diamondcli/org.veupathdb.lib.cli.diamond/DiamondCommand

DiamondCommand

enum DiamondCommand : Enum<DiamondCommand>

Enum of DIAMOND commands.

DIAMOND Docs:

Commands are issued as the first parameter on the command line and set the task to be run by the program.

Since

v1.0.0

Entries

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MakeDB

Create a DIAMOND formatted reference database from a FASTA input file.

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PrepDB

Prepare BLAST database for use with Diamond. This call requires the path to the BLAST database (option -d) and will write a number of small auxiliary files into the database directory.

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BlastP

Align protein query sequences against a protein reference database.

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BlastX

Align translated DNA query sequences against a protein reference database.

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View

Generate formatted output from DAA files.

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DBInfo

Print information about a database file.

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Version

Print version information.

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Help

Print help message.

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Test

Run a series of test cases and verify the output against reference hashes.

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Cluster

Cluster protein sequences

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LinearCluster

Cluster protein sequences in linear time

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ClusterRealign

Realign clustered sequences against their centroids

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RecomputeClustering

Recompute clustering to fix errors

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ReassignClusters

Reassign clustered sequences to the closest centroid

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MergeDAA

Merge DAA files

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GetSeq

Retrieve sequences from a DIAMOND database file

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MakeIndex

Make database index

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GreedyVortexCover

Compute greedy vertex cover

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ROC

???

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@DiamondExtras
BlastN

Align DNA query sequences against a DNA reference database.

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Types

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object Companion

Properties

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val entries: EnumEntries<DiamondCommand>

Returns a representation of an immutable list of all enum entries, in the order they're declared.

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val name: String
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val ordinal: Int

Functions

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fun valueOf(value: String): DiamondCommand

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

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fun values(): Array<DiamondCommand>

Returns an array containing the constants of this enum type, in the order they're declared.