/**
* If a read ends in INSERTION, returns the last element length.
*
* <p>Warning: If the read has Hard or Soft clips after the insertion this function will return 0.
*
* @param read
* @return the length of the last insertion, or 0 if there is none (see warning).
*/
public static int getLastInsertionOffset(final GATKRead read) {
final CigarElement e = read.getCigar().getCigarElement(read.getCigar().numCigarElements() - 1);
if (e.getOperator() == CigarOperator.I) {
return e.getLength();
} else {
return 0;
}
}
/**
* Pre-processes the results of {@link #getReadCoordinateForReferenceCoordinate(int, Cigar, int,
* boolean)} to take care of two corner cases:
*
* <p>1. If clipping the right tail (end of the read) getReadCoordinateForReferenceCoordinate and
* fall inside a deletion return the base after the deletion. If clipping the left tail (beginning
* of the read) it doesn't matter because it already returns the previous base by default.
*
* <p>2. If clipping the left tail (beginning of the read) getReadCoordinateForReferenceCoordinate
* and the read starts with an insertion, and you're requesting the first read based coordinate,
* it will skip the leading insertion (because it has the same reference coordinate as the
* following base).
*
* @return the read coordinate corresponding to the requested reference coordinate for clipping.
*/
public static int getReadCoordinateForReferenceCoordinate(
final GATKRead read, final int refCoord, final ClippingTail tail) {
return getReadCoordinateForReferenceCoordinate(
getSoftStart(read), read.getCigar(), refCoord, tail, false);
}
public static int getReadCoordinateForReferenceCoordinateUpToEndOfRead(
final GATKRead read, final int refCoord, final ClippingTail tail) {
final int leftmostSafeVariantPosition = Math.max(getSoftStart(read), refCoord);
return getReadCoordinateForReferenceCoordinate(
getSoftStart(read), read.getCigar(), leftmostSafeVariantPosition, tail, false);
}
/**
* Calculates the reference coordinate for the end of the read taking into account soft clips but
* not hard clips.
*
* <p>Note: getUnclippedEnd() adds soft and hard clips, this function only adds soft clips.
*
* @return the unclipped end of the read taking soft clips (but not hard clips) into account
*/
public static int getSoftEnd(final GATKRead read) {
return getSoftEnd(read, read.getCigar());
}
/**
* Calculates the reference coordinate for the beginning of the read taking into account soft
* clips but not hard clips.
*
* <p>Note: getUnclippedStart() adds soft and hard clips, this function only adds soft clips.
*
* @return the unclipped start of the read taking soft clips (but not hard clips) into account
*/
public static int getSoftStart(final GATKRead read) {
Utils.nonNull(read);
return getSoftStart(read, read.getCigar());
}