index

Documentation

Index

• Constants
• Variables
• type Header
  • func (h Header) Compatible(b Header) bool
  • func (h Header) String() string
• type Reader
  • func NewReader(r io.Reader) (reader *Reader, err error)
  • func (reader *Reader) Read() ([]byte, error)
• type Writer
  • func NewWriter(w io.Writer, k int, canonical bool, numHashes uint8, numSigs uint64, ...) (*Writer, error)
  • func (writer *Writer) Flush() (err error)
  • func (writer *Writer) Write(data []byte) (err error)
  • func (writer *Writer) WriteBatch(data []byte, n int) (err error)
  • func (writer *Writer) WriteHeader() (err error)

Constants

const Version uint8 = 2

Version is the version of index format

Variables

var ErrInvalidIndexFileFormat = errors.New("unikmer/index: invalid index format")

ErrInvalidIndexFileFormat means invalid index format.

var ErrNameAndIndexMismatch = errors.New("unikmer/index: size of names and indices unequal")

ErrNameAndIndexMismatch means size of names and sizes are not equal.

var ErrNameAndSizeMismatch = errors.New("unikmer/index: size of names and sizes unequal")

ErrNameAndSizeMismatch means size of names and sizes are not equal.

var ErrTruncateIndexFile = errors.New("unikmer/index: truncated index file")

ErrTruncateIndexFile means the file is truncated

var ErrUnfishedWrite = errors.New("unikmer/index: index not fished writing")

ErrUnfishedWrite means writing not finished

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

ErrVersionMismatch means version mismatch between files and program

var ErrWrongWriteDataSize = errors.New("unikmer/index: write data with wrong size")

ErrWrongWriteDataSize means the size of data to write is invalid

var Magic = [8]byte{'.', 'u', 'n', 'i', 'k', 'i', 'd', 'x'}

Magic number of index file.

Types

type Header

type Header struct {
	Version   uint8 // uint8
	K         int   // uint8
	Canonical bool  // uint8
	NumHashes uint8 // uint8
	NumSigs   uint64
	Names     []string
	Indices   []uint32
	Sizes     []uint64

	NumRowBytes int // length of bytes for storing one row of signiture for n names
}

Header contains metadata

func (Header) Compatible

func (h Header) Compatible(b Header) bool

Compatible checks compatibility

func (Header) String

func (h Header) String() string

type Reader

type Reader struct {
	Header
	// contains filtered or unexported fields
}

Reader is for reading KmerCode.

func NewReader

func NewReader(r io.Reader) (reader *Reader, err error)

NewReader returns a Reader.

func (*Reader) Read

func (reader *Reader) Read() ([]byte, error)

Read reads one code.

type Writer

type Writer struct {
	Header
	// contains filtered or unexported fields
}

Writer writes KmerCode.

func NewWriter

func NewWriter(w io.Writer, k int, canonical bool, numHashes uint8, numSigs uint64, names []string, indices []uint32, sizes []uint64) (*Writer, error)

NewWriter creates a Writer.

func (*Writer) Flush

func (writer *Writer) Flush() (err error)

Flush check completeness

func (*Writer) Write

func (writer *Writer) Write(data []byte) (err error)

Write writes some thing

func (*Writer) WriteBatch

func (writer *Writer) WriteBatch(data []byte, n int) (err error)

WriteBatch writes a batch of data

func (*Writer) WriteHeader

func (writer *Writer) WriteHeader() (err error)

WriteHeader writes file header