if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
{
System.err.println("Couldn't reconstruct sequence.\n" +
- gen_sgapped_s.getSequence() + "\n" +
- s_gapped.getSequence());
+ gen_sgapped_s.getSequenceAsString() + "\n" +
+ s_gapped.getSequenceAsString());
return false;
}
return true;
+ "\nCigar String:" + sub_se_gp.getCigarstring() + "\n"
);
SequenceI ssgp = sub_se_gp.getSeq('-');
- System.out.println("\t " + ssgp.getSequence());
+ System.out.println("\t " + ssgp.getSequenceAsString());
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" +
- al.getSequenceAt(i).getSequence());
+ al.getSequenceAt(i).getSequenceAsString());
}
}
{
System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
al.getSequenceAt(i).getStart() + "\t" +
al.getSequenceAt(i).getEnd() + "\t" +
- al.getSequenceAt(i).getSequence());
+ al.getSequenceAt(i).getSequenceAsString());
}
}
// if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))