develop: bug fixed regarding start_lost DELETION annotations
@@ -119,7 +119,8 @@ public class ConsequenceTypeDeletionCalculator extends ConsequenceTypeGenericReg
// ---NNNNNNNNCATTTTTTT
// deletion |---|
if (cdnaVariantStart != -1 && cdnaVariantEnd != -1
- && transcript.getCdnaCodingStart() - cdnaVariantEnd < 3) {
+ && (cdnaVariantEnd - transcript.getCdnaCodingStart()) < 3
+ && (cdnaVariantEnd - transcript.getCdnaCodingStart()) >= 0) {
solveStartCodonNegativeVariant(transcriptSequence, transcript.getCdnaCodingStart(),
cdnaVariantStart, cdnaVariantEnd);
} else {
@@ -229,7 +230,8 @@ public class ConsequenceTypeDeletionCalculator extends ConsequenceTypeGenericReg
// ---NNNNNNNNCATTTTTTT
// deletion |---|
if (cdnaVariantStart != -1 && cdnaVariantEnd != -1
- && transcript.getCdnaCodingStart() - cdnaVariantEnd < 3) {
+ && (cdnaVariantEnd - transcript.getCdnaCodingStart()) < 3
+ && (cdnaVariantEnd - transcript.getCdnaCodingStart()) >= 0) {
solveStartCodonPositiveVariant(transcriptSequence, transcript.getCdnaCodingStart(),
cdnaVariantStart, cdnaVariantEnd);
} else {
