15     TLiteInDels indels;  in BEGIN_SCOPE()  local
16     indels.reserve(sam_indels.size());  in BEGIN_SCOPE()
34                 indels.push_back(CLiteIndel(loc, insertlen));  in BEGIN_SCOPE()
36                 indels.push_back(CLiteIndel(loc+insertlen,deletion.size(),deletion));  in BEGIN_SCOPE()
50             indels.push_back(CLiteIndel(loc, insertlen));  in BEGIN_SCOPE()
52             indels.push_back(CLiteIndel(loc+insertlen,deletion.size(),deletion));  in BEGIN_SCOPE()
55     return indels;  in BEGIN_SCOPE()
58 CLiteAlign::CLiteAlign(TSignedSeqRange range, const TLiteInDels& indels, set<CLiteIndel>& indel_hol…  in CLiteAlign()  argument
61     m_indels.reserve(indels.size());  in CLiteAlign()
62     ITERATE( TLiteInDels, indl, indels) {  in CLiteAlign()
140     TLiteInDels indels = GroupInDels(sam_indels);  in CLiteAlign()  local
142     m_indels.reserve(indels.size());  in CLiteAlign()
143     ITERATE(TLiteInDels, indl, indels) {  in CLiteAlign()
233         TLiteInDels indels;  in AddAlignment()  local
236                 indels.push_back(CLiteIndel(indl->Loc(), indl->Len()));  in AddAlignment()
237 …    indels.push_back(CLiteIndel(indl->InDelEnd(), indl->Len(), indl->GetInDelV()));                  in AddAlignment()
239                 indels.push_back(CLiteIndel(indl->Loc(), indl->Len()));  in AddAlignment()
241                 indels.push_back(CLiteIndel(indl->Loc(), indl->Len(), indl->GetInDelV()));  in AddAlignment()
245 …m_aligns.push_back(CLiteAlign(exon_lim, GroupInDels(indels), m_indel_holder, align.Weight(), error…  in AddAlignment()
356         TLiteInDelsP indels = m_alignsp[ir]->GetInDels();  in InsertDashesInBase()  local
357         ITERATE(TLiteInDelsP, indl, indels) {  in InsertDashesInBase()
360                 if(indl != indels.begin()) {  in InsertDashesInBase()
421         TLiteInDelsP indels = m_alignsp[ir]->GetInDels();  in InsertDashesInReads()  local
423         ITERATE(TLiteInDelsP, indl, indels) {  in InsertDashesInReads()