void Realigner::SetClipping(int clipping, bool is_forward_strand)
{
//DVK
// These settings are set for a forward strand read
switch (clipping) {
case 0: // align full strings, no clipping in read or ref
start_anywhere_in_ref_ = false;
stop_anywhere_in_ref_ = false;
soft_clip_left_ = false;
soft_clip_right_ = false; break;
case 1: // start or end anywhere in ref
start_anywhere_in_ref_ = true;
stop_anywhere_in_ref_ = true;
soft_clip_left_ = false;
soft_clip_right_ = false; break;
case 2: // semi-global + soft-clip bead end of the read
start_anywhere_in_ref_ = true;
stop_anywhere_in_ref_ = true;
soft_clip_left_ = false;
soft_clip_right_ = true; break;
case 3: // semi-global + soft-clip key end of the read
start_anywhere_in_ref_ = true;
stop_anywhere_in_ref_ = true;
soft_clip_left_ = true;
soft_clip_right_ = false; break;
case 4: // semi-global + soft-clip both ends of read
start_anywhere_in_ref_ = true;
stop_anywhere_in_ref_ = true;
soft_clip_left_ = true;
soft_clip_right_ = true; break;
}
// Adjust for read strand
SetStrand(is_forward_strand);
if (!is_forward_strand)
ReverseClipping();
if (verbose_ and debug_) {
cout << "Clipping settings for read from the ";
if (is_forward_strand) cout << "forward ";
else cout << "reverse ";
cout << "strand:" << endl
<< "start_anywhere_in_ref_" << start_anywhere_in_ref_ << endl
<< "stop_anywhere_in_ref_" << stop_anywhere_in_ref_ << endl
<< "soft_clip_left_" << soft_clip_left_ << endl
<< "soft_clip_right_" << soft_clip_right_ << endl << endl;
}
}
// ----------------------------------------------------------------------------
void CGffFeatureRecord::SetLocation(
const CSeq_interval& interval)
// ----------------------------------------------------------------------------
{
m_pLoc.Reset(new CSeq_loc());
m_pLoc->SetInt().Assign(interval);
if ( interval.CanGetFrom() ) {
mSeqStart = interval.GetFrom();
}
if ( interval.CanGetTo() ) {
mSeqStop = interval.GetTo();
}
unsigned int seqStart = Location().GetStart(eExtreme_Positional);
unsigned int seqStop = Location().GetStop(eExtreme_Positional);
string min = NStr::IntToString(seqStart + 1);
string max = NStr::IntToString(seqStop + 1);
if (Location().IsPartialStart(eExtreme_Biological)) {
if (Location().GetStrand() == eNa_strand_minus) {
SetAttribute("end_range", max + string(",."));
}
else {
SetAttribute("start_range", string(".,") + min);
}
}
if (Location().IsPartialStop(eExtreme_Biological)) {
if (Location().GetStrand() == eNa_strand_minus) {
SetAttribute("start_range", string(".,") + min);
}
else {
SetAttribute("end_range", max + string(",."));
}
}
if ( interval.IsSetStrand() ) {
SetStrand(interval.GetStrand());
}
}
void CPacked_seqpnt::FlipStrand(void)
{
if (IsSetStrand()) {
SetStrand(Reverse(GetStrand()));
}
}
void CSeq_interval::FlipStrand(void)
{
if (IsSetStrand()) {
SetStrand(Reverse(GetStrand()));
}
}
