Module dentist.common.scaffold

Work with scaffold graphs. A scaffold graph is an undirected graph with optional edge payloads.

For each contig of the input assembly there exist four nodes in the graph: ContigPart.pre, ContigPart.begin, ContigPart.end and ContigPart.post. These represent four locations relative to the contig.

Canonical edges are categorized by isDefault (the contig itself), isUnkown (a gap marked by ns), isGap (pile up or insertion that connects two contigs), isFrontExtension or isBackExtension (pile up or insertion that extends beyond the begin/end of a contig).

Gap edges are further categorized as isParallel or isAntiParallel depending on weather the involved contigs are connected in the same (parallel) or opposite (anti-parallel) orientation.

The scaffold graph is used to collect pile ups of read alignments and represent the final assembly.

Functions

Name	Description
`buildScaffold(numReferenceContigs, rawJoins)`	Build a scaffold graph using `rawJoins`. This creates default edges for contigs `1 .. numReferenceContigs + 1` and inserts the `rawJoins`. Multi-edges are merged using `mergeMultiEdges`.
`buildScaffold(rawJoins)`	Build a scaffold graph using `rawJoins`. The nodes are deduced from `rawJoins`.
`concatenatePayloads()`	Combine joins by concatenating their payloads.
`enforceJoinPolicy(scaffold, joinPolicy)`	Enforce `joinPolicy` in `scaffold`. Write discarded joins to `forbiddenJoins` if given.
`getDefaultJoin(contigId)`	Construct the default join for `contigId`. Initialize `payload` with `getPayload(contigId)` if given.
`getUnkownJoin(preContigId, postContigId, payload)`	Get join for a stretch of unknown sequence (`n`s).
`initScaffold(numReferenceContigs)`	Creates a scaffold the default edges for contigs `1 .. numReferenceContigs + 1`. Optionally specify a function that produces the payloads.
`isAntiParallel(join)`	Returns true iff join is a gap edge and anti-parallel.
`isBackExtension(join)`	Returns true iff join is a back extension edge of the scaffold graph.
`isCyclic(scaffold, startNode, incidentEdgesCache)`	Use `linearWalk` to determine if `startNode` is part of a cycle.
`isDefault(join)`	Returns true iff join is a default/contig edge of the scaffold graph.
`isExtension(join)`	Returns true iff join is an extension edge of the scaffold graph.
`isFrontExtension(join)`	Returns true iff join is a front extension edge of the scaffold graph.
`isGap(join)`	Returns true iff join is a gap edge of the scaffold graph.
`isParallel(join)`	Returns true iff join is a gap edge and parallel.
`isReal(contigPart)`	True for the two real locations `begin` and `end`.
`isTranscendent(contigPart)`	True for the two symbolic locations `pre` and `post`.
`isUnkown(join)`	Returns true iff join is a unknown edge, ie. an edge for unknown sequence (`n`s) of the scaffold graph.
`isValid(join)`	Returns true iff join is a valid canonical edge of the scaffold graph.
`linearWalk(scaffold, startNode, incidentEdgesCache)`	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, i.e. for every node the degree must be at most two. If the component of `startNode` is cyclic then the walk will end in `startNode` and the `isCyclic` flag will be set.
`mergeExtensionsWithGaps(scaffold)`	Remove extension edges were they coincide with a gap edge combining their payloads. This is intended to build pile ups with all reads that contribute to each gap.
`normalizeUnkownJoins(scaffold)`	Normalizes unknown joins such that they join contigs or are removed as applicable. Afterwards the gap joins may not be canonical anymore, i.e. `isUnkown` may be false.
`removeBlacklisted(scaffold, blacklist)`	Remove blacklisted gap joins. Write discarded joins to `forbiddenJoins` if given.
`removeNoneJoins(scaffold)`	Remove marked edges from the graph. This always keeps the default edges.
`scaffoldStarts(scaffold, incidentEdgesCache)`	Returns a range of `ContigNode`s where full contig walks should start.
`sumPayloads()`	Combine joins by summing their payloads.

Structs

Name	Description
`LinearWalk`	Range that walks linearly through its scaffold graph.

Enums

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

Aliases

Name	Type	Description
`ContigNode`	`std.typecons.Tuple!(ulong,"contigId",dentist.common.scaffold.ContigPart,"contigPart")`	A contig is represented by four `ContigNodes` in the scaffold graph: one for each `ContigPart`.
`IncidentEdgesCache`	`Scaffold!T`	`IncidentEdgesCache` for `Scaffold!T`.
`Join`	`Scaffold!T`	An edge of the scaffold graph.
`Scaffold`	`Graph!(ContigNode,void,No.isDirected,T)`	Data structure for the scaffold graph described in the module documentation.

Authors	Arne Ludwig
Copyright	© 2018 Arne Ludwig
License	Subject to the terms of the MIT license, as written in the included LICENSE file.

Generated using the DDOX documentation generator

Module dentist.common.scaffold

See also

Functions

Structs

Enums

Aliases