/** * Returns the read's unclipped start if the read is on the forward strand, or the read's * unclipped end if the read is on the reverse strand. * * @param read read whose stranded unclipped start to retrieve * @return the read's unclipped start if the read is on the forward strand, or the read's * unclipped end if the read is on the reverse strand. */ public static int getStrandedUnclippedStart(final GATKRead read) { return read.isReverseStrand() ? read.getUnclippedEnd() : read.getUnclippedStart(); }