From 20fe80d7c113e2d4be1697becbfe92ec6258ef40 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 25 Jan 2016 12:35:16 +0100
Subject: [PATCH] Remove old code
---
.../pipelines/gentrap/measures/BaseCounts.scala | 2 +-
.../gentrap/measures/FragmentsPerGene.scala | 15 ---------------
2 files changed, 1 insertion(+), 16 deletions(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
index 7a56733ea..1f2bdaed6 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
@@ -25,6 +25,6 @@ class BaseCounts(val root: Configurable) extends QScript with Measurement with A
}
//TODO: merges
- //TODO heatmaps
+ //TODO: heatmaps
}
}
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 fd94996f6..440dc1246 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
@@ -9,21 +9,6 @@ import org.broadinstitute.gatk.queue.QScript
* Created by pjvan_thof on 1/12/16.
*/
class FragmentsPerGene(val root: Configurable) extends QScript with Measurement with AnnotationGtf {
- def bamToCountFile(id: String, bamFile: File): (String, File) = {
- //TODO: ID sorting job
-
- val job = new HtseqCount(this)
- job.inputAnnotation = annotationGtf
- job.inputAlignment = bamFile
- job.output = new File(outputDir, s"$name.$id.counts")
- job.format = Option("bam")
- // 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.output
- }
-
def mergeArgs = MergeArgs(List(1), 2, numHeaderLines = 1, fallback = "0")
/** Pipeline itself */
--
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