Merge branch 'fix-BIOPET-477' into 'develop'

Fix BIOPET-477

This feature was required by a project

See merge request !485

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala

@@ -44,6 +44,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFunction with Refe
   var minAP: Option[Int] = config("min_ap")
   var homoFraction: Option[Double] = config("homoFraction")
   var ploidy: Option[Int] = config("ploidy")
+  var refCalls: Boolean = config("ref_calls", default = false)
   var sample: String = _
   var reference: String = _
 
@@ -72,6 +73,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFunction with Refe
     optional("--minAP", minAP) +
     optional("--homoFraction", homoFraction) +
     optional("--ploidy", ploidy) +
+    conditional(refCalls, "--refCalls") +
     required("--sample", sample) +
     (if (inputAsStdin) "" else required("-I", inputMpileup))
 }

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

@@ -27,7 +27,7 @@ import scala.math.{ floor, round }
 
 object MpileupToVcf extends ToolCommand {
   case class Args(input: File = null, output: File = null, sample: String = null, minDP: Int = 8, minAP: Int = 2,
-                  homoFraction: Double = 0.8, ploidy: Int = 2, seqError: Double = 0.005) extends AbstractArgs
+                  homoFraction: Double = 0.8, ploidy: Int = 2, seqError: Double = 0.005, refCalls: Boolean = false) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
     opt[File]('I', "input") valueName "<file>" action { (x, c) =>
@@ -54,6 +54,9 @@ object MpileupToVcf extends ToolCommand {
     opt[Double]("seqError") action { (x, c) =>
       c.copy(seqError = x)
     }
+    opt[Unit]("refCalls") action { (x, c) =>
+      c.copy(refCalls = true)
+    }
   }
 
   /**
@@ -66,6 +69,7 @@ object MpileupToVcf extends ToolCommand {
 
     val writer = new PrintWriter(commandArgs.output)
     writer.println("##fileformat=VCFv4.1")
+    writer.println("##ALT=<ID=REF,Description=\"Placeholder if location has no ALT alleles\">")
     writer.println("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">")
     writer.println("##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">")
     writer.println("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">")
@@ -172,7 +176,7 @@ object MpileupToVcf extends ToolCommand {
         case _       =>
       }
 
-      if (alt.nonEmpty) {
+      if (alt.nonEmpty || commandArgs.refCalls) {
         val ad = for (ad <- format("AD").toString.split(",")) yield ad.toInt
         var left = reads - dels
         val gt = ArrayBuffer[Int]()
@@ -187,11 +191,11 @@ object MpileupToVcf extends ToolCommand {
           }
           left -= ad(max)
         }
-        writer.println(Array(chr, pos, ".", ref.toUpperCase, alt.mkString(","), ".", ".", info.mkString(";"),
+        writer.println(Array(chr, pos, ".", ref.toUpperCase, if (alt.nonEmpty) alt.mkString(",") else "<REF>", ".", ".", info.mkString(";"),
           "GT:" + format.keys.mkString(":"), gt.sortWith(_ < _).mkString("/") + ":" + format.values.mkString(":")
         ).mkString("\t"))
       }
     }
     writer.close()
   }
-}
\ No newline at end of file
+}