Searched refs:ai_rf (Results 1 – 1 of 1) sorted by relevance
2345 if(!Include(ai_rf,aj_rf)) in CanIncludeJinI()2348 if(ai_rf.GetFrom() != aj_rf.GetFrom()) { in CanIncludeJinI()2352 TSignedSeqPos i_from = mi.m_align_map->MapOrigToEdited(ai_rf.GetFrom()); in CanIncludeJinI()2561 int genome_overlap = ai_rf.GetLength()+aj_rf.GetLength()-(ai_rf+aj_rf).GetLength(); in LRCanChainItoJ()2570 …if((Include(ai_rf,aj_rf) || Include(aj_rf,ai_rf)) && ai_rf.GetFrom() != aj_rf.GetFrom() && ai_rf.G… in LRCanChainItoJ()2573 cds_overlap = mi.m_align_map->FShiftedLen(ai_rf&aj_rf,false); in LRCanChainItoJ()2621 mi.m_cds = mi.m_align_map->FShiftedLen(ai_rf,false); in LRIinit()2801 int genome_overlap = ai_rf.GetLength()+aj_rf.GetLength()-(ai_rf+aj_rf).GetLength(); in RightLeft()2810 …if((Include(ai_rf,aj_rf) || Include(aj_rf,ai_rf)) && ai_rf.GetFrom() != aj_rf.GetFrom() && ai_rf.G… in RightLeft()2813 cds_overlap = mi.m_align_map->FShiftedLen(ai_rf&aj_rf,false); in RightLeft()[all …]