feature-vep-comparison: attempt to refine start_lost annotation for SNVs
@@ -267,9 +267,10 @@ public class ConsequenceTypeSNVCalculator extends ConsequenceTypeCalculator {
// The !transcript.unconfirmedStart condition may seem weird but it's correct. If coding start
// is clearly defined, can be considered start_lost variant
if (cdnaVariantPosition < (cdnaCodingStart + 3)
- && (!transcript.unconfirmedStart()
- || VariantAnnotationUtils.isStartCodon(MT.equals(variant.getChromosome()),
- String.valueOf(referenceCodon)))) {
+ && !transcript.unconfirmedStart()) {
+// && (!transcript.unconfirmedStart()
+// || VariantAnnotationUtils.isStartCodon(MT.equals(variant.getChromosome()),
+// String.valueOf(referenceCodon)))) {
// Gary - initiator codon SO terms not compatible with the terms below
SoNames.add(VariantAnnotationUtils.START_LOST);
if (VariantAnnotationUtils.isStopCodon(variant.getChromosome().equals("MT"),
@@ -528,8 +529,10 @@ public class ConsequenceTypeSNVCalculator extends ConsequenceTypeCalculator {
}
} else {
if (cdnaVariantPosition < (cdnaCodingStart + 3)
- && (!transcript.unconfirmedStart()
- || VariantAnnotationUtils.isStartCodon(MT.equals(variant.getChromosome()), referenceCodon))) {
+ && !transcript.unconfirmedStart()) {
+
+// && (!transcript.unconfirmedStart()
+// || VariantAnnotationUtils.isStartCodon(MT.equals(variant.getChromosome()), referenceCodon))) {
// Gary - initiator codon SO terms not compatible with the terms below
SoNames.add(VariantAnnotationUtils.START_LOST);
if (VariantAnnotationUtils.isStopCodon(MT.equals(variant.getChromosome()),
