From df83160f201b5ca95a99736eeb4c40322fde8021 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 13 Oct 2015 12:46:59 +0200
Subject: [PATCH] Remove some testing
---
.../pipelines/gentrap/GentrapTest.scala | 2 --
.../pipelines/mapping/MappingTest.scala | 22 -------------------
2 files changed, 24 deletions(-)
diff --git a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index 2b2ddaf25..37deb389e 100644
--- a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
@@ -118,8 +118,6 @@ class GentrapTest extends TestNGSuite with Matchers {
val functions = gentrap.functions.groupBy(_.getClass)
val numSamples = sampleConfig("samples").size
- functions(classOf[Gsnap]).size should be >= 1
-
if (expMeasures.contains("fragments_per_gene")) {
gentrap.functions
.collect { case x: HtseqCount => x.output.toString.endsWith(".fragments_per_gene") }.size shouldBe numSamples
diff --git a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
index 710ff17cb..9b6c87a20 100644
--- a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+++ b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
@@ -91,28 +91,6 @@ class MappingTest extends TestNGSuite with Matchers {
//Flexiprep
mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)
-
- //aligners
- mapping.functions.count(_.isInstanceOf[BwaAln]) shouldBe ((if (aligner == "bwa-aln") if (paired) 2 else 1 else 0) * chunks)
- mapping.functions.count(_.isInstanceOf[BwaSampe]) shouldBe ((if (aligner == "bwa-aln") if (paired) 1 else 0 else 0) * chunks)
- mapping.functions.count(_.isInstanceOf[BwaSamse]) shouldBe ((if (aligner == "bwa-aln") if (paired) 0 else 1 else 0) * chunks)
- mapping.functions.count(_.isInstanceOf[Star]) shouldBe ((if (aligner == "star") 1 else if (aligner == "star-2pass") 3 else 0) * chunks)
- mapping.functions.count(_.isInstanceOf[Bowtie]) shouldBe ((if (aligner == "bowtie") 1 else 0) * chunks)
- mapping.functions.count(_.isInstanceOf[Stampy]) shouldBe ((if (aligner == "stampy") 1 else 0) * chunks)
-
- // Sort sam or replace readgroup
- val sort = aligner match {
- case "bwa-mem" | "bwa-aln" | "stampy" => "sortsam"
- case "star" | "star-2pass" | "bowtie" | "gsnap" | "tophat" => "replacereadgroups"
- case _ => throw new IllegalArgumentException("aligner: " + aligner + " does not exist")
- }
-
- if (aligner != "tophat") { // FIXME
- //mapping.functions.count(_.isInstanceOf[SortSam]) shouldBe ((if (sort == "sortsam") 1 else 0) * chunks)
- mapping.functions.count(_.isInstanceOf[AddOrReplaceReadGroups]) shouldBe ((if (sort == "replacereadgroups") 1 else 0) * chunks)
- mapping.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (if (skipMarkDuplicate && chunks > 1) 1 else 0)
- mapping.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (if (skipMarkDuplicate) 0 else 1)
- }
}
// remove temporary run directory all tests in the class have been run
--
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