From dd458aef00c1049a50c00cc1585e0e21fa628890 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@e-sensei.nl>
Date: Wed, 29 Jun 2016 09:36:10 +0200
Subject: [PATCH] Update code with fixes from Peter
---
.../lumc/sasc/biopet/extensions/tools/WipeReads.scala | 10 +++++++++-
.../sasc/biopet/pipelines/gentrap/GentrapTest.scala | 5 ++---
2 files changed, 11 insertions(+), 4 deletions(-)
diff --git a/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala b/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
index 81012df74..a2e66a482 100644
--- a/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
+++ b/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
@@ -42,7 +42,7 @@ class WipeReads(val root: Configurable) extends ToolCommandFunction {
var readgroup: Set[String] = config("read_group", default = Nil)
@Argument(doc = "Whether to remove multiple-mapped reads outside the target regions (default: yes)")
- var limitRemoval: Boolean = config("limit_removal", default=true)
+ var limitRemoval: Boolean = config("limit_removal", default=false)
@Argument(doc = "Whether to index output BAM file or not")
var noMakeIndex: Boolean = config("no_make_index", default=false)
@@ -59,9 +59,17 @@ class WipeReads(val root: Configurable) extends ToolCommandFunction {
@Output(doc = "Output BAM", shortName = "o", required = true)
var outputBam: File = null
+ @Output(required = false)
+ private var outputIndex: Option[File] = None
+
@Output(doc = "BAM containing discarded reads", shortName = "f", required = false)
var discardedBam: Option[File] = None
+ override def beforeGraph() {
+ super.beforeGraph()
+ if (! noMakeIndex) outputIndex = Some(new File(outputBam.getPath.stripSuffix(".bam") + ".bai"))
+ }
+
override def cmdLine = super.cmdLine +
required("-I", inputBam) +
required("-r", intervalFile) +
diff --git a/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index 9b834708d..090c8099e 100644
--- a/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
@@ -138,9 +138,8 @@ abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: O
assert(gentrap.functions.exists(_.isInstanceOf[Ln]))
}
- if (gentrap.removeRibosomalReads) {
- assert(gentrap.functions.exists(_.isInstanceOf[WipeReads]))
- }
+ gentrap.removeRibosomalReads shouldBe removeRiboReads
+ gentrap.functions.exists(_.isInstanceOf[WipeReads]) shouldBe removeRiboReads
val classMap = Map(
"gsnap" -> classOf[Gsnap],
--
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