Struct AlignmentChain

Holds a chain of local alignments that form a compound alignment. An AlignmentChain should contain at least one element.

Fields

Name	Type	Description
contigA	Contig
contigB	Contig
flags	std.typecons.BitFlags!(dentist.common.alignments.base.Flag,0)
id	ulong
localAlignments	AlignmentChain.LocalAlignment[]
tracePointDistance	ushort

Properties

Name	Type	Description
averageErrorRate[get]	double	Average diffs per base pair over all local alignments.
beginsWith[set]	bool	This alignment begins within allowance of the begin of contig.
completelyCovers[set]	bool	Returns true iff this alignment covers contig completely within allowance.
coveredBases[get]	size_t	Sum of bases covered by each local alignment on contig A. Some bases may be counted multiple times.
disabledInstance[get]	AlignmentChain	Return a minimal AlignmentChain with the disabled flag set.
endsWith[set]	bool	This alignment ends within allowance of the end of contig.
first[get]	const(AlignmentChain.LocalAlignment)	Return first local alignment.
isProper[set]	bool	This alignment is called proper iff it starts and ends at a contig boundary within allowance.
last[get]	const(AlignmentChain.LocalAlignment)	Return last local alignment.
totalDiffs[get]	ulong	Sum of differences in each local alignment.

Methods

Name	Description
cartoon ()	Generate a cartoon of this alignment relative to contig.
compareIds (other)	Compare this alignment chain to other only by contig IDs.
cropToTracePoint (startingSeed, contigPos, roundingMode)	Crops this local alignment from startingSeed (begin or end of alignment chain) to contigPos.
disableIf (disable)	Set the disable flag if disable == true unless it is already set.
fromJson (json)	Convert to/from vibed.data.json.Json.
isFullyContained ()	Returns true if the aligned read contigB (with extensions on either end) is fully contained in the reference contigA.
opCmp (other)	Compare this alignment chain to other. Sort order is determined by these criteria:
toFlatLocalAlignments ()	Split this alignment chain into a range of FlatLocalAlignments. The resulting alignment are flagged appropriately to make reconstruction of the chain possible.
toJson ()	Convert to/from vibed.data.json.Json.
translateTracePoint (contigPos, roundingMode)	Translate contigPos on contig to a position on the other contig without exact alignment reconstruction. The first local alignment that covers contigPos is selected for translation.
coveringLocalAlignmentIndex (contigPos, roundingMode)	Return the index of the first local alignment that covers contigPos.

Inner structs

Name	Description
LocalAlignment