Fixes/remove phased check (#13)

* Remove phased check since its decided on user specification. * remove unused phasing autodetect method
genepi · Dec 18, 2024 · ace1b08 · ace1b08
1 parent d3403f9
commit ace1b08
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diff --git a/src/main/java/genepi/imputationserver/steps/InputValidationCommand.java b/src/main/java/genepi/imputationserver/steps/InputValidationCommand.java
@@ -194,11 +194,6 @@ private boolean checkVcfFiles() throws Exception {
 
 				phased = phased && vcfFile.isPhased();
 
-				if (vcfFile.isPhasedAutodetect() && !vcfFile.isPhased()) {
-					output.error("File should be phased, but also includes unphased and/or missing genotypes! Please double-check!");
-					return false;
-				}
-
 				if (noSamples < minSamples && minSamples != 0) {
 					output.error("At least " + minSamples + " samples must be uploaded.");
 					return false;

diff --git a/src/main/java/genepi/imputationserver/steps/vcf/VcfFile.java b/src/main/java/genepi/imputationserver/steps/vcf/VcfFile.java
@@ -23,8 +23,6 @@ public class VcfFile {
 
 	private boolean chrX = false;
 
-	private boolean phasedAutodetect = true;
-
 	private int chunkSize;
 
 	private boolean chrPrefix;
@@ -135,14 +133,6 @@ public String getType() {
 		}
 	}
 
-	public boolean isPhasedAutodetect() {
-		return phasedAutodetect;
-	}
-
-	public void setPhasedAutodetect(boolean phasedAutodetect) {
-		this.phasedAutodetect = phasedAutodetect;
-	}
-
 	public void setChunkSize(int chunkSize) {
 		this.chunkSize = chunkSize;
 	}

diff --git a/src/main/java/genepi/imputationserver/steps/vcf/VcfFileUtil.java b/src/main/java/genepi/imputationserver/steps/vcf/VcfFileUtil.java
@@ -36,7 +36,6 @@ public static VcfFile load(String vcfFilename, int chunksize, boolean createInde
 			LineReader lineReader = new LineReader(vcfFilename);
 
 			boolean phased = true;
-			boolean phasedAutodetect = true;
 			boolean firstLine = true;
 			while (lineReader.next()) {
 
@@ -64,20 +63,6 @@ public static VcfFile load(String vcfFilename, int chunksize, boolean createInde
 
 					}
 
-					if (firstLine) {
-						boolean containsSymbol = tiles[9].contains("/") || tiles[9].contains(".");
-
-						if (!containsSymbol) {
-							phasedAutodetect = true;
-						} else {
-							phasedAutodetect = false;
-						}
-						firstLine = false;
-
-					}
-
-					// TODO: check that all are phased
-					// context.getGenotypes().get(0).isPhased();
 					chromosomes.add(chromosome);
 					if (chromosomes.size() > 1) {
 						throw new IOException(
@@ -154,7 +139,6 @@ public static VcfFile load(String vcfFilename, int chunksize, boolean createInde
 			pair.setRawChromosomes(rawChromosomes);
 			pair.setChrPrefix(hasChrPrefix);
 			pair.setPhased(phased);
-			pair.setPhasedAutodetect(phasedAutodetect);
 			pair.setChunkSize(chunksize);
 			return pair;