From 9cc925040f45fc026d9937e19bebd72ccc904f0a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 3 Nov 2014 17:47:17 +0100
Subject: [PATCH] Added index as output file
---
.../sasc/biopet/extensions/picard/MarkDuplicates.scala | 8 ++++++++
.../nl/lumc/sasc/biopet/extensions/picard/SortSam.scala | 8 ++++++++
2 files changed, 16 insertions(+)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
index 0b4169ab1..bb9575e1a 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
@@ -52,6 +52,14 @@ class MarkDuplicates(val root: Configurable) extends Picard {
@Argument(doc = "OPTICAL_DUPLICATE_PIXEL_DISTANCE", required = false)
var opticalDuplicatePixelDistance: Option[Int] = config("opticalDuplicatePixelDistance")
+ @Output(doc = "Bam Index", required = true)
+ private var outputIndex: File = _
+
+ override def afterGraph {
+ super.afterGraph
+ if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
+ }
+
override def commandLine = super.commandLine +
repeat("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
index 119d411e7..82f1fac3d 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
@@ -16,6 +16,14 @@ class SortSam(val root: Configurable) extends Picard {
@Argument(doc = "Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} ", required = true)
var sortOrder: String = _
+ @Output(doc = "Bam Index", required = true)
+ private var outputIndex: File = _
+
+ override def afterGraph {
+ super.afterGraph
+ if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
+ }
+
override def commandLine = super.commandLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false) +
--
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