Add refpanel option to limit allowed allele switches

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

@@ -189,6 +189,7 @@ public boolean run(WorkflowContext context) {
 		double sampleCallrate = panel.getQcFilterByKey("sampleCallrate");
 		double mixedGenotypesChrX = panel.getQcFilterByKey("mixedGenotypeschrX");
 		int strandFlips = (int) (panel.getQcFilterByKey("strandFlips"));
+		int alleleSwitches = (int) (panel.getQcFilterByKey("alleleSwitches"));
 		String ranges = panel.getRange();
 
 		if (ranges != null) {
@@ -336,6 +337,15 @@ else if (task.getStrandFlipSimple() + task.getStrandFlipAndAlleleSwitch() > stra
 			return false;
 		}
 
+		// Check if too many allele switches are detected
+		else if (task.getAlleleSwitch() > alleleSwitches) {
+			text.append("<br><b>Error:</b> More than " + alleleSwitches
+					+ " allele switches have been detected. Imputation cannot be started!");
+			context.error(text.toString());
+
+			return false;
+		}
+
 		else if (task.isChrXMissingRate()) {
 			text.append(
 					"<br><b>Error:</b> Chromosome X nonPAR region includes > 10 % mixed genotypes. Imputation cannot be started!");

src/main/java/genepi/imputationserver/util/RefPanel.java

@@ -13,6 +13,7 @@
 
 public class RefPanel {
 
+	public static final String ALLELE_SWITCHES = String.valueOf(Integer.MAX_VALUE);
 	public static final String STRAMD_FLIPS = "100";
 	public static final String SAMPLE_CALL_RATE = "0.5";
 	public static final String MIN_SNPS = "3";
@@ -57,6 +58,7 @@ public RefPanel() {
 		defaultQcFilter.put("sampleCallrate", SAMPLE_CALL_RATE);
 		defaultQcFilter.put("mixedGenotypeschrX", CHR_X_MIXED_GENOTYPES);
 		defaultQcFilter.put("strandFlips", STRAMD_FLIPS);
+		defaultQcFilter.put("alleleSwitches", ALLELE_SWITCHES);
 	}
 
 	public String getId() {

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

@@ -519,6 +519,47 @@ public void testQcStatisticsDontAllowStrandFlips() throws IOException {
 				"<b>Error:</b> More than -1 obvious strand flips have been detected. Please check strand. Imputation cannot be started!"));
 
 	}
+
+	public void testQcStatisticsAllowAlleleSwitches() throws IOException {
+
+		String configFolder = "test-data/configs/hapmap-3chr";
+		String inputFolder = "test-data/data/simulated-chip-3chr-imputation-switches";
+
+		// create workflow context
+		WorkflowTestContext context = buildContext(inputFolder, "hapmap2");
+
+		// create step instance
+		FastQualityControlMock qcStats = new FastQualityControlMock(configFolder);
+
+		// run and test
+		boolean result = run(context, qcStats);
+
+		// check statistics
+
+		assertTrue(context.hasInMemory("Excluded sites in total: 2,967"));
+		assertTrue(context.hasInMemory("Allele switch: 118,209"));
+	}
+
+	public void testQcStatisticsDontAllowAlleleSwitches() throws IOException {
+
+		String configFolder = "test-data/configs/hapmap-3chr";
+		String inputFolder = "test-data/data/simulated-chip-3chr-imputation-switches";
+
+		// create workflow context
+		WorkflowTestContext context = buildContext(inputFolder, "hapmap2-qcfilter-alleleswitches");
+
+		// create step instance
+		FastQualityControlMock qcStats = new FastQualityControlMock(configFolder);
+
+		// run and test
+		boolean result = run(context, qcStats);
+
+		// check statistics
+
+		assertTrue(context.hasInMemory("Excluded sites in total: 2,967"));
+		assertTrue(context.hasInMemory("Allele switch: 118,209"));
+		assertTrue(context.hasInMemory("<b>Error:</b> More than 33 allele switches have been detected. Instructions to solve this issue can be found in our documentation. Imputation cannot be started!"));
+	}
 
 	public void testQcStatisticsFilterOverlap() throws IOException {
 

test-data/configs/hapmap-3chr/panels.txt

@@ -71,4 +71,18 @@ panels:
     qcFilter:
      sampleCallrate: 1.01   
      strandFlips: 100
+
+  - id: hapmap2-qcfilter-alleleswitches
+    hdfs: ref-panels/hapmap_r22.chr$chr.CEU.hg19.msav
+    legend: ref-panels/hapmap_r22.chr$chr.CEU.hg19_impute.legend.gz
+    mapEagle: ref-panels/genetic_map_hg19_chr1.txt
+    refEagle: ref-panels/hapmap_r22.eagle/hapmap_r22.chr$chr.CEU.hg19.recode.bcf
+    samples:
+      eur: 60
+      mixed: -1
+    populations:
+      eur: EUR
+      mixed: Mixed
+    qcFilter:
+      alleleSwitches: 33