unikmer

Jul 26, 2021

Changes in this version

+ var ErrUnkownRank = errors.New("unikmer: unknown rank")

type Taxonomy

+ func (t *Taxonomy) AtOrBelowRank(taxid uint32, rank string) bool

Apr 26, 2021

Changes in this version

+ type ProteinIterator struct

+ func NewProteinIterator(s *seq.Seq, k int, codonTable int, frame int) (*ProteinIterator, error)

+ func (iter *ProteinIterator) Index() int

+ func (iter *ProteinIterator) Next() (code uint64, ok bool)

+ type ProteinMinimizerSketch struct

+ func NewProteinMinimizerSketch(S *seq.Seq, k int, codonTable int, frame int, w int) (*ProteinMinimizerSketch, error)

+ func (s *ProteinMinimizerSketch) Index() int

+ func (s *ProteinMinimizerSketch) Next() (code uint64, ok bool)

Apr 6, 2021

Changes in this version

+ var ErrNamesNotLoaded = errors.New("unikmer: taxonomy names not loaded, please call: LoadNames")

type Taxonomy

+ Names map[uint32]string

+ func (t *Taxonomy) LineageNames(taxid uint32) []string

+ func (t *Taxonomy) LineageTaxIds(taxid uint32) []uint32

+ func (t *Taxonomy) LoadNames(file string, taxidColumn int, nameColumn int, typeColumn int, _type string) error

+ func (t *Taxonomy) LoadNamesFromNCBI(file string) error

Dec 25, 2020

Changes in this version

+ var ErrBufNil = fmt.Errorf("unikmer: buffer slice is nil")

+ var ErrBufNotEmpty = fmt.Errorf("unikmer: buffer has elements")

+ type IdxValue struct

+ Idx int

+ Val uint64

type Sketch

+ func NewMinimizerSketchWithBuffer(S *seq.Seq, k int, w int, circular bool, buf []IdxValue) (*Sketch, error)

+ func NewSyncmerSketchWithBuffer(S *seq.Seq, k int, s int, circular bool, buf []IdxValue) (*Sketch, error)

+ func (s *Sketch) ResetMinimizer(S *seq.Seq) error

+ func (s *Sketch) ResetSyncmer(S *seq.Seq) error

Nov 25, 2020

Changes in this version

+ const UnikCanonical

+ const UnikCompact

+ const UnikHashed

+ const UnikIncludeTaxID

+ const UnikScaled

+ const UnikSorted

+ var ErrInvalidS = fmt.Errorf("unikmer: invalid s-mer size")

+ var ErrInvalidW = fmt.Errorf("unikmer: invalid minimimzer window")

+ func MustCanonical(code uint64, k int) uint64

+ func MustComplement(code uint64, k int) uint64

+ func MustDecode(code uint64, k int) []byte

+ func MustRevComp(code uint64, k int) (c uint64)

+ func MustReverse(code uint64, k int) (c uint64)

type Header

+ MaxHash uint64

+ Scale uint32

type Iterator

+ func (iter *Iterator) Index() int

type Reader

+ func (reader *Reader) GetMaxHash() uint64

+ func (reader *Reader) GetScale() uint32

+ func (reader *Reader) IsScaled() bool

+ type Sketch struct

+ S []byte

+ func NewMinimizerSketch(S *seq.Seq, k int, w int, circular bool) (*Sketch, error)

+ func NewSyncmerSketch(S *seq.Seq, k int, s int, circular bool) (*Sketch, error)

+ func (s *Sketch) Index() int

+ func (s *Sketch) Next() (uint64, bool)

+ func (s *Sketch) NextMinimizer() (code uint64, ok bool)

+ func (s *Sketch) NextSyncmer() (code uint64, ok bool)

type Writer

+ func (writer *Writer) SetMaxHash(maxHash uint64) error

+ func (writer *Writer) SetScale(scale uint32) error

Sep 24, 2020

Changes in this version

+ const UNIK_HASHED

+ var ErrEmptySeq = fmt.Errorf("unikmer: empty sequence")

+ var ErrInvalidK = fmt.Errorf("unikmer: invalid k-mer size")

+ var ErrShortSeq = fmt.Errorf("unikmer: sequence shorter than k")

+ var ErrVersionMismatch = errors.New("unikmer: version mismatch")

+ func Canonical(code uint64, k int) (c uint64)

