internal

package

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

Details

Valid go.mod file

The Go module system was introduced in Go 1.11 and is the official dependency management solution for Go.
Redistributable license

Redistributable licenses place minimal restrictions on how software can be used, modified, and redistributed.
Tagged version

Modules with tagged versions give importers more predictable builds.
Stable version

When a project reaches major version v1 it is considered stable.
Learn more about best practices

Repository

github.com/AlanRace/hts

Links

Open Source Insights

Documentation ¶

Overview ¶

Package internal provides shared code for BAI and tabix index implementations.

Index ¶

Constants
func BinFor(beg, end int) uint32
func IsValidIndexPos(i int) bool
func OverlappingBinsFor(beg, end int) []uint32
func WriteIndex(w io.Writer, idx *Index, typ string) error
type Bin
type Index
- func ReadIndex(r io.Reader, n int32, typ string) (Index, error)
type Record
type RefIndex
type ReferenceStats

Constants ¶

View Source

const (
	// TileWidth is the length of the interval tiling used
	// in BAI and tabix indexes.
	TileWidth = 0x4000

	// StatsDummyBin is the bin number of the reference
	// statistics bin used in BAI and tabix indexes.
	StatsDummyBin = 0x924a
)

Variables ¶

This section is empty.

Functions ¶

func BinFor ¶

func BinFor(beg, end int) uint32

BinFor returns the bin number for given an interval covering [beg,end) (zero-based, half-close-half-open).

func IsValidIndexPos ¶

func IsValidIndexPos(i int) bool

IsValidIndexPos returns a boolean indicating whether the given position is in the valid range for BAM/SAM.

func OverlappingBinsFor ¶

func OverlappingBinsFor(beg, end int) []uint32

OverlappingBinsFor returns the bin numbers for all bins overlapping an interval covering [beg,end) (zero-based, half-close-half-open).

func WriteIndex ¶

func WriteIndex(w io.Writer, idx *Index, typ string) error

WriteIndex writes the Index to the given io.Writer.

Types ¶

type Bin ¶

type Bin struct {
	Bin    uint32
	Chunks []bgzf.Chunk
}

Bin is an index bin.

type Index ¶

type Index struct {
	Refs       []RefIndex
	Unmapped   *uint64
	IsSorted   bool
	LastRecord int
}

Index is a coordinate based index.

func ReadIndex ¶

func ReadIndex(r io.Reader, n int32, typ string) (Index, error)

ReadIndex reads the Index from the given io.Reader.

func (*Index) Add ¶

func (i *Index) Add(r Record, bin uint32, 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(rid, beg, end int) ([]bgzf.Chunk, error)

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

func (*Index) MergeChunks ¶

func (i *Index) MergeChunks(s func([]bgzf.Chunk) []bgzf.Chunk)

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

type Record ¶

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

Record wraps types that may be indexed by an Index.

type RefIndex ¶

type RefIndex struct {
	Bins      []Bin
	Stats     *ReferenceStats
	Intervals []bgzf.Offset
}

RefIndex is the index of a single reference.

type ReferenceStats ¶

type ReferenceStats struct {
	// Chunk is the span of the indexed BGZF
	// holding alignments to the reference.
	Chunk bgzf.Chunk

	// Mapped is the count of mapped reads.
	Mapped uint64

	// Unmapped is the count of unmapped reads.
	Unmapped uint64
}

ReferenceStats holds mapping statistics for a genomic reference.

Source Files ¶

View all Source files

?	: This menu
/	: Search site
f or F	: Jump to
y or Y	: Canonical URL