From 3ff377eb0bed66895216f7ea11a8b56529e6ca6e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 16 Apr 2015 09:53:02 +0200
Subject: [PATCH] Added BedToIntervalList extension
---
.../extensions/picard/BedToIntervalList.scala | 36 +++++++++++++++++++
1 file changed, 36 insertions(+)
create mode 100644 public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
new file mode 100644
index 000000000..2faef859c
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
@@ -0,0 +1,36 @@
+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+
+/**
+ * Created by pjvan_thof on 4/15/15.
+ */
+class BedToIntervalList(val root: Configurable) extends Picard {
+ javaMainClass = new picard.util.BedToIntervalList().getClass.getName
+
+ @Input(doc = "Input bed file", required = true)
+ var input: File = null
+
+ @Input(doc = "Reference dict file", required = true)
+ var dict: File = new File(config("reference").asString.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
+
+ @Output(doc = "Output interval list", required = true)
+ var output: File = null
+
+ override def commandLine = super.commandLine +
+ required("SEQUENCE_DICTIONARY=", dict, spaceSeparated = false) +
+ required("INPUT=", input, spaceSeparated = false) +
+ required("OUTPUT=", output, spaceSeparated = false)
+}
+
+object BedToIntervalList {
+ def apply(root:Configurable, input:File, output:File): BedToIntervalList = {
+ val bi = new BedToIntervalList(root)
+ bi.input = input
+ bi.output = output
+ bi
+ }
+}
\ No newline at end of file
--
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