https://www.biostars.org/p/394289/ : Extracting reads mapping to CDS regions but not the first 45bp after ATG gtf cds

bioalcidae.code

stream().
	flatMap(G->G.getTranscripts().stream()).
	filter(T->T.getCodonStart().isPresent() && T.getCodonStop().isPresent() && T.hasStrand()).
	forEach(T->{
	
	List<Integer> positions = new ArrayList<>();
	for(com.github.lindenb.jvarkit.util.bio.structure.Cds cds : T.getAllCds()) {
		for(int x=cds.getStart();x<=cds.getEnd();++x) positions.add(x);
		}
	if(positions.size() <= 45) return;
	if(T.isPositiveStrand()) {
		positions = positions.subList(45,positions.size());	
		}
	else {
		positions = positions.subList(0,positions.size()-45);	
		}
	int i=0;
	while(i<positions.size()) {
		int beg =i;
		while(i+1 < positions.size() && positions.get(i)+1==positions.get(i+1))
			{
			i++;
			}
		println(T.getContig()+"\t"+(positions.get(beg)-1)+"\t"+positions.get(i)+"\t"+T.getId());
		i++;
		}
	});