From 95ebd1c911863ff16904fc9e8a51d426357c200e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 25 Jan 2016 19:08:01 +0100
Subject: [PATCH] Fixed htseq-count
---
.../biopet/pipelines/gentrap/measures/FragmentsPerGene.scala | 1 +
1 file changed, 1 insertion(+)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
index b12501da0..a383874f1 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
@@ -22,6 +22,7 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
job.inputAlignment = file
job.output = new File(outputDir, s"$name.$id.counts")
job.format = Option("bam")
+ add(job)
// We are forcing the sort order to be ID-sorted, since HTSeq-count often chokes when using position-sorting due
// to its buffer not being large enough.
//TODO: ID sorting job
--
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