cmd

Sep 28, 2022

Changes in this version

+ func BinomialCoeff(n int, k int) float64

+ func BinomialCoeffWithCache(bufSize int) func(n int, k int) float64

+ func CalcFPR(numElements uint64, numHashes int, signatureSize uint64) float64

+ func QueryFPR(n int, k int, fpr float64) float64

+ func QueryFPRWithCache(bufSize int) func(n int, k int, fpr float64) float64

+ func QueryFPRWithCacheWithConstantFPR(bufSize int, fpr float64) func(n int, k int) float64

+ func QueryFPRWithCacheWithFPRBins(bufSize int, maxFPR float64, bins int) func(n int, k int, fpr float64) float64

+ type GenomeInfo struct

+ Contigs int

+ File string

+ Size int

type SearchOptions

+ FPRBufSize int

Aug 15, 2022

Changes in this version

type SearchOptions

+ MaxFPR float64

Mar 26, 2022

Changes in this version

+ var HicUreadsMinProp0 float64 = 0.1

Mar 7, 2022

Changes in this version

type UnikIndex

+ func NewUnikIndex(file string, opt SearchOptions, fpr float64, nextraWorkers int) (*UnikIndex, error)

Feb 24, 2022

Changes in this version

type Match

+ FPR float64

Feb 8, 2022

Changes in this version

type Target

+ StatsA *stats.Quantiler

Jan 24, 2022

Changes in this version

+ func MeanStdev(values []float64) (float64, float64)

+ type MatchResult2 struct

+ FPR float64

+ Line *string

+ QCov float64

+ Query string

+ Target string

+ type MatchResult3 struct

+ Begin int

+ End int

+ FPR float64

+ QCov float64

+ Query string

+ Ref string

+ Target string

type Query

+ Seq2 *seq.Seq

type SearchOptions

+ LoadWholeFile bool

+ TrySingleEnd bool

type SearchResult

+ QuerySeqId string

type Target

+ RelDepth []float64

+ RelDepthStd float64

+ Stats *stats.Quantiler

Aug 13, 2021

Changes in this version

+ func NewSearchResultParser(file string, poolMatches *sync.Pool, scoreField int, numFields int, ...) (chan *SearchResult, error)

type IndexQuery

+ Hashes1 []uint64

type Options

+ Log2File bool

type SearchOptions

+ DoNotSort bool

+ Verbose bool

+ type SearchResult struct

+ Matches []_Match

+ QueryIdx uint64

type Uint64Slice

+ func (s *Uint64Slice) Pop() interface{}

+ func (s *Uint64Slice) Push(x interface{})

type UnikIndex

+ ExtraWorkers int

type UnikIndexDB

+ ExtraWorkers int

type UnikIndexDBInfo

+ CompactSize bool

Jun 24, 2021

Changes in this version

+ func IntSlice2StringSlice(vals []int) []string

type MatchResult

+ K int

type Meta

+ Ks []int

type Options

+ LogFile string

type QueryResult

+ K int

type SearchOptions

+ DeduplicateThreshold int

+ MinQLen int

type Target

+ Score float64

+ Scores []float64

+ SumUniqMatchHic float64

+ UniqMatchHic []float64

type UnikIndexDBInfo

+ Ks []int

+ SplitNum int

Apr 8, 2021

Changes in this version

+ func Combinations(set []uint64, n int) (subsets [][]uint64)

+ func Combinations2(set []uint64) [][2]uint64

type Match

+ GenomeSize []uint64

+ type MatchResult struct

+ FPR float64

+ FragIdx int

+ GSize uint64

+ Hits int

+ IdxNum int

+ MKmers int

+ QCov float64

+ QKmers int

+ QLen int

+ Query string

+ Target string

type Meta

+ GenomeSize uint64

+ SplitNum int

+ type ProfileNode struct

+ LineageNames []string

+ LineageTaxids []uint32

+ Percentage float64

+ Rank string

+ Taxid uint32

+ TaxonName string

type SearchOptions

+ TopNScores int

+ type Target struct

+ CompleteLineageNames []string

+ CompleteLineageTaxids []uint32

+ Coverage float64

+ FragsProp float64

+ GenomeSize uint64

+ LineageNames []string

+ LineageTaxids []string

+ Match []float64

+ Name string

+ Percentage float64

+ QLen []float64

+ Qlens float64

+ Rank string

+ RefName string

+ SumMatch float64

+ SumUniqMatch float64

+ Taxid uint32

+ TaxonName string

+ UniqMatch []float64

+ func (t *Target) AddTaxonomy(taxdb *unikmer.Taxonomy, showRanksMap map[string]interface{}, taxid uint32)

+ func (t Target) String() string

+ type Targets []*Target

+ func (t Targets) Len() int

+ func (t Targets) Less(i, j int) bool

+ func (t Targets) Swap(i, j int)

+ type Uint64Slice []uint64

+ func (s Uint64Slice) Len() int

+ func (s Uint64Slice) Less(i, j int) bool

+ func (s Uint64Slice) Swap(i, j int)

type UnikFileInfo

+ GenomeSize uint64

+ Indexes uint32

Mar 16, 2021

Changes in this version

type Match

+ JaccardIndex float64

type SearchOptions

+ NameMap map[string]string

+ type SortByJacc struct

+ func (ms SortByJacc) Less(i int, j int) bool

Dec 30, 2020

Changes in this version

+ const PosPopCountBufSize

+ const UnikIndexDBVersion

+ var BufferSize = 65536

+ var ErrVersionMismatch = errors.New("kmcp/index: version mismatch")

