bbi

package
v0.0.19 Latest Latest
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 Go to latest Published: Apr 27, 2021 License: GPL-2.0 Imports: 17 Imported by: 2

Documentation

Overview

　add support to io.ReadSeeker interface by Xiaopeng Zhu 

*

Index

Constants

View Source 
const BIGBED_MAGIC = 0x8789F2EB
View Source 
const BIGWIG_MAGIC = 0x888FFC26
View Source 
const BbiMaxZoomLevels = 10 /* Max number of zoom levels */
View Source 
const BbiResIncrement = 4 /* Amount to reduce at each zoom level */
View Source 
const CIRTREE_MAGIC = 0x78ca8c91
View Source 
const IDX_MAGIC = 0x2468ace0

Variables

This section is empty.

Functions

This section is empty.

Types

type BData 

type BData struct {
	KeySize       uint32
	ValueSize     uint32
	ItemsPerBlock uint32
	ItemCount     uint64

	Keys   [][]byte
	Values [][]byte
}

func NewBData 

func NewBData() *BData

func (*BData) Add 

func (data *BData) Add(key, value []byte) error

func (*BData) Read 

func (data *BData) Read(file io.ReadSeeker) error

func (*BData) Write 

func (data *BData) Write(file io.WriteSeeker) error

type BTree 

type BTree struct {
	KeySize       uint32
	ValueSize     uint32
	ItemsPerBlock uint32
	ItemCount     uint64
	Root          BVertex
}

func NewBTree 

func NewBTree(data *BData) *BTree

func (*BTree) Write 

func (tree *BTree) Write(file io.WriteSeeker) error

type BVertex 

type BVertex struct {
	IsLeaf   uint8
	Keys     [][]byte
	Values   [][]byte
	Children []BVertex
}

func (*BVertex) BuildTree 

func (vertex *BVertex) BuildTree(data *BData, from, to uint64, level int) (uint64, error)

type BbiBlockDecoder 

type BbiBlockDecoder struct {
	Header BbiDataHeader
	Buffer []byte
}

func NewBbiBlockDecoder 

func NewBbiBlockDecoder(buