From 1df0636d5d1d2c15b99d88464f943c02cf02d299 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Tue, 6 Oct 2015 15:24:49 +0200
Subject: [PATCH] add BuildBamIndex to biopet
---
.../extensions/picard/BuildBamIndex.scala | 24 +++++++++++++++++++
1 file changed, 24 insertions(+)
create mode 100644 public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
new file mode 100644
index 000000000..e68c4ded5
--- /dev/null
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
@@ -0,0 +1,24 @@
+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+
+/**
+ * Created by sajvanderzeeuw on 6-10-15.
+ */
+class BuildBamIndex (val root: Configurable) extends Picard {
+
+ javaMainClass = new picard.sam.BuildBamIndex().getClass.getName
+
+ @Input(doc = "The input SAM or BAM files to analyze.", required = true)
+ var input: File = _
+
+ @Output(doc = "The output file to bam file to", required = true)
+ var output: File = _
+
+ override def cmdLine = super.cmdLine +
+ required("INPUT=", input, spaceSeparated = false) +
+ required("OUTPUT=", output, spaceSeparated = false)
+}
--
GitLab