Commit df83160f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove some testing

parent f03c70ff
......@@ -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
......
......@@ -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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