dentist.common.scaffold

Work with scaffold graphs.

Members

Aliases

ContigNode alias ContigNode = Tuple!(size_t, "contigId", ContigPart, "contigPart"): A contig is represented by four ContigNodes in the scaffold graph.
Scaffold alias Scaffold(T) = Graph!(ContigNode, void, No.isDirected, T): Represents a set of joins which conclude possibly several scaffolding variants.

Enums

ContigPart enum ContigPart: Each contig has four designated parts where joins can start or end.
JoinPolicy enum JoinPolicy: Determine which kinds of joins are allowed.

Functions

buildScaffold Scaffold!T buildScaffold(in size_t numReferenceContigs, R rawJoins): Build a scaffold graph using rawJoins. This creates default edges and inserts the rawJoins.
discardAmbiguousJoins Scaffold!T discardAmbiguousJoins(Scaffold!T scaffold, in double bestPileUpMargin): This removes ambiguous gap insertions.
enforceJoinPolicy Scaffold!T enforceJoinPolicy(Scaffold!T scaffold, in JoinPolicy joinPolicy): Enforce joinPolicy in scaffold.
getDefaultJoin Join!T getDefaultJoin(size_t contigId)
Join!T getDefaultJoin(size_t contigId): Get the default join for contigId. Initialize payload with getPayload(contigId) if given.
getUnkownJoin Join!T getUnkownJoin(size_t preContigId, size_t postContigId, T payload): Get join for a stretch of unknown sequence (ns).
initScaffold Scaffold!T initScaffold(in size_t numReferenceContigs)
Scaffold!T initScaffold(in size_t numReferenceContigs): Creates a scaffold with all the default edges. Optionally specify a function that produces the payloads.
isAntiParallel bool isAntiParallel(in J join): Returns true iff join is a gap edge and anti-parallel.
isBackExtension bool isBackExtension(in J join): Returns true iff join is a back extension edge of the scaffold graph.
isDefault bool isDefault(in J join): Returns true iff join is a default edge of the scaffold graph.
isExtension bool isExtension(in J join): Returns true iff join is an extension edge of the scaffold graph.
isFrontExtension bool isFrontExtension(in J join): Returns true iff join is a front extension edge of the scaffold graph.
isGap bool isGap(in J join): Returns true iff join is a gap edge of the scaffold graph.
isParallel bool isParallel(in J join): Returns true iff join is a gap edge and parallel.
isUnkown bool isUnkown(in J join): Returns true iff join is a unknown edge, ie. an edge for unknown sequence (ns) of the scaffold graph.
isValid bool isValid(in J join): Returns true iff join is a valid edge of the scaffold graph.
linearWalk LinearWalk!T linearWalk(Scaffold!T scaffold, ContigNode startNode, Scaffold!T.IncidentEdgesCache incidentEdgesCache = Scaffold!T.IncidentEdgesCache.init)
LinearWalk!T linearWalk(Scaffold!T scaffold, ContigNode startNode, Join!T firstJoin, Scaffold!T.IncidentEdgesCache incidentEdgesCache = Scaffold!T.IncidentEdgesCache.init): Performs a linear walk through a scaffold graph starting in startNode. A linear walk is a sequence of adjacent joins where no node is visited twice unless the graph is cyclic in which case the first node will appear twice. The implementation requires the graph to have linear components, ie. for every node the degree must be at most two. If the component of startNode is cyclic then the walk will in startNode and the isCyclic flag will be set.
mergeExtensionsWithGaps Scaffold!T mergeExtensionsWithGaps(Scaffold!T scaffold): Remove extension edges were they coincide with a gap edge combining their payload. This is intended to build pile ups with all reads that contribute to each gap.
normalizeUnkownJoins Scaffold!T normalizeUnkownJoins(Scaffold!T scaffold): Normalizes unknown joins such that they join contigs or are removed as applicable.
removeExtensions Scaffold!T removeExtensions(Scaffold!T scaffold): Enforce joinPolicy in scaffold.
removeNoneJoins Scaffold!T removeNoneJoins(Scaffold!T scaffold): Remove marked edges from the graph. This always keeps the default edges.
scaffoldStarts auto scaffoldStarts(Scaffold!T scaffold, Scaffold!T.IncidentEdgesCache incidentEdgesCache = Scaffold!T.IncidentEdgesCache.init): Get a range of ContigNodes where full contig walks should start.

Structs

LinearWalk struct LinearWalk(T)

dentist.common.scaffold

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