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D

DBFile - class in org.veupathdb.lib.blast.common.fields

-db <String>BLAST database name

DBGenCode - class in org.veupathdb.lib.blast.common.fields

-db_gencode <Integer>Permissible values between:

• 1..6

• 9..16

• 21..31

• 33

Genetic code to use to translate database/subjects (see user manual for details)Default = 1

DBHardMask - class in org.veupathdb.lib.blast.common.fields

-db_hard_mask <String>Filtering algorithm ID to apply to the BLAST database as hard masking

DBSize - class in org.veupathdb.lib.blast.common.fields

-dbsize <Int8>Effective length of the database

DBSoftMask - class in org.veupathdb.lib.blast.common.fields

-db_soft_mask <String>Filtering algorithm ID to apply to the BLAST database as soft masking

deltablast(ObjectNode) - function in org.veupathdb.lib.blast.Blast

Creates a new DeltaBlast instance by parsing the given JSON input.

deltablast() - function in org.veupathdb.lib.blast.Blast

Creates a new, defaulted DeltaBlast instance.

DeltaBlast - enum entry in org.veupathdb.lib.blast.BlastTool

 

DeltaBlast - class in org.veupathdb.lib.blast.deltablast

 

Disable - enum entry in org.veupathdb.lib.blast.common.fields.AutoCPUCoresValue

 

DiscontiguousMegablast - enum entry in org.veupathdb.lib.blast.blastn.fields.BlastNTaskType

 

DomainInclusionEValueThreshold - class in org.veupathdb.lib.blast.deltablast.fields

-domain_inclusion_ethresh <Real>E-value inclusion threshold for alignments with conserved domainsDefault = 0.05

Dust - class in org.veupathdb.lib.blast.blastn.fields

-dust <String>Filter query sequence with DUST (Format: 'yes', 'level window linker', or 'no' to disable)Default = "20 64 1"

Dust.Companion - class in org.veupathdb.lib.blast.blastn.fields.Dust

 

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