bamat

Documentation

Index

• type BamAt
  • func New(path string) (*BamAt, error)
  • func (b *BamAt) Close() error
  • func (b *BamAt) Query(chrom string, start int, end int) (*bam.Iterator, error)

Types

type BamAt

type BamAt struct {
	*bam.Reader

	Refs map[string]*sam.Reference
	// contains filtered or unexported fields
}

BamAt holds bam index and the Bam Reader. Because BamAt holds the underlying os.File open, it is not safe to query from multiple go routines.

func New

func New(path string) (*BamAt, error)

New returns a BamAt from the given path to the indexed bam

func (*BamAt) Close

func (b *BamAt) Close() error

Close closes the underlying file and the Bam.Reader

func (*BamAt) Query

func (b *BamAt) Query(chrom string, start int, end int) (*bam.Iterator, error)

Query the BamAt with 0-base half-open interval.