Merge pull request #130 from biopet/fix-BIOPET-697

Disable insertsize metrics for single end

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -42,6 +42,9 @@ class BamMetrics(val parent: Configurable)
   @Input(doc = "Bam File", shortName = "BAM", required = true)
   var inputBam: File = _
 
+  @Argument(required = false)
+  var paired: Boolean = true
+
   override def defaults = Map("bedtoolscoverage" -> Map("sorted" -> true))
 
   /** returns files to store in summary */
@@ -87,6 +90,9 @@ class BamMetrics(val parent: Configurable)
     val multiMetrics = new CollectMultipleMetrics(this)
     multiMetrics.input = inputBam
     multiMetrics.outputName = new File(outputDir, inputBam.getName.stripSuffix(".bam"))
+    if (!paired)
+      multiMetrics.program = multiMetrics.program
+        .filter(_ != CollectMultipleMetrics.Programs.CollectInsertSizeMetrics)
     add(multiMetrics)
     addSummarizable(multiMetrics, "multi_metrics")
 
@@ -212,6 +218,7 @@ object BamMetrics extends PipelineCommand {
   def apply(root: Configurable,
             bamFile: File,
             outputDir: File,
+            paired: Boolean,
             sampleId: Option[String] = None,
             libId: Option[String] = None): BamMetrics = {
     val bamMetrics = new BamMetrics(root)
@@ -219,6 +226,7 @@ object BamMetrics extends PipelineCommand {
     bamMetrics.libId = libId
     bamMetrics.inputBam = bamFile
     bamMetrics.outputDir = outputDir
+    bamMetrics.paired = paired
 
     bamMetrics.init()
     bamMetrics.biopetScript()

carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -78,6 +78,7 @@ class Carp(val parent: Configurable) extends QScript with MultisampleMappingTrai
       val bamMetricsFilter = BamMetrics(qscript,
                                         preProcessBam.get,
                                         new File(sampleDir, "metrics-filter"),
+                                        paired,
                                         sampleId = Some(sampleId))
       addAll(bamMetricsFilter.functions)
       bamMetricsFilter.summaryName = "bammetrics-filter"

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -305,7 +305,7 @@ class Mapping(val parent: Configurable)
       }
       if (chunking && numberChunks.getOrElse(1) > 1 && config("chunk_metrics", default = false))
         addAll(
-          BamMetrics(this, outputBam, new File(chunkDir, "metrics"), sampleId, libId).functions)
+          BamMetrics(this, outputBam, new File(chunkDir, "metrics"), paired, sampleId, libId).functions)
     }
 
     if (!skipFlexiprep) {
@@ -334,7 +334,7 @@ class Mapping(val parent: Configurable)
 
     if (!skipMetrics) {
       val bamMetrics =
-        BamMetrics(this, finalBamFile, new File(outputDir, "metrics"), sampleId, libId)
+        BamMetrics(this, finalBamFile, new File(outputDir, "metrics"), paired, sampleId, libId)
       addAll(bamMetrics.functions)
       addSummaryQScript(bamMetrics)
     }

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala

@@ -236,6 +236,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript with Reference { qscrip
             bamMetrics.libId = Some(libId)
             bamMetrics.inputBam = bamFile.get
             bamMetrics.outputDir = new File(libDir, "metrics")
+            bamMetrics.paired = inputR2.isDefined
             add(bamMetrics)
 
             if (config("execute_bam2wig", default = true)) add(Bam2Wig(qscript, bamFile.get))
@@ -340,6 +341,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript with Reference { qscrip
         bamMetrics.sampleId = Some(sampleId)
         bamMetrics.inputBam = if (metricsPreprogressBam) preProcessBam.get else bamFile.get
         bamMetrics.outputDir = new File(sampleDir, "metrics")
+        bamMetrics.paired = libraries.exists(_._2.inputR1.isDefined)
         add(bamMetrics)
 
         if (config("execute_bam2wig", default = true)) add(Bam2Wig(qscript, preProcessBam.get))