+ type Iterator struct

+ func NewHashIterator(s *seq.Seq, k int, canonical bool, circular bool) (*Iterator, error)

+ func NewKmerIterator(s *seq.Seq, k int, canonical bool, circular bool) (*Iterator, error)

+ func (iter *Iterator) CurrentIndex() int

+ func (iter *Iterator) Next() (code uint64, ok bool, err error)

+ func (iter *Iterator) NextHash() (code uint64, ok bool)

+ func (iter *Iterator) NextKmer() (code uint64, ok bool, err error)

type Reader

+ func (reader *Reader) IsHashed() bool

Jul 6, 2020

Changes in this version

+ var ErrRankNotLoaded = errors.New("unikmer: ranks not loaded, please call: NewTaxonomyWithRank")

+ var ErrTooManyRanks = errors.New("unikmer: number of ranks exceed limit of 255")

type Taxonomy

+ Ranks map[string]interface{}

+ func NewTaxonomyWithRank(file string, childColumn int, parentColumn int, rankColumn int) (*Taxonomy, error)

+ func NewTaxonomyWithRankFromNCBI(file string) (*Taxonomy, error)

+ func (t *Taxonomy) Rank(taxid uint32) string

Feb 18, 2020

Changes in this version

+ const UNIK_INCLUDETAXID

+ var ErrCallLate = errors.New(...)

+ var ErrCallOrder = errors.New("unikmer: WriteTaxid/ReadTaxid should be called after WriteCode/ReadCode")

+ var ErrCallReadWriteTaxid = errors.New(...)

+ var ErrDescTooLong = errors.New("unikmer: description too long, 128 bytes at most")

+ var ErrIllegalColumnIndex = errors.New("unikmer: illegal column index, positive integer needed")

+ var ErrInvalidTaxid = errors.New("unikmer: invalid taxid, 0 not allowed")

+ type CodeTaxid struct

+ Code uint64

+ Taxid uint32

+ type CodeTaxidSlice []CodeTaxid

+ func (pairs CodeTaxidSlice) Len() int

+ func (pairs CodeTaxidSlice) Less(i, j int) bool

+ func (pairs CodeTaxidSlice) Swap(i, j int)

type Header

+ Description []byte

type Reader

+ func (reader *Reader) GetGlobalTaxid() uint32

+ func (reader *Reader) GetTaxidBytesLength() int

+ func (reader *Reader) HasGlobalTaxid() bool

+ func (reader *Reader) HasTaxidInfo() bool

+ func (reader *Reader) IsCanonical() bool

+ func (reader *Reader) IsCompact() bool

+ func (reader *Reader) IsIncludeTaxid() bool

+ func (reader *Reader) IsSorted() bool

+ func (reader *Reader) ReadCodeWithTaxid() (code uint64, taxid uint32, err error)

+ func (reader *Reader) ReadTaxid() (taxid uint32, err error)

+ func (reader *Reader) ReadWithTaxid() (KmerCode, uint32, error)

+ type Taxonomy struct

+ DelNodes map[uint32]struct{}

+ MergeNodes map[uint32]uint32

+ Nodes map[uint32]uint32

+ func NewTaxonomy(file string, childColumn int, parentColumn int) (*Taxonomy, error)

+ func NewTaxonomyFromNCBI(file string) (*Taxonomy, error)

+ func (t *Taxonomy) CacheLCA()

+ func (t *Taxonomy) LCA(a uint32, b uint32) uint32

+ func (t *Taxonomy) LoadDeletedNodes(file string, column int) error

+ func (t *Taxonomy) LoadDeletedNodesFromNCBI(file string) error

+ func (t *Taxonomy) LoadMergedNodes(file string, oldColumn int, newColumn int) error

+ func (t *Taxonomy) LoadMergedNodesFromNCBI(file string) error

+ func (t *Taxonomy) MaxTaxid() uint32

type Writer

+ func (writer *Writer) SetGlobalTaxid(taxid uint32) error

+ func (writer *Writer) SetMaxTaxid(taxid uint32) error

+ func (writer *Writer) WriteCodeWithTaxid(code uint64, taxid uint32) (err error)

+ func (writer *Writer) WriteKmerWithTaxid(mer []byte, taxid uint32) error

+ func (writer *Writer) WriteTaxid(taxid uint32) (err error)

