if (!block.isSoftClipped()) {
final int vrPos = var.getPosition() + entry.getPosition();
if (hasReadDeletion(var) && vrPos >= block.getStart() && vrPos <= block.getEnd()) {
ByteList leftBases = new ByteArrayList(block.getBases());
ByteList leftScores = new ByteArrayList(block.getQualities());
ByteList rightBases = new ByteArrayList(block.getBases());
ByteList rightScores = new ByteArrayList(block.getQualities());
int deletionPosition = var.getPosition() - 1;
leftBases = leftBases.subList(0, deletionPosition);
rightBases = rightBases.subList(deletionPosition, rightBases.size());
leftScores = leftScores.subList(0, deletionPosition);
rightScores = rightScores.subList(deletionPosition, rightScores.size());
AlignmentBlock left = AlignmentBlock.getInstance(getChr(), block.getStart(),
leftBases.toByteArray(new byte[leftBases.size()]),
leftScores.toByteArray(new byte[leftScores.size()]));
AlignmentBlock right = AlignmentBlock.getInstance(getChr(), block.getStart() + leftBases.size()
+ var.getFrom().length(),
rightBases.toByteArray(new byte[rightBases.size()]),
rightScores.toByteArray(new byte[rightScores.size()]));
blocks.remove(block);
newBlocks.add(left);
newBlocks.add(right);