csi

package

v1.0.1 Latest Latest Go to latest Published: Jan 31, 2017 License: BSD-3-Clause Imports: 7 Imported by: 0

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Repository

github.com/AlanRace/hts

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Documentation ¶

Overview ¶

Package csi implements CSIv1 and CSIv2 coordinate sorted indexing.

Index ¶

Constants
func MinimumDepthFor(max int64, shift uint32) (uint32, bool)
func MinimumShiftFor(max int64, depth uint32) (uint32, bool)
func WriteTo(w io.Writer, idx *Index) error
type Index
- func New(minShift, depth int) *Index
- func ReadFrom(r io.Reader) (*Index, error)
type Record

Constants ¶

View Source

const (
	// DefaultShift is the default minimum shift setting for a CSI.
	DefaultShift = 14

	// DefaultDepth is the default index depth for a CSI.
	DefaultDepth = 5
)

Variables ¶

This section is empty.

Functions ¶

func MinimumDepthFor ¶

func MinimumDepthFor(max int64, shift uint32) (uint32, bool)

MinimumDepthFor returns the lowest depth value that can be used to index the given maximum position with the given index minimum shift.

func MinimumShiftFor ¶

func MinimumShiftFor(max int64, depth uint32) (uint32, bool)

MinimumShiftFor returns the lowest minimum shift value that can be used to index the given maximum position with the given index depth.

func WriteTo ¶

func WriteTo(w io.Writer, idx *Index) error

WriteTo writes the CSI index to the given io.Writer. Note that the csi specification states that the index is stored as BGZF, but WriteTo does not perform compression.

Types ¶

type Index ¶

type Index struct {
	Auxilliary []byte
	Version    byte
	// contains filtered or unexported fields
}

Index implements coordinate sorted indexing.

func New ¶

func New(minShift, depth int) *Index

New returns a CSI index with the given minimum shift and depth. The returned index defaults to CSI version 2.

func ReadFrom ¶

func ReadFrom(r io.Reader) (*Index, error)

ReadFrom reads the CSI index from the given io.Reader. Note that the csi specification states that the index is stored as BGZF, but ReadFrom does not perform decompression.

func (*Index) Add ¶

func (i *Index) Add(r Record, c bgzf.Chunk, mapped, placed bool) error

Add records the Record as having being located at the given chunk with the given mapping and placement status.

func (*Index) Chunks ¶

func (i *Index) Chunks(rid int, beg, end int) []bgzf.Chunk

Chunks returns a []bgzf.Chunk that corresponds to the given interval.

func (*Index) MergeChunks ¶

func (i *Index) MergeChunks(s index.MergeStrategy)

MergeChunks applies the given MergeStrategy to all bins in the Index.

func (*Index) NumRefs ¶

func (i *Index) NumRefs() int

NumRefs returns the number of references in the index.

func (*Index) ReferenceStats ¶

func (i *Index) ReferenceStats(id int) (stats index.ReferenceStats, ok bool)

ReferenceStats returns the index statistics for the given reference and true if the statistics are valid.

func (*Index) Unmapped ¶

func (i *Index) Unmapped() (n uint64, ok bool)

Unmapped returns the number of unmapped reads and true if the count is valid.

type Record ¶

type Record interface {
	RefID() int
	Start() int
	End() int
}

Record wraps types that may be indexed by an Index.

Source Files ¶

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