tabix

package

v1.0.1 Latest Latest Go to latest Published: Jan 31, 2017 License: BSD-3-Clause Imports: 8 Imported by: 0

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Repository

github.com/AlanRace/hts

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Documentation ¶

Overview ¶

Package tabix implements tabix coordinate sorted indexing.

Index ¶

func WriteTo(w io.Writer, idx *Index) error
type Index
- func New() *Index
- func ReadFrom(r io.Reader) (*Index, error)
type Record

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func WriteTo ¶

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

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

Types ¶

type Index ¶

type Index struct {
	Format    byte
	ZeroBased bool

	NameColumn  int32
	BeginColumn int32
	EndColumn   int32

	MetaChar rune
	Skip     int32
	// contains filtered or unexported fields
}

Index is a tabix index.

func New ¶

func New() *Index

New returns a new tabix index.

func ReadFrom ¶

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

ReadFrom reads the tabix index from the given io.Reader. Note that the tabix 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, placed, mapped bool) error

Add records the SAM record as having being located at the given chunk.

func (*Index) Chunks ¶

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

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

func (*Index) IDs ¶

func (i *Index) IDs() map[string]int

IDs returns a map of strings to integer IDs. The returned map should not be altered.

func (*Index) MergeChunks ¶

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

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

func (*Index) Names ¶

func (i *Index) Names() []string

Names returns the reference names in the index. The returned slice should not be altered.

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 {
	RefName() string
	Start() int
	End() int
}

Record wraps types that may be indexed by an Index.

Source Files ¶

View all Source files

tabix.go

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