Array[String], List[Array[String]])] =
 
-    val start = lines.indexWhere(_.startsWith("## METRICS CLASS")) + 1
-    val end = lines.indexOf("", start)
+    if (file.exists) {
+      val lines = Source.fromFile(file).getLines().toArray
 
-    val header = lines(start).split("\t")
-    val content = (for (i <- (start + 1) until end) yield lines(i).split("\t")).toList
+      val start = lines.indexWhere(_.startsWith("## METRICS CLASS")) + 1
+      val end = lines.indexOf("", start)
+
+      val header = lines(start).split("\t")
+      val content = (for (i <- (start + 1) until end) yield lines(i).split("\t")).toList
+
+      Option((header, content))
+    } else {
+      None
+    }
 
-    (header, content)
-  }
 }
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