From b34a09a05ce12a294a81ede0f43543b4af12a185 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 15 May 2016 11:57:42 +0200
Subject: [PATCH] Fixed test
---
.../biopet/pipelines/bammetrics/BamMetricsTest.scala | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala b/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
index 4a75d99e0..6da49168e 100644
--- a/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+++ b/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
@@ -61,9 +61,9 @@ class BamMetricsTest extends TestNGSuite with Matchers {
def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean, wgs: Boolean) = {
val map = ConfigUtils.mergeMaps(Map("output_dir" -> BamMetricsTest.outputDir, "rna_metrics" -> rna, "wgs_metrics" -> wgs),
Map(BamMetricsTest.executables.toSeq: _*)) ++
- (if (amplicon) Map("amplicon_bed" -> "amplicon.bed") else Map()) ++
+ (if (amplicon) Map("amplicon_bed" -> BamMetricsTest.ampliconBed.getAbsolutePath) else Map()) ++
(if (rna) Map("annotation_refflat" -> "transcripts.refFlat") else Map()) ++
- Map("regions_of_interest" -> (1 to rois).map("roi_" + _ + ".bed").toList)
+ Map("regions_of_interest" -> (1 to rois).map(BamMetricsTest.roi(_).getAbsolutePath).toList)
val bammetrics: BamMetrics = initPipeline(map)
bammetrics.inputBam = BamMetricsTest.bam
@@ -94,6 +94,14 @@ object BamMetricsTest {
val bam = new File(outputDir, "input" + File.separator + "bla.bam")
Files.touch(bam)
+ val ampliconBed = new File(outputDir, "input" + File.separator + "amplicon_bed.bed")
+ Files.touch(ampliconBed)
+
+ def roi(i: Int): File = {
+ val roi = new File(outputDir, "input" + File.separator + s"roi${i}.bed")
+ Files.touch(roi)
+ roi
+ }
private def copyFile(name: String): Unit = {
val is = getClass.getResourceAsStream("/" + name)
--
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