From 78a9fc74c0a05da4d197f6e371b2f27ca667b64a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= Date: Wed, 18 Dec 2024 11:18:15 +0100 Subject: [PATCH 1/2] Remove phased check since its decided on user specification. --- .../imputationserver/steps/InputValidationCommand.java | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/main/java/genepi/imputationserver/steps/InputValidationCommand.java b/src/main/java/genepi/imputationserver/steps/InputValidationCommand.java index 94baa1c..a4aa529 100644 --- 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; From 921c8d5daa276df53e3c42d79c6ccbd1a453738a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= Date: Wed, 18 Dec 2024 13:34:01 +0100 Subject: [PATCH 2/2] remove unused phasing autodetect method --- .../imputationserver/steps/vcf/VcfFile.java | 10 ---------- .../imputationserver/steps/vcf/VcfFileUtil.java | 16 ---------------- 2 files changed, 26 deletions(-) diff --git a/src/main/java/genepi/imputationserver/steps/vcf/VcfFile.java b/src/main/java/genepi/imputationserver/steps/vcf/VcfFile.java index 72b694e..16e75a8 100644 --- 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 index 6bfd034..caa2762 100644 --- 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;