From 5ff11a3cf000f5b734f7f2816bde2309e46979ec Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 1 Jun 2016 19:16:50 +0200
Subject: [PATCH] Switch to picard for id sorting
---
.../biopet/pipelines/gentrap/measures/FragmentsPerGene.scala | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala b/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
index e5f8a13ba..ffcb35bad 100644
--- a/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
+++ b/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.measures
import nl.lumc.sasc.biopet.core.annotations.AnnotationGtf
import nl.lumc.sasc.biopet.extensions.HtseqCount
+import nl.lumc.sasc.biopet.extensions.picard.SortSam
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsSort
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
@@ -37,10 +38,10 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
case (id, file) =>
val bamFile = if (sortOnId) {
- val samtoolsSort = new SamtoolsSort(this)
+ val samtoolsSort = new SortSam(this)
samtoolsSort.input = file
samtoolsSort.output = swapExt(outputDir, file, ".bam", ".idsorted.bam")
- samtoolsSort.sortByName = true
+ samtoolsSort.sortOrder = "queryname"
samtoolsSort.isIntermediate = true
add(samtoolsSort)
samtoolsSort.output
--
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