update test case for invalid chrX alleles

genepi · Apr 10, 2018 · 1064905 · 1064905
1 parent f49c8c4
commit 1064905
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/src/main/java/genepi/imputationserver/steps/fastqc/StatisticsTask.java b/src/main/java/genepi/imputationserver/steps/fastqc/StatisticsTask.java
@@ -661,7 +661,7 @@ public List<String> prepareChrX(String filename, boolean phased, LineWriter chrX
 		vcfChunkWriterNonPar.writeHeader(header);
 		vcfChunkWriterPar1.writeHeader(header);
 		vcfChunkWriterPar2.writeHeader(header);
-		
+
 		int mixedGenotypes[] = null;
 		int count = 0;
 
@@ -673,7 +673,6 @@ public List<String> prepareChrX(String filename, boolean phased, LineWriter chrX
 			nonParEnd = 155701383;
 		}
 
-
 		VCFCodec codec = new VCFCodec();
 		codec.setVCFHeader(vcfReader.getFileHeader(), VCFHeaderVersion.VCF4_1);
 		LineReader reader = new LineReader(filename);
@@ -696,7 +695,7 @@ public List<String> prepareChrX(String filename, boolean phased, LineWriter chrX
 					continue;
 				}
 
-				//now decode, since it's valid
+				// now decode, since it's a valid VCF
 				VariantContext line = codec.decode(lineString);
 
 				if (line.getContig().equals("23")) {

diff --git a/src/test/java/genepi/imputationserver/steps/FastQualityControlTest.java b/src/test/java/genepi/imputationserver/steps/FastQualityControlTest.java
@@ -371,7 +371,10 @@ public void testChrXInvalidAlleles() throws IOException, ZipException {
 		FastQualityControlMock qcStats = new FastQualityControlMock(configFolder);
 		boolean result = run(context, qcStats);
 
-		//FileUtil.deleteDirectory(file);
+		assertTrue(result);
+		assertTrue(context.hasInMemory("Invalid alleles: 190"));
+
+		FileUtil.deleteDirectory(file);
 
 	}