if  (fullName.contains("BaseCalled_2D")){
<BUG>toks[0] = toks[0].substring(1) + "_twodimentional" + " length=" + toks[1].length() ;
</BUG>
seqList.add(new BaseCalledFastq(DNA.DNA16(), toks, BaseCalledFastq.TWODIM));
}else if (fullName.contains("BaseCalled_complement")){
<BUG>toks[0] = toks[0].substring(1) + "_complement" + " length=" + toks[1].length() ;
</BUG>
seqList.add(new BaseCalledFastq(DNA.DNA16(), toks, BaseCalledFastq.COMPLEMENT));
}else if (fullName.contains("BaseCalled_template")){
<BUG>toks[0] = toks[0].substring(1) + "_template" + " length=" + toks[1].length();
</BUG>
seqList.add(new BaseCalledFastq(DNA.DNA16(), toks, BaseCalledFastq.TEMPLATE));

if  (fullName.contains("BaseCalled_2D")){
out.print(toks[0] + "_twodimentional path=" + fullName);
}else if (fullName.contains("BaseCalled_complement")){
out.print(toks[0] + "_complement path=" + fullName);
}else if (fullName.contains("BaseCalled_template")){
out.print(toks[0] + "_template path=" + fullName);
}else
out.print(toks[0] + "_unknown path=" + fullName);
out.print('\n');
out.print(toks[1]);
out.print('\n');
