private AlignmentBlock[] keepSoftClips(AlignmentBlock[] blocks) {
int numSoftCLippedBlocks = 0;
for (AlignmentBlock block : blocks) {
if (block.isSoftClipped()) numSoftCLippedBlocks++;
}
AlignmentBlock[] tmp = new AlignmentBlock[numSoftCLippedBlocks];
int j = 0;
for (int i = 0; i < numSoftCLippedBlocks; i++) {
AlignmentBlock block = blocks[j++];
if (block.isSoftClipped()) {
tmp[i] = block;
}
}
return tmp;
}
/**
* This method splits blocks whose boundaries contain a read deletion.
*
* @param blocks
* @param alignmentEntry
* @return
*/
private ObjectArrayList<AlignmentBlock> introduceDeletions(
ObjectArrayList<AlignmentBlock> blocks, Alignments.AlignmentEntry alignmentEntry) {
ObjectArrayList<AlignmentBlock> newBlocks = new ObjectArrayList<AlignmentBlock>();
for (Alignments.SequenceVariation var : alignmentEntry.getSequenceVariationsList()) {
for (AlignmentBlock block : blocks) {
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(
block.getStart(),
leftBases.toByteArray(new byte[leftBases.size()]),
leftScores.toByteArray(new byte[leftScores.size()]),
this);
AlignmentBlock right =
AlignmentBlock.getInstance(
block.getStart() + leftBases.size() + var.getFrom().length(),
rightBases.toByteArray(new byte[rightBases.size()]),
rightScores.toByteArray(new byte[rightScores.size()]),
this);
blocks.remove(block);
newBlocks.add(left);
newBlocks.add(right);
}
}
}
}
newBlocks.addAll(blocks);
return newBlocks;
}