cmd

package

Go to main page

Versions in this module

v0

v0.5.0

Dec 18, 2024

Changes in this version

+ const FileGenomeChunks

+ func TrimSubStrPairs(subs *[]*SubstrPair, k int)

type Chaining2Options

+ BandBase int

+ BandCount int

type IndexBuildingOptions

+ Debug bool

type IndexInfo

+ InputGenomes int

type IndexSearchingOptions

+ Debug bool

type SearchResult

+ BatchGenomeIndex uint64

v0.4.0

Aug 15, 2024

Changes in this version

+ const BITS_BATCH_IDX

+ const BITS_FLAGS

+ const BITS_GENOME_IDX

+ const BITS_IDX

+ const BITS_IDX_FLAGS

+ const BITS_NONE_IDX

+ const BITS_NONE_POS

+ const BITS_POSITION

+ const BITS_REVERSE

+ const BITS_STRAND

+ const MASK_GENOME_IDX

+ const MASK_NONE_IDX

+ const MASK_REVERSE

+ const MAX_GENOME_SIZE

+ const NO_VALID_SEQS

+ const TOO_LARGE_GENOME

+ const TOO_MANY_SEQS

+ var COMMIT = func() string { ... }()

+ func ParseByteSize(val string) (int64, error)

type Chain2Result

+ AlignedFraction float64

+ AlignedLength int

+ Alignment []byte

+ CIGAR []byte

+ Gaps int

+ PIdent float64

+ QSeq []byte

+ TSeq []byte

type ChainingOptions

+ MinLen uint8

type IndexBuildingOptions

+ DisableDesertFilling bool

+ MergeThreads int

+ MinSeqLen int

type IndexInfo

+ MaxDesert int

+ SeedDistInDesert int

type IndexSearchingOptions

+ MoreAccurateAlignment bool

type SearchResult

+ func (sr *SearchResult) SortBySeqID()

type SeqComparatorResult

+ func (r *SeqComparatorResult) Update2(chains *[]*Chain2Result, queryLen int)

v0.3.0

May 14, 2024

Changes in this version

+ const FileSeedPositions

+ func GenerateMasks(files []string, opt *IndexBuildingOptions, outFile string) ([]uint64, []string, error)

+ type Chain2Result struct

+ AlignedBasesQ int

+ AlignedBasesT int

+ MatchedBases int

+ NAnchors int

+ Pident float64

+ QBegin int

+ QEnd int

+ TBegin int

+ TEnd int

+ func (r *Chain2Result) Reset()

type Chaining2Options

+ MinAlignLen int

+ MinIdentity float64

type ChainingOptions

+ MaxDistance float64

+ type File2GSize struct

+ File string

+ Size int

+ type File2GSizes []File2GSize

+ func (h *File2GSizes) Pop() any

+ func (h *File2GSizes) Push(x any)

+ func (h File2GSizes) Len() int

+ func (h File2GSizes) Less(i, j int) bool

+ func (h File2GSizes) Swap(i, j int)

type Index

+ InMemorySearchers []*kv.InMemorySearcher

+ func (idx *Index) RecycleSimilarityDetails(sds *[]*SimilarityDetail)

type IndexBuildingOptions

+ BigGenomeFile string

+ ContigInterval int

+ DesertExpectedSeedDist int

+ DesertMaxLen uint32

+ DesertSeedPosRange int

+ MaskFile string

+ MaxGenomeSize int

+ Prefix int

+ PrefixExt int

+ SaveSeedPositions bool

+ TopN int

type IndexInfo

+ ContigInterval int

type IndexSearchingOptions

+ ExtendLength int

+ InMemorySearch bool

+ MaxDistance float64

+ MinQueryAlignedFractionInAGenome float64

+ OutputSeq bool

+ type Kmer2Locs [][2]uint64

+ func (h Kmer2Locs) Len() int

+ func (h Kmer2Locs) Less(i, j int) bool

+ func (h Kmer2Locs) Swap(i, j int)

type SearchResult

+ AlignedFraction float64

type SeqComparatorResult

+ Chains *[]*Chain2Result

+ PIdent float64

+ QBegin int

+ QEnd int

+ QueryLen int

+ TBegin int

+ TEnd int

+ TSeq []byte

+ func (r *SeqComparatorResult) Update(chains *[]*Chain2Result, queryLen int)

type SimilarityDetail

+ NSeeds int

type SubstrPair

+ QRC bool

+ TRC bool

v0.2.0

Feb 2, 2024

Changes in this version

+ const DirGenomes

+ const DirSeeds

+ const ExtSeeds

+ const ExtTmpDir

+ const FileGenomeIndex

+ const FileGenomes

+ const FileInfo

+ const FileMasks

+ var DefaultChaining2Options = Chaining2Options

+ var DefaultChainingOptions = ChainingOptions

+ var DefaultIndexSearchingOptions = IndexSearchingOptions

+ var DefaultSeqComparatorOptions = SeqComparatorOptions

+ var MainVersion uint8 = 0

+ var MinorVersion uint8 = 1

+ func BuildIndex(outdir string, infiles []string, opt *IndexBuildingOptions) error

