(FORK COMMIT) Consider flip+switch in QC filters; add these variants …

…to excluded snps filter Refs genepi#137
statgen · Apr 18, 2024 · 0d15b69 · 0d15b69
1 parent d24f2e5
commit 0d15b69
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/src/main/java/genepi/imputationserver/steps/FastQualityControl.java b/src/main/java/genepi/imputationserver/steps/FastQualityControl.java
@@ -338,7 +338,7 @@ else if (task.getStrandFlipSimple() + task.getStrandFlipAndAlleleSwitch() > stra
 		}
 
 		// Check if too many allele switches are detected
-		else if (task.getAlleleSwitch() > alleleSwitches) {
+		else if ((task.getAlleleSwitch() + task.getStrandFlipAndAlleleSwitch()) > alleleSwitches) {
 			text.append("<br><b>Error:</b> More than " + alleleSwitches
 					+ " allele switches have been detected. Imputation cannot be started!");
 			context.error(text.toString());

diff --git a/src/main/java/genepi/imputationserver/steps/fastqc/StatisticsTask.java b/src/main/java/genepi/imputationserver/steps/fastqc/StatisticsTask.java
@@ -481,12 +481,15 @@ else if (GenomicTools.alleleSwitch(snp, refSnp)) {
 				if (insideChunk) {
 
 					alleleSwitch++;
+					filtered++;
+					excludedSnpsWriter.write(snp + "\t" + "Allele switch" + "\t" + "Ref:" + legendRef + "/" + legendAlt);
 					/*
 					 * logWriter.write("Allele switch" + snp.getID() + "\t" + chr + ":"+
 					 * snp.getStart() + "\t" + "ref: " + legendRef + "/" + legendAlt + "; data: " +
 					 * studyRef + "/" + studyAlt + ")");
 					 */
 				}
+				return;
 
 			}