Searched refs:MapOrigToEdited (Results 1 – 5 of 5) sorted by relevance
101 int p = amap.MapOrigToEdited(Exons()[i-1].GetTo()); in TranscriptExon()108 int p = amap.MapOrigToEdited(Exons()[i+1].GetFrom()); in TranscriptExon()126 l = amap.MapOrigToEdited(Exons()[1].GetFrom())-Exons().front().m_seq.length(); in TranscriptLimits()132 … r = amap.MapOrigToEdited(Exons()[Exons().size()-2].GetTo()) + Exons().back().m_seq.length(); in TranscriptLimits()139 r = amap.MapOrigToEdited(Exons()[1].GetFrom())+Exons().front().m_seq.length(); in TranscriptLimits()361 new_cds.Set5PrimeCdsLimit(amap.MapOrigToEdited(Start().GetFrom())); in MapFromOrigToEdited()363 new_cds.Set5PrimeCdsLimit(amap.MapOrigToEdited(Start().GetTo())); in MapFromOrigToEdited()1026 afirst = pmapa->MapOrigToEdited(firstcommonpoint); in isCompatible()1027 bfirst = pmapb->MapOrigToEdited(firstcommonpoint); in isCompatible()1031 TSignedSeqPos asecond = pmapa->MapOrigToEdited(left); in isCompatible()[all …]
175 _ASSERT( m_map.MapEditedToOrig(0) == From() && m_map.MapOrigToEdited(From()) == 0 ); in ConstructSequenceAndMaps()176 …_ASSERT( m_map.MapEditedToOrig((int)sequence.size()-1) == To() && m_map.MapOrigToEdited(To()) == (… in ConstructSequenceAndMaps()315 left = m_map.MapOrigToEdited(max(left,m_chunk_start)); in Init()317 right = m_map.MapOrigToEdited(min(right,m_chunk_stop)); in Init()334 int j = m_map.MapOrigToEdited(jj); in Init()
536 TSignedSeqPos p = amap.MapOrigToEdited(k); in IsAlternative()551 TSignedSeqPos p = gmap.MapOrigToEdited(k); in IsAlternative()3970 int jtr = amap.MapOrigToEdited(j); in SetFlagsForChains()4024 int jtr = amap.MapOrigToEdited(j); in SetFlagsForChains()4680 int a = amap.MapOrigToEdited(start.GetFrom()); in RestoreReasonableConfirmedStart()4681 int b = amap.MapOrigToEdited(start.GetTo()); in RestoreReasonableConfirmedStart()5287 int p = amap.MapOrigToEdited(abs(ithird_peak->first)); in MainPeaks()6653 …if(alignmap_clipped.MapOrigToEdited(left) < 0 || alignmap_clipped.MapOrigToEdited(right) < 0) … in transform_align()8102 int left_end = m_edited_contig_map.MapOrigToEdited(ig->Loc()); in SetGenomic()8118 int loc = m_edited_contig_map.MapOrigToEdited(ig->InDelEnd()); in SetGenomic()[all …]
814 orig_pos = MapOrigToEdited(orig_pos); in FShiftedMove()878 TSignedSeqPos CAlignMap::MapOrigToEdited(TSignedSeqPos orig_pos) const { in MapOrigToEdited() function in CAlignMap
648 TSignedSeqPos MapOrigToEdited(TSignedSeqPos orig_pos) const;