Fix issue with hg38 and tabix (#6)

src/main/java/genepi/imputationserver/steps/QualityControlCommand.java

@@ -434,4 +434,7 @@ protected TaskResults runTask(final OutputWriter output, ITask task) {
 
 	}
 
+	public void setBuild(String build) {
+		this.build = build;
+	}
 }

src/main/java/genepi/imputationserver/steps/fastqc/StatisticsTask.java

@@ -239,7 +239,7 @@ public void processFile(VcfFile myvcfFile, LineWriter mafWriter, LineWriter excl
 			}
 
 			// load reference snp
-			SitesEntry refSnp = legendReader.findByPosition(myvcfFile.getChromosome(), snp.getStart());
+			SitesEntry refSnp = legendReader.findByPosition(myvcfFile.getRawChromosome(), snp.getStart());
 
 			for (VcfChunk openChunk : chunks.values()) {
 				if (snp.getStart() <= openChunk.getEnd() + phasingWindow) {

src/test/java/genepi/imputationserver/steps/QualityControlCommandTest.java

@@ -45,6 +45,38 @@ public void testQcStatistics() throws Exception {
 
 	}
 
+	@Test
+	public void testQcStatisticsChr20Hg19() throws Exception {
+
+		String inputFolder = "test-data/data/chr20-phased";
+
+		QualityControlCommand command = buildCommand(inputFolder);
+		command.setPopulation("eur");
+		command.setReference("test-data/configs/hapmap-chr20/hapmap2.json");
+		command.call();
+		OutputReader log = new OutputReader(CLOUDGENE_LOG);
+		assertTrue(log.hasInMemory("Remaining sites in total: 7,735"));
+
+	}
+	@Test
+	public void testQcStatisticsChr20Hg38() throws Exception {
+
+		String inputFolder = "test-data/data/chr20-phased-hg38";
+
+		QualityControlCommand command = buildCommand(inputFolder);
+		command.setPopulation("eur");
+		command.setBuild("hg38");
+		//set the following file in hapmap2: hapmap_r22.chr20.CEU.hg38_impute.legend.gz
+		command.setReference("test-data/configs/hapmap-chr20-hg38/hapmap2.json");
+		command.call();
+
+		OutputReader log = new OutputReader(CLOUDGENE_LOG);
+		log.view();
+		assertTrue(log.hasInMemory("Remaining sites in total: 7,735"));
+
+	}
+
+
 	@Test
 	public void testQcStatisticAllChunksExcluded() throws Exception {