From f095411493353ffbb919589e87113fd8a9b4d6e4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 4 Mar 2015 14:39:00 +0100
Subject: [PATCH] Added tabix
---
.../lumc/sasc/biopet/extensions/Tabix.scala | 30 +++++++++++++++++++
1 file changed, 30 insertions(+)
create mode 100644 public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
new file mode 100644
index 000000000..0653abf52
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
@@ -0,0 +1,30 @@
+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+
+/**
+ * Created by pjvan_thof on 3/4/15.
+ */
+class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
+
+ @Input(doc = "Input files", required = true)
+ var input: File = null
+
+ @Output(doc = "Compressed output file", required = true)
+ protected var output: File = null
+
+ var p: Option[String] = config("p")
+ executable = config("exe", default = "bgzip")
+
+ override def beforeGraph: Unit = {
+ output = new File(input.getAbsolutePath + ".tbi")
+ }
+
+ def cmdLine = required(executable) +
+ optional("-p", p) +
+ required(input)
+}
\ No newline at end of file
--
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