int gapsToAdd = calculateGapsToInsert(preserveMappedGaps,
preserveUnmappedGaps, sourceGapMappedLength, inExon,
trailingCopiedGap.length(), intronLength, startOfCodon);
int gapsToAdd = calculateGapsToInsert(preserveMappedGaps,
preserveUnmappedGaps, sourceGapMappedLength, inExon,
trailingCopiedGap.length(), intronLength, startOfCodon);