Removed unnecessary print line from the bgen writer.

Renamed erroneously named method. Resolved issues still present in the vcf field picker
molgenis · Dec 15, 2022 · c3588bd · c3588bd
1 parent 79f8df9
commit c3588bd
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Showing 3 changed files with 55 additions and 22 deletions.
diff --git a/Genotype-IO/src/main/java/org/molgenis/genotype/bgen/BgenGenotypeWriter.java b/Genotype-IO/src/main/java/org/molgenis/genotype/bgen/BgenGenotypeWriter.java
@@ -301,8 +301,7 @@ private void addMetaData(File bgenFile, BgenixWriter bgenixWriter) throws IOExce
 		byte[] firstBytes = new byte[1000];
 		randomAccessBgenFile.read(firstBytes, 0, 1000);
 
-		//Add current time in int.
-		System.out.println((System.currentTimeMillis() / 1000L));
+		// Add current time in int.
 		// Create and write new metadata.
 		BgenixMetadata m = new BgenixMetadata(
 				bgenFile.getName(),

diff --git a/Genotype-IO/src/main/java/org/molgenis/genotype/vcf/VcfGenotypeData.java b/Genotype-IO/src/main/java/org/molgenis/genotype/vcf/VcfGenotypeData.java
@@ -324,7 +324,7 @@ public boolean arePhasedProbabilitiesPresent(GeneticVariant variant) {
         LinkedHashSet<VcfGenotypeFormat> haplotypeProbabilitiesFields = getVcfHaplotypeFormats(variant);
 
         // If the requested format is set and present for this variant base decision on this format
-        return genotypeFormatSupplier.VcfGenotypeFormatReadable(
+        return genotypeFormatSupplier.vcfGenotypeFormatReadable(
                 vcfRecord, haplotypeProbabilitiesFields);
     }
 

diff --git a/...O/src/main/java/org/molgenis/genotype/vcf/VcfGenotypeField/VcfGenotypeFormatSupplier.java b/...O/src/main/java/org/molgenis/genotype/vcf/VcfGenotypeField/VcfGenotypeFormatSupplier.java
@@ -54,24 +54,36 @@ public VcfGenotypeFormat getVcfGenotypeFormat(
 
         List<String> formatIdentifiers = Arrays.asList(vcfRecord.getFormat());
 
-        if (preferredGenotypeFormat != null
-                && genotypeDosageFieldPrecedence.contains(preferredGenotypeFormat)
-                && formatIdentifiers.contains(this.getGenotypeFormatIdentifier(preferredGenotypeFormat))) {
-            return preferredGenotypeFormat;
-        }
-
-        if (this.forcePreferredGenotypeFormat) {
-            throw new GenotypeDataException(String.format(
-                    "Preferred genotype format field (%s) is unavailable for vcf record: %n%s (%s:%s). " +
-                            "Available format fields: %s",
-                    preferredGenotypeFormatIdentifier,
-                    String.join(", ", vcfRecord.getIdentifiers()),
-                    vcfRecord.getChromosome(), vcfRecord.getPosition(),
-                    String.join(", ", vcfRecord.getFormat())));
+        // Check if the preferred genotype format is set
+        if (preferredGenotypeFormat != null) {
+            // If it is set, check if it is available, and, if it is not, if we should write exceptions or not.
+            if (genotypeDosageFieldPrecedence.contains(preferredGenotypeFormat)
+                    && isGenotypeFormatPresent(formatIdentifiers, preferredGenotypeFormat)) {
+                return preferredGenotypeFormat;
+            } else if (this.forcePreferredGenotypeFormat) {
+                if (!isGenotypeFormatPresent(formatIdentifiers, preferredGenotypeFormat)) {
+                    throw new GenotypeDataException(String.format(
+                            "Preferred genotype format field (%s) is unavailable for vcf record: %n%s (%s:%s). " +
+                                    "Available format fields: %s",
+                            preferredGenotypeFormatIdentifier,
+                            String.join(", ", vcfRecord.getIdentifiers()),
+                            vcfRecord.getChromosome(), vcfRecord.getPosition(),
+                            String.join(", ", vcfRecord.getFormat())));
+                } else if (!genotypeDosageFieldPrecedence.contains(preferredGenotypeFormat)) {
+                    throw new GenotypeDataException(String.format(
+                            "Preferred genotype format field (%s) cannot be used. " +
+                                    "Requested to load vcf record %n%s (%s:%s). " +
+                                    "Possible format fields: %s",
+                            preferredGenotypeFormatIdentifier,
+                            String.join(", ", vcfRecord.getIdentifiers()),
+                            vcfRecord.getChromosome(), vcfRecord.getPosition(),
+                            String.join(", ", Arrays.toString(genotypeDosageFieldPrecedence.toArray()))));
+                }
+            }
         }
 
