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merge in MNV fixes from hotfix 1.5.x branch #198

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merge in MNV fixes from hotfix 1.5.x branch #198

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b26f49f
merge in MNV fixes from hotfix 1.5.x branch
julie-sullivan Jan 20, 2021
c723a3b
fix merge error
julie-sullivan Feb 26, 2021
8d66574
Merge branch 'opencb:develop' into develop
julie-sullivan Sep 28, 2022
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13 changes: 10 additions & 3 deletions biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantNormalizer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -978,10 +978,15 @@ public static List<VariantKeyFields> decomposeAlignmentSingleVariants(String ref
VariantKeyFields keyFields = null;
char previousReferenceChar = 0;
char previousAlternateChar = 0;
int originalKeyFieldsIndex = 0;
// Assume that as a result of the alignment "reference" and "alternate" Strings are of the same length
for (int i = 0; i < reference.length(); i++) {
char referenceChar = reference.charAt(i);
char alternateChar = alternate.charAt(i);
if (referenceChar != '-') {
// keep track where we are in the original reference
originalKeyFieldsIndex++;
}
// Insertion
if (referenceChar == '-') {
// Assume there cannot be a '-' at the reference and alternate aligned sequences at the same position
Expand All @@ -1003,16 +1008,18 @@ public static List<VariantKeyFields> decomposeAlignmentSingleVariants(String ref
// Current character is a continuation of a deletion
if (previousAlternateChar == '-') {
keyFields.setReference(keyFields.getReference() + referenceChar);
keyFields.setEnd(keyFields.getEnd()+1);
keyFields.setEnd(keyFields.getEnd() + 1);
// New deletion found, create new keyFields
} else {
keyFields = new VariantKeyFields(genomicStart + i, genomicStart + i,
int originalPosition = genomicStart + originalKeyFieldsIndex - 1;
keyFields = new VariantKeyFields(originalPosition, originalPosition,
String.valueOf(referenceChar),"", originalKeyFields);
keyFieldsList.add(keyFields);
}
// SNV
} else if (referenceChar != alternateChar) {
keyFields = new VariantKeyFields(genomicStart + i, genomicStart + i,
int originalPosition = genomicStart + originalKeyFieldsIndex - 1;
keyFields = new VariantKeyFields(originalPosition, originalPosition,
String.valueOf(referenceChar), String.valueOf(alternateChar), originalKeyFields);
keyFieldsList.add(keyFields);
}
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