Package org.veupathdb.lib.blast.blastn.fields

Object Summary
Object	Description
Companion

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

Class Summary
Class	Description
FilteringDB	-filtering_db `<String>`BLAST database containing filtering elements (i.e.
IndexName	-index_name `<String>`MegaBLAST database index name (deprecated; use only for old style indices)
MinRawGappedScore	-min_raw_gapped_score `<Integer>`Minimum raw gapped score to keep an alignment in the preliminary gapped and traceback stages
NonGreedy	-no_greedyUse non-greedy dynamic programming extension
OffDiagonalRange	-off_diagonal_range `<Integer, >=0>`Number of off-diagonals to search for the 2nd hit, use 0 to turn offDefault = `0`
Penalty	-penalty `<Integer, <=0>`Penalty for a nucleotide mismatch
PercentIdentity	-perc_identity `<Real, 0..100>`Percent identity
Reward	-reward `<Integer, >=0>`Reward for a nucleotide match
SoftMaskingN	-soft_masking `<Boolean>`Apply filtering locations as soft masksDefault = `true`
BlastNTask	-task `<String>`Permissible values: 'blastn' 'blastn-short' 'dc-megablast' 'megablast' 'rmblastn' Task to executeDefault = `megablast`
TemplateLength	-template_length `<Integer>`Permissible values: 16 18 21 Discontiguous MegaBLAST template length
TemplateType	-template_type `<String>`Permissible Values: coding coding_and_optimal optimal Discontiguous MegaBLAST template type
UseIndex	-use_index `<Boolean>`Use MegaBLAST database indexDefault = `false`
WindowMaskerDB	-window_masker_db `<String>`Enable WindowMasker filtering using this repeats database.
WindowMaskerTaxID	-window_masker_taxid `<Integer>`Enable WindowMasker filtering using a Taxonomic ID