+ func CheckIndexBuildingOptions(opt *IndexBuildingOptions) error

+ func CheckIndexSearchingOptions(opt *IndexSearchingOptions) error

+ func ClearSubstrPairs(subs *[]*SubstrPair, k int)

+ func RC(s []byte) []byte

+ func RecycleChaining2Result(chains *[]*[]int)

+ func RecycleChainingResult(chains *[]*[]int)

+ func RecycleSeqComparatorResult(r *SeqComparatorResult)

+ func RecycleSubstrPairs(subs *[]*SubstrPair)

+ type Chainer struct

+ func NewChainer(options *ChainingOptions) *Chainer

+ func (ce *Chainer) Chain(subs *[]*SubstrPair) (*[]*[]int, float64)

+ type Chainer2 struct

+ func NewChainer2(options *Chaining2Options) *Chainer2

+ func (ce *Chainer2) Chain(subs *[]*SubstrPair) (*[]*[]int, int, int)

+ type Chaining2Options struct

+ Band int

+ MaxDistance int

+ MaxGap int

+ MinScore int

+ type ChainingOptions struct

+ MaxGap float64

+ MinScore float64

+ type Index struct

+ Searchers []*kv.Searcher

+ func NewIndexSearcher(outDir string, opt *IndexSearchingOptions) (*Index, error)

+ func (idx *Index) Close() error

+ func (idx *Index) RecycleSearchResult(r *SearchResult)

+ func (idx *Index) RecycleSearchResults(sr *[]*SearchResult)

+ func (idx *Index) Search(s []byte) (*[]*SearchResult, error)

+ func (idx *Index) SetSeqCompareOptions(sco *SeqComparatorOptions)

+ type IndexBuildingOptions struct

+ Chunks int

+ Force bool

+ GenomeBatchSize int

+ K int

+ Log2File bool

+ Masks int

+ MaxOpenFiles int

+ NumCPUs int

+ Partitions int

+ PrefixForCheckLC int

+ RandSeed int64

+ ReRefName *regexp.Regexp

+ ReSeqExclude []*regexp.Regexp

+ Verbose bool

+ type IndexInfo struct

+ Chunks int

+ GenomeBatchSize int

+ GenomeBatches int

+ Genomes int

+ K uint8

+ MainVersion uint8

+ Masks int

+ MinorVersion uint8

+ Partitions int

+ RandSeed int64

+ type IndexSearchingOptions struct

+ Log2File bool

+ MaxGap float64

+ MaxMismatch int

+ MaxOpenFiles int

+ MinPrefix uint8

+ MinSinglePrefix uint8

+ NumCPUs int

+ TopN int

+ Verbose bool

+ type SearchResult struct

+ Chains *[]*[]int

+ GenomeBatch int

+ GenomeIndex int

+ GenomeSize int

+ ID []byte

+ Score float64

+ SimilarityDetails *[]*SimilarityDetail

+ Subs *[]*SubstrPair

+ func (r *SearchResult) Reset()

+ type SeqComparator struct

+ func NewSeqComparator(options *SeqComparatorOptions) *SeqComparator

+ func (cpr *SeqComparator) Compare(s []byte) (*SeqComparatorResult, error)

+ func (cpr *SeqComparator) Index(s []byte) error

+ func (cpr *SeqComparator) RecycleIndex()

+ type SeqComparatorOptions struct

+ K uint8

+ MinAlignedFraction float64

+ MinIdentity float64

+ MinPrefix uint8

+ type SeqComparatorResult struct

+ AlignedBases int

+ AlignedFraction float64

+ Identity float64

+ MatchedBases int

+ NumChains int

+ type SimilarityDetail struct

+ Chain *[]int

+ RC bool

+ SeqID []byte

+ SeqLen int

+ Similarity *SeqComparatorResult

+ SimilarityScore float64

+ TBegin int

+ TEnd int

+ type SubstrPair struct

+ Code uint64

+ Len int

+ Mismatch uint8

+ QBegin int

+ RC bool

+ TBegin int

+ func (s SubstrPair) String() string

v0.1.0

Jan 15, 2024

Changes in this version

+ var BufferSize = 65536

+ var RootCmd = &cobra.Command

+ var Strands = [2]byte

+ var VERSION = "0.1.0"

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

+ func Execute()

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

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

+ type Options struct

+ Compress bool

+ CompressionLevel int

+ Log2File bool

+ LogFile string

+ NumCPUs int

+ Verbose bool

+ type Query struct

+ func (q *Query) Reset()

+ type Uint64Slice []uint64

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

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

+ func (s Uint64Slice) Len() int

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

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

?	: This menu
/	: Search site
f or F	: Jump to
y or Y	: Canonical URL