Index

Modules: unoisenim, unoisenim/nbc_algo, unoisenim/remove_phix_utils, unoisenim/sintax_algo, unoisenim/uchime2_algo, unoisenim/unoise_algo, unoisenim/utils.

API symbols

AlignPath:

• uchime2_algo: type AlignPath

buildIndex:

• sintax_algo: proc buildIndex(seqs: seq[string]; taxStrings: seq[string]): SintaxIndex

buildNbcIndex:

• nbc_algo: proc buildNbcIndex(seqs: seq[string]; taxStrings: seq[string]): NbcIndex

Centroid:

• unoise_algo: object Centroid

classifyOneDir:

• sintax_algo: proc classifyOneDir(query: string; idx: SintaxIndex; bootSubset: int = 32; bootIters: int = 100): tuple[topCount: int, hit: SintaxHit]

editDistanceLimit:

• unoise_algo: proc editDistanceLimit(s1, s2: string; limit: int): int

extractKmers:

• unoise_algo: proc extractKmers(s: string; kmers: var seq[uint16])

extractTaxRanks:

• sintax_algo: proc extractTaxRanks(tax: string): seq[string]

getLeftRight:

• uchime2_algo: proc getLeftRight(q, t: string; path: AlignPath): tuple[ diffs, posL0, posL1, posR0, posR1: int]

globalAlign:

• uchime2_algo: proc globalAlign(q, t: string; path: var AlignPath): int

initSintaxState:

• sintax_algo: proc initSintaxState(idx: SintaxIndex): SintaxState

isPhix:

• remove_phix_utils: proc isPhix(query: string; minId: float = 0.97; minKmers: int = 8): bool

nbc:

• nbc_algo: proc nbc(query: string; idx: NbcIndex; bootIters: int = 100; minWords: int = 5): NbcHit

NbcHit:

• nbc_algo: object NbcHit

NbcIndex:

• nbc_algo: object NbcIndex

NbcKmerSize:

• nbc_algo: const NbcKmerSize

parseSize:

• utils: proc parseSize(label: string): int

parseTaxRanks:

• nbc_algo: proc parseTaxRanks(tax: string): seq[string]

phixKmers:

• remove_phix_utils: const phixKmers

phixScore:

• remove_phix_utils: proc phixScore(query: string): float

phixSeqLen:

• remove_phix_utils: const phixSeqLen

postingFirst:

• sintax_algo: proc postingFirst(idx: SintaxIndex; word: uint16): int32

postingLen:

• sintax_algo: proc postingLen(idx: SintaxIndex; word: uint16): int

rc:

• sintax_algo: proc rc(s: string): string

reverseComplement:

• nbc_algo: proc reverseComplement(s: string): string

sintax:

• sintax_algo: proc sintax(query: string; idx: SintaxIndex; bootSubset: int = 32; bootIters: int = 100): SintaxHit

SintaxHit:

• sintax_algo: object SintaxHit

SintaxIndex:

• sintax_algo: object SintaxIndex

SintaxState:

• sintax_algo: object SintaxState

sintaxWithState:

• sintax_algo: proc sintaxWithState(query: string; idx: SintaxIndex; state: var SintaxState; bootSubset: int = 32; bootIters: int = 100): SintaxHit

uchime:

• uchime2_algo: proc uchime(centroids: seq[Centroid]; minAbSkew: float = 16.0; threads: int = 1): seq[ bool]

unoise:

• unoise_algo: proc unoise(sequences: seq[UnoiseSeq]; alpha: float = 2.0; minsize: int = 8): seq[ Centroid]

UnoiseSeq:

• unoise_algo: object UnoiseSeq