         for (VcfGenotypeFormat genotypeFormat: genotypeDosageFieldPrecedence) {
-            if (formatIdentifiers.contains(this.getGenotypeFormatIdentifier(genotypeFormat))) {
+            if (isGenotypeFormatPresent(formatIdentifiers, genotypeFormat)) {
                 return genotypeFormat;
             }
         }
@@ -90,26 +102,48 @@ public VcfGenotypeFormat getVcfGenotypeFormat(
      * the genotype field formats from the precedence list can be read from the vcf record.
      * If nothing matches these conditions, false is returned.
      */
-    public boolean VcfGenotypeFormatReadable(
+    public boolean vcfGenotypeFormatReadable(
             VcfRecord vcfRecord,
             LinkedHashSet<VcfGenotypeFormat> genotypeDosageFieldPrecedence) {
 
         List<String> formatIdentifiers = Arrays.asList(vcfRecord.getFormat());
 
+        // Test if the preferred genotype format is present
+        // Test if we should suppress exception if this is not the case
+        // Test if the
+
         if (preferredGenotypeFormat != null) {
-            return genotypeDosageFieldPrecedence.contains(preferredGenotypeFormat)
-                    && formatIdentifiers.contains(this.getGenotypeFormatIdentifier(preferredGenotypeFormat));
+            if (isGenotypeFormatPresent(formatIdentifiers, preferredGenotypeFormat)) {
+                return genotypeDosageFieldPrecedence.contains(preferredGenotypeFormat);
+            } else if (this.forcePreferredGenotypeFormat) {
+                throw new GenotypeDataException(String.format(
+                        "Preferred genotype format field (%s) is unavailable for vcf record: %n%s (%s:%s). " +
+                                "Available format fields: %s",
+                        preferredGenotypeFormatIdentifier,
+                        String.join(", ", vcfRecord.getIdentifiers()),
+                        vcfRecord.getChromosome(), vcfRecord.getPosition(),
+                        String.join(", ", vcfRecord.getFormat())));
+            }
         }
 
         for (VcfGenotypeFormat genotypeFormat: genotypeDosageFieldPrecedence) {
-            if (formatIdentifiers.contains(this.getGenotypeFormatIdentifier(genotypeFormat))) {
+            if (isGenotypeFormatPresent(formatIdentifiers, genotypeFormat)) {
                 return true;
             }
         }
 
         return false;
     }
 
+    public boolean isPreferredGenotypeFormatPresent(VcfRecord vcfRecord) {
+        List<String> formatIdentifiers = Arrays.asList(vcfRecord.getFormat());
+        return isGenotypeFormatPresent(formatIdentifiers, preferredGenotypeFormat);
+    }
+
+    private boolean isGenotypeFormatPresent(List<String> formatIdentifiers, VcfGenotypeFormat genotypeFormat) {
+        return formatIdentifiers.contains(this.getGenotypeFormatIdentifier(genotypeFormat));
+    }
+
     public VcfGenotypeFormat getPreferredGenotypeFormat() {
         return preferredGenotypeFormat;
     }