+ func (writer *Writer) WriteWithTaxid(kcode KmerCode, taxid uint32) (err error)

Feb 9, 2020

Changes in this version

type Reader

+ func (reader *Reader) ReadCode() (uint64, error)

type Writer

+ func (writer *Writer) WriteCode(code uint64) (err error)

Jan 21, 2019

Changes in this version

type KmerCode

+ func (kcode KmerCode) BitsString() string

Jan 20, 2019

Changes in this version

+ var ErrCodeOverflow = errors.New("unikmer: code value overflow")

+ var MaxCode []uint64

Oct 10, 2018

Changes in this version

+ var ErrBrokenFile = errors.New("unikmer: broken file")

Oct 9, 2018

Changes in this version

+ const UNIK_SORTED

+ func PutUint64s(buf []byte, v1, v2 uint64) (ctrl byte, n int)

+ func Uint64s(ctrl byte, buf []byte) (values [2]uint64, n int)

+ type CodeSlice []uint64

+ func (codes CodeSlice) Len() int

+ func (codes CodeSlice) Less(i, j int) bool

+ func (codes CodeSlice) Swap(i, j int)

type Header

+ Number int64

+ type KmerCodeSlice []KmerCode

+ func (codes KmerCodeSlice) Len() int

+ func (codes KmerCodeSlice) Less(i, j int) bool

+ func (codes KmerCodeSlice) Swap(i, j int)

type Writer

+ func (writer *Writer) WriteHeader() error

Sep 24, 2018

Changes in this version

+ const UNIK_CANONICAL

+ const UNIK_COMPACT

type Header

+ Flag uint32

Sep 22, 2018

Changes in this version

+ var ErrNotConsecutiveKmers = errors.New("unikmer: not consecutive Kmers")

+ func EncodeFromFormerKmer(kmer []byte, leftKmer []byte, leftCode uint64) (uint64, error)

+ func EncodeFromLatterKmer(kmer []byte, rightKmer []byte, rightCode uint64) (uint64, error)

+ func MustEncodeFromFormerKmer(kmer []byte, leftKmer []byte, leftCode uint64) (uint64, error)

+ func MustEncodeFromLatterKmer(kmer []byte, rightKmer []byte, rightCode uint64) (uint64, error)

+ func RevComp(code uint64, k int) (c uint64)

type Header

+ MainVersion int64

+ MinorVersion int64

type KmerCode

+ func NewKmerCodeFromFormerOne(kmer []byte, leftKmer []byte, preKcode KmerCode) (KmerCode, error)

+ func NewKmerCodeMustFromFormerOne(kmer []byte, leftKmer []byte, preKcode KmerCode) (KmerCode, error)

+ func (kcode KmerCode) Canonical() KmerCode

type Reader

+ Compact bool

type Writer

+ Compact bool

Aug 9, 2018

Changes in this version

+ const MainVersion

+ const MinorVersion

+ var ErrIllegalBase = errors.New("unikmer: illegal base")

+ var ErrInvalidFileFormat = errors.New("unikmer: invalid binary format")

+ var ErrKMismatch = errors.New("unikmer: K mismatch")

+ var ErrKOverflow = errors.New("unikmer: K (1-32) overflow")

+ var Magic = [8]byte

+ func Complement(code uint64, k int) (c uint64)

+ func Decode(code uint64, k int) []byte

+ func Encode(mer []byte) (code uint64, err error)

+ func Reverse(code uint64, k int) (c uint64)

+ type Header struct

+ K int

+ Version string

+ func (h Header) String() string

+ type KmerCode struct

+ Code uint64

+ K int

+ func NewKmerCode(mer []byte) (KmerCode, error)

+ func (kcode KmerCode) Bytes() []byte

+ func (kcode KmerCode) Comp() KmerCode

+ func (kcode KmerCode) Equal(kcode2 KmerCode) bool

+ func (kcode KmerCode) Rev() KmerCode

+ func (kcode KmerCode) RevComp() KmerCode

+ func (kcode KmerCode) String() string

+ type Reader struct

+ func NewReader(r io.Reader) (*Reader, error)

+ func (reader *Reader) Read() (KmerCode, error)

+ type Writer struct

+ func NewWriter(w io.Writer, k int) *Writer

+ func (writer *Writer) Flush() error

+ func (writer *Writer) Write(kcode KmerCode) error

+ func (writer *Writer) WriteKmer(mer []byte) error