From 480684fb9bcb9b2c4acc362573aeb0aa76a507bc Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Fri, 14 Aug 2015 11:43:04 +0200
Subject: [PATCH] > 85% class coverage for BastyGenerateFasta
---
.../nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala | 3 +++
.../lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala | 9 +++++++++
2 files changed, 12 insertions(+)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
index deb9aa38c..b682eda9d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
@@ -172,9 +172,12 @@ object BastyGenerateFasta extends ToolCommand {
if (cmdArgs.outputConsensus != null || cmdArgs.outputConsensusVariants != null) {
writeConsensus()
}
+
+ //FIXME: what to do if outputcConsensus is set, but not outputConsensusVariants (and vice versa)?
}
protected def writeConsensus() {
+ //FIXME: preferably split this up in functions, so that they can be unit tested
val referenceFile = new IndexedFastaSequenceFile(cmdArgs.reference)
val referenceDict = referenceFile.getSequenceDictionary
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
index dea9abb7f..d67f36517 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
@@ -47,6 +47,15 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
main(arguments)
}
+ @Test def testMainVcfAndBamMore = {
+ val tmp = File.createTempFile("basty_out", ".fa")
+ val tmppath = tmp.getAbsolutePath
+ tmp.deleteOnExit()
+
+ val arguments = Array("-V", chrQ_path, "--outputConsensus", tmppath, "--outputConsensusVariants", tmppath, "--bamFile", bam_path, "--sampleName", "Child_7006504", "--reference", chrQRef_path, "--outputName", "test")
+ main(arguments)
+ }
+
@Test def testGetMaxAllele = {
val reader = new VCFFileReader(vepped, false)
val record = reader.iterator().next()
--
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