positionGapToSeq

Function

positionGapToSeq

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

positionGapToSeq(gaps, pos)

Include Headers

seqan/store.h

Parameters

gaps	Contig gaps from fragment store. Types: AnchorGaps
pos	Position in gap space.

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 sequence space.

Examples

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

Converts position aligned read with index idx in the aligned read store.

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

typedef typename TFragmentStore::TAlignedReadStore                   TAlignedReadStore;
typedef typename Value<TAlignedReadStore>::Type                      TAlignedRead;
typedef typename TAlignedRead::TPos                                  TAlignedReadPos;

unsigned contigId = alignedReadStore[idx].contigId;
TContigGaps contigGaps(contigStore[contigId].seq, contigStore[contigId].gaps);
TAlignedRead const & alignedRead = alignedReadStore[idx];
// Translate end position from aligned read record to sequence space in reference.
TAlignedReadPos endPos = positionGapToSeq(contigGaps, alignedRead.endPos);

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

Converts position aligned read with index idx in the aligned read store.

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

typedef typename TFragmentStore::TAlignedReadStore                   TAlignedReadStore;
typedef typename Value<TAlignedReadStore>::Type                      TAlignedRead;
typedef typename TAlignedRead::TPos                                  TAlignedReadPos;

unsigned contigId = alignedReadStore[idx].contigId;
TContigGaps contigGaps(Nothing(), contigStore[contigId].gaps);
TAlignedRead const & alignedRead = alignedReadStore[idx];
// Translate end position from aligned read record to sequence space in reference.
TAlignedReadPos endPos = positionGapToSeq(contigGaps, alignedRead.endPos);