positionSeqToGap

Function

positionSeqToGap

Convert from sequence space on the reference to gap space in the global alignment.

positionGapToSeq(gaps, pos)

Include Headers

seqan/store.h

Parameters

gaps	Contig gaps from fragment store. Types: AnchorGaps
pos	Position in the reference.

Remarks

See the example below to construct the gaps object. Note that this construction is fast since it is only a thin wrapper around underlying objects.

Return Values

Position in the gap space of the global alignment space.

Examples

Convert from gap space to position space on contig contigId when the contigs required to be loaded.

typedef typename TFragmentStore::TContigStore                        TContigStore;
typedef typename Value<TContigStore>::Type                           TContig;
typedef typename TFragmentStore::TContigSeq                          TContigSeq;
typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;

TContigGaps contigGaps(contigStore[contigId].seq, contigStore[contigId].gaps);
TAlignedReadPos pos = positionGapToSeq(contigGaps, 33);

Convert from gap space to position space on contig contigId when the contigs are not required.

typedef typename TFragmentStore::TContigStore TContigStore;
typedef typename Value<TContigStore>::Type TContig;
typedef Gaps<Nothing, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;

TContigGaps contigGaps(Nothing(), contigStore[contigId].gaps);
TAlignedReadPos endPos = positionGapToSeq(contigGaps, 33);