From c4c5dc60bb14b22c4d18f67c1662a474a4e38b41 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Wed, 23 Mar 2016 12:45:48 +0100
Subject: [PATCH] Set default htseq-count sorting order to pos
---
.../pipelines/gentrap/measures/FragmentsPerGene.scala | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
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 78224cc18..bcfc41786 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
@@ -26,6 +26,8 @@ import org.broadinstitute.gatk.queue.QScript
class FragmentsPerGene(val root: Configurable) extends QScript with Measurement with AnnotationGtf {
def mergeArgs = MergeArgs(idCols = List(1), valCol = 2, numHeaderLines = 0, fallback = "0")
+ override def fixedValues: Map[String, Any] = Map("htseqcount" -> Map("order" -> "pos"))
+
/** Pipeline itself */
def biopetScript(): Unit = {
val jobs = bamFiles.map {
@@ -38,10 +40,6 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
job.output = new File(outputDir, s"$id.$name.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
- //job.order = Option("name")
id -> job
}
--
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