/** appends a sorted list of hits to an existing set of hits. */ public void appendSingleHits(SingleHit[] hits, String prefix, int chrom) throws IOException { if (hits.length == 0) { return; } int s = getPositionsBuffer().limit() - 1; SingleHit last = new SingleHit( chrom, getPositionsBuffer().get(s), getWeightsBuffer().get(s), Hits.getStrandOne(getLASBuffer().get(s)), Hits.getLengthOne(getLASBuffer().get(s))); if (hits[0].compareTo(last) > 0) { append(hits, prefix, chrom); } else { merge(hits, prefix, chrom); } }