bed

Documentation

Overview

Package bed handles BED I/O.

Format

This package uses the format described in: https://en.wikipedia.org/wiki/BED_(file_format)

Index

• Constants
• type BED
• type Reader
  • func NewReader(r io.Reader) *Reader
  • func (r *Reader) Next() (*BED, int, error)

Constants

const (
	PlusStrand  = "+"
	MinusStrand = "-"
	NoStrand    = "."
)

Valid values for the strand field.

Types

type BED

type BED struct {
	Chrom       string
	ChromStart  int // 0-based
	ChromEnd    int // 0-based exclusive
	Name        string
	Score       int
	Strand      string
	ThickStart  int
	ThickEnd    int
	ItemRGB     [3]byte
	BlockCount  int
	BlockSizes  []int // Length should match BlockCount
	BlockStarts []int // Length should match BlockCount
}

BED is a single line in a BED file.

type Reader

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

A Reader reads and parses BED lines.

func NewReader

func NewReader(r io.Reader) *Reader

NewReader returns a new BED reader that reads from r.

func (*Reader) Next

func (r *Reader) Next() (*BED, int, error)

Next returns the next BED line, and the number of fields that were found. That number of fields will be populated in the result BED, by order of appearance. The rest will have zero values.