bix

README

bix

Tabix files in go.

Bixis a pure go tabix reader. Tabix has a minimum resolution of 16K bases. So, for dense annotations like ExAC, repeated queries will have to re-parse the same intervals. To mitigate this, Bix caches all annotations for the blocks from each query and re-uses them for later querires to the same block. In practice, this results in 10X-100X speedup for any type of data.

tbx, err := bix.New(f)

// Query returns an io.Reader
ph := true // print header ?
rdr, err := tbx.Query(chrom, start, end, ph)
buf := bufio.NewReader(rdr)
for {
	line, err := bufr.ReadString('\n')
	if err == io.EOF {
		break
	}
	fmt.Println(line)
}
// or

intervals := tbx.Get(chrom, start, end)

where intervals will be either a vcfgo.Variant or an Interval object with a Chrom(), Start(), and End() method.

Documentation

Overview

Tabix queries for go

Tabix queries for go

Index

• func NewCSI(r io.Reader) (cIndex, error)
• type Bix
  • func New(path string, workers ...int) (*Bix, error)
  • func NewGCP(path string, client *storage.Client, workers ...int) (*Bix, error)
  • func (tbx *Bix) AddInfoToHeader(id, number, vtype, desc string)
  • func (tbx *Bix) ChunkedReader(chrom string, start, end int) (io.ReadCloser, error)
  • func (b *Bix) Close() error
  • func (tbx *Bix) FastQuery(region interfaces.IPosition) (interfaces.RelatableIterator, error)
  • func (tbx *Bix) GetHeaderDescription(field string) string
  • func (tbx *Bix) GetHeaderNumber(field string) string
  • func (tbx *Bix) GetHeaderType(field string) string
  • func (tbx *Bix) Query(region interfaces.IPosition) (interfaces.RelatableIterator, error)
• type Index

Functions

func NewCSI

func NewCSI(r io.Reader) (cIndex, error)

Types

type Bix

type Bix struct {
	Index

	VReader *vcfgo.Reader
	// contains filtered or unexported fields
}

Bix provides read access to tabix files.

func New

func New(path string, workers ...int) (*Bix, error)

New returns a &Bix from on-disk files.

func NewGCP

func NewGCP(path string, client *storage.Client, workers ...int) (*Bix, error)

NewGCP returns a &Bix from either on-disk files or, if a GCP client is specified and the .vcf file begins with 'gs://', from a Google Storage object connection that simulates seeking capabilities.

func (*Bix) AddInfoToHeader

func (tbx *Bix) AddInfoToHeader(id, number, vtype, desc string)

func (*Bix) ChunkedReader

func (tbx *Bix) ChunkedReader(chrom string, start, end int) (io.ReadCloser, error)

func (*Bix) Close

func (b *Bix) Close() error

func (*Bix) FastQuery

func (tbx *Bix) FastQuery(region interfaces.IPosition) (interfaces.RelatableIterator, error)

FastQuery allows extracting intervals from an indexed file. Use this function if concurrency is *not* required, otherwise use Query

func (*Bix) GetHeaderDescription

func (tbx *Bix) GetHeaderDescription(field string) string

func (*Bix) GetHeaderNumber

func (tbx *Bix) GetHeaderNumber(field string) string

func (*Bix) GetHeaderType

func (tbx *Bix) GetHeaderType(field string) string

func (*Bix) Query

func (tbx *Bix) Query(region interfaces.IPosition) (interfaces.RelatableIterator, error)

Query allows extracting intervals from an indexed file. Use this function if concurrency is required, otherwise use FastQuery

type Index

type Index interface {
	Chunks(string, int, int) ([]bgzf.Chunk, error)
	NameColumn() int
	BeginColumn() int
	EndColumn() int
	ZeroBased() bool
	MetaChar() rune
	Skip() int
}

Index unifies CSI and tabix.