Commit 5301853f authored by bow's avatar bow
Browse files

Update BamMetrics RNA mode and its tests

parent a8a816b5
......@@ -80,11 +80,13 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
add(gcBiasMetrics)
addSummarizable(gcBiasMetrics, "gc_bias")
val wgsMetrics = new CollectWgsMetrics(this)
wgsMetrics.input = inputBam
wgsMetrics.output = swapExt(outputDir, inputBam, ".bam", ".wgs.metrics")
add(wgsMetrics)
addSummarizable(wgsMetrics, "wgs")
if (transcriptRefFlatFile.isEmpty) {
val wgsMetrics = new CollectWgsMetrics(this)
wgsMetrics.input = inputBam
wgsMetrics.output = swapExt(outputDir, inputBam, ".bam", ".wgs.metrics")
add(wgsMetrics)
addSummarizable(wgsMetrics, "wgs")
}
if (transcriptRefFlatFile.isDefined) {
val rnaMetrics = new CollectRnaSeqMetrics(this)
......
......@@ -45,9 +45,10 @@ class BamMetricsTest extends TestNGSuite with Matchers {
@Test(dataProvider = "bammetricsOptions")
def testFlexiprep(rois: Int, amplicon: Boolean, rna: Boolean) = {
val map = ConfigUtils.mergeMaps(Map("output_dir" -> BamMetricsTest.outputDir, "rna_metrcis" -> rna
), Map(BamMetricsTest.executables.toSeq: _*)) ++
val map = ConfigUtils.mergeMaps(Map("output_dir" -> BamMetricsTest.outputDir),
Map(BamMetricsTest.executables.toSeq: _*)) ++
(if (amplicon) Map("amplicon_bed" -> "amplicon.bed") else Map()) ++
(if (rna) Map("transcript_refflat" -> "transcripts.refFlat") else Map()) ++
Map("regions_of_interest" -> (1 to rois).map("roi_" + _ + ".bed").toList)
val bammetrics: BamMetrics = initPipeline(map)
......@@ -59,7 +60,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
var regions: Int = rois + (if (amplicon) 1 else 0)
bammetrics.functions.count(_.isInstanceOf[CollectRnaSeqMetrics]) shouldBe (if (rna) 1 else 0)
bammetrics.functions.count(_.isInstanceOf[CollectWgsMetrics]) shouldBe 1
bammetrics.functions.count(_.isInstanceOf[CollectWgsMetrics]) shouldBe (if (rna) 0 else 1)
bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1
bammetrics.functions.count(_.isInstanceOf[CalculateHsMetrics]) shouldBe (if (amplicon) 1 else 0)
bammetrics.functions.count(_.isInstanceOf[CollectTargetedPcrMetrics]) shouldBe (if (amplicon) 1 else 0)
......
......@@ -114,11 +114,12 @@ class MappingTest extends TestNGSuite with Matchers {
case _ => throw new IllegalArgumentException("aligner: " + aligner + " does not exist")
}
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)
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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