refseq.getStart() + start+((bounds[2]==0) ? -1 : bounds[2]));
// seq.checkValidRange(); probably not needed
seq.setDatasetSequence(refseq);
refseq.getStart() + start+((bounds[2]==0) ? -1 : bounds[2]));
// seq.checkValidRange(); probably not needed
seq.setDatasetSequence(refseq);
if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
{
System.err.println("Couldn't reconstruct sequence.\n" +
if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
{
System.err.println("Couldn't reconstruct sequence.\n" +
for (int r = 0; r < 10; r++)
{
sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
for (int r = 0; r < 10; r++)
{
sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
al.getSequenceAt(i).getStart() + "\t" +
al.getSequenceAt(i).getEnd() + "\t" +
System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
al.getSequenceAt(i).getStart() + "\t" +
al.getSequenceAt(i).getEnd() + "\t" +
System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
al.getSequenceAt(i).getStart() + "\t" +
al.getSequenceAt(i).getEnd() + "\t" +
System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
al.getSequenceAt(i).getStart() + "\t" +
al.getSequenceAt(i).getEnd() + "\t" +