dentist.common

This package holds common code for the dentist algorithm.

Modules

alignments module dentist.common.alignments: Everything to handle local alignments and friends.
binio module dentist.common.binio: This package contains methods to handle the proprietary binary data containers.
insertions module dentist.common.insertions: Everything to handle insertions.
scaffold module dentist.common.scaffold: Work with scaffold graphs.

Public Imports

dentist.common.alignments public import dentist.common.alignments;

dentist.common.binio public import dentist.common.binio;

dentist.common.scaffold public import dentist.common.scaffold;

Members

Aliases

ReadInterval alias ReadInterval = ReadRegion.TaggedInterval: An interval of a read contig.
ReadPoint alias ReadPoint = ReadRegion.TaggedPoint: A point on a read.
ReadRegion alias ReadRegion = Region!(size_t, size_t, "readId"): A region of a read aka. mask.
ReferenceInterval alias ReferenceInterval = ReferenceRegion.TaggedInterval: An interval of a reference contig.
ReferencePoint alias ReferencePoint = ReferenceRegion.TaggedPoint: A point on the reference.
ReferenceRegion alias ReferenceRegion = Region!(size_t, size_t, "contigId"): A region of the reference aka. mask.

Classes

DentistException class DentistException: Thrown if some runtime error in the dentist algorithm occurs.

Functions

to R to(in AlignmentChain alignmentChain): Returns the alignment region of alignmentChain.

Manifest constants

isTesting enum isTesting;: True iff building with testing commands.

Structs

OutputCoordinate struct OutputCoordinate: A point on the output assembly.

Templates

testingOnly template testingOnly(alias value): Evaluate to value if building with testing command; otherwise to typeof(value).init.

Meta

Source

See Source File

License

Subject to the terms of the MIT license, as written in the included LICENSE file.

Copyright

© 2018 Arne Ludwig <arne.ludwig@posteo.de>

Authors

Arne Ludwig <arne.ludwig@posteo.de>

dentist modules