+ var RootCmd = &cobra.Command

+ var VERSION = "0.2.0"

+ func CalcSignatureSize(numElements uint64, numHashes int, falsePositiveRate float64) uint64

+ func Execute()

+ type IndexQuery struct

+ Ch chan []Match

+ Hashes [][]uint64

+ type Match struct

+ NumKmers int

+ QCov float64

+ TCov float64

+ Target []string

+ TargetIdx []uint32

+ type Matches []Match

+ func (ms Matches) Len() int

+ func (ms Matches) Less(i int, j int) bool

+ func (ms Matches) Swap(i int, j int)

+ type Meta struct

+ FragIdx uint32

+ Minimizer bool

+ MinimizerW int

+ SeqID string

+ SplitOverlap int

+ SplitSeq bool

+ SplitSize int

+ Syncmer bool

+ SyncmerS int

+ func (m Meta) String() string

+ type Name2Idx struct

+ Index uint32

+ Name string

+ type Options struct

+ Compress bool

+ CompressionLevel int

+ NumCPUs int

+ Verbose bool

+ type Query struct

+ Ch chan QueryResult

+ ID []byte

+ Idx uint64

+ Seq *seq.Seq

+ type QueryResult struct

+ DBId int

+ FPR float64

+ Matches []Match

+ NumKmers int

+ QueryID []byte

+ QueryIdx uint64

+ QueryLen int

+ func (r QueryResult) Recycle()

+ type SearchOptions struct

+ KeepUnmatched bool

+ LoadDefaultNameMap bool

+ MinMatched int

+ MinQueryCov float64

+ MinTargetCov float64

+ SortBy string

+ Threads int

+ TopN int

+ UseMMap bool

+ type SortByQCov struct

+ type SortBySum struct

+ func (ms SortBySum) Less(i int, j int) bool

+ type SortByTCov struct

+ func (ms SortByTCov) Less(i int, j int) bool

+ type UnikFileInfo struct

+ Index uint32

+ Kmers uint64

+ Name string

+ Path string

+ func (i UnikFileInfo) String() string

+ type UnikFileInfoGroup struct

+ Infos []UnikFileInfo

+ Kmers uint64

+ func (i UnikFileInfoGroup) String() string

+ type UnikFileInfoGroups []UnikFileInfoGroup

+ func (l UnikFileInfoGroups) Len() int

+ func (l UnikFileInfoGroups) Less(i int, j int) bool

+ func (l UnikFileInfoGroups) Swap(i int, j int)

+ type UnikFileInfos []UnikFileInfo

+ func (l UnikFileInfos) Len() int

+ func (l UnikFileInfos) Less(i int, j int) bool

+ func (l UnikFileInfos) Swap(i int, j int)

+ type UnikFileInfosByName []UnikFileInfo

+ func (l UnikFileInfosByName) Len() int

+ func (l UnikFileInfosByName) Less(i int, j int) bool

+ func (l UnikFileInfosByName) Swap(i int, j int)

+ type UnikIndex struct

+ Header index.Header

+ InCh chan IndexQuery

+ Options SearchOptions

+ Path string

+ func NewUnixIndex(file string, opt SearchOptions) (*UnikIndex, error)

+ func (idx *UnikIndex) Close() error

+ func (idx *UnikIndex) String() string

+ type UnikIndexDB struct

+ DBId int

+ Header index.Header

+ InCh chan Query

+ Indices []*UnikIndex

+ Info UnikIndexDBInfo

+ Options SearchOptions

+ func NewUnikIndexDB(path string, opt SearchOptions, dbID int) (*UnikIndexDB, error)

+ func (db *UnikIndexDB) Close() error

+ func (db *UnikIndexDB) CompatibleWith(db2 *UnikIndexDB) bool

+ func (db *UnikIndexDB) String() string

+ type UnikIndexDBInfo struct

+ Alias string

+ BlockSize int

+ Canonical bool

+ FPR float64

+ Files []string

+ Hashed bool

+ IndexVersion uint8

+ K int

+ Kmers uint64

+ MappingNames bool

+ Minimizer bool

+ MinimizerW uint32

+ NameMapping map[string]string

+ NumHashes int

+ NumNames int

+ Scale uint32

+ Scaled bool

+ SplitOverlap int

+ SplitSeq bool

+ SplitSize int

+ Syncmer bool

+ SyncmerS uint32

+ Version uint8

+ func NewUnikIndexDBInfo(files []string) UnikIndexDBInfo

+ func UnikIndexDBInfoFromFile(file string) (UnikIndexDBInfo, error)

+ func (i UnikIndexDBInfo) Check() error

+ func (i UnikIndexDBInfo) CompatibleWith(j UnikIndexDBInfo) bool

+ func (i UnikIndexDBInfo) String() string

+ func (i UnikIndexDBInfo) WriteTo(file string) (int, error)

+ type UnikIndexDBSearchEngine struct

+ DBNames []string

+ DBs []*UnikIndexDB

+ InCh chan Query

+ Options SearchOptions

+ OutCh chan QueryResult

+ func NewUnikIndexDBSearchEngine(opt SearchOptions, dbPaths ...string) (*UnikIndexDBSearchEngine, error)

+ func (sg *UnikIndexDBSearchEngine) Close() error

+ func (sg *UnikIndexDBSearchEngine) Wait()