void Application::processReverseFeature(int featureBegin,
const BOOM::String &seq)
{
int end=featureBegin;
int begin=featureBegin-margin;
if(begin<0) begin=0;
BOOM::String subseq=
BOOM::ProteinTrans::reverseComplement(seq.substr(begin,end-begin));
margins.push_back(subseq);
}
void Application::processForwardFeature(int featureEnd,
const BOOM::String &seq)
{
int begin=featureEnd;
int end=begin+margin;
int len=seq.length();
if(end>=len) end=len-1;
BOOM::String subseq=seq.substr(begin,end-begin);
margins.push_back(subseq);
}