Module dentist.common.insertions
Everything to handle insertions. Insertions are generated by DENTIST
command process-pile-ups. They are essentially a consensus sequence
alongside alignment that allow precise splicing into the assembly. In
addition, the IDs of the reads involved in the consensus are included.
See also
Functions
| Name | Description |
|---|---|
getCroppingPosition(overlap)
|
Return the cropping position on contig according to overlap.
|
getInfoForExistingContig(begin, insertion, globalComplement)
|
Returns information required when building the assembly. |
getInfoForGap(insertion)
|
Returns information required when building the assembly. |
getInfoForNewSequenceInsertion(begin, insertion, globalComplement)
|
Returns information required when building the assembly. |
hasSequence(insertion)
|
Returns true if insertion has a non-empty sequence attached. |
isOutputGap(insertion)
|
Returns true iff a sequence of ns should be written.
|
isValidInsertion(insertion)
|
Returns true iff insertion describes a contig (isDefault), gap
(isOutputGap) or insertion (isGap, isExtension, hasSequence).
|
Structs
| Name | Description |
|---|---|
InsertionInfo
|
This describes an insertion, existing contig or gap. |
Aliases
| Name | Type | Description |
|---|---|---|
Insertion
|
Graph!(std.typecons.Tuple!(ulong,"contigId",dentist.common.scaffold.ContigPart,"contigPart").Tuple,void,0,dentist.common.insertions.InsertionInfo)
|
This represents a contig, gap or insertion edge with InsertionInfo
payload.
|
OutputScaffold
|
Graph!(std.typecons.Tuple!(ulong,"contigId",dentist.common.scaffold.ContigPart,"contigPart").Tuple,void,0,dentist.common.insertions.InsertionInfo)
|
This is used to collect all sub-sequences (contigs, gaps, insertions) of the output. |