Module dentist.commands.output

This is the output command of DENTIST.

Command Summary

Generate the output assembly by closing gaps.

Name	Description
`execute(options)`	Execute the `output` command with `options`.
`fixCropping(scaffold)`	Remove contig cropping where no new sequence is to be inserted and adjust cropping where cropped regions overlap.
`insertionToSimpleJson(insertion)`	Converts the pileup into a simple JSON object for diagnostic purposes.
`transferCroppingFromIncidentJoins(contigJoin, incidentEdgesCache)`

Name	Description
`AssemblyWriter`

Name	Description
`AGPComponentType`
`AGPLinkageEvidence`

Name	Type	Description
`Options`	`OptionsFor!(16)`	Options for the `output` command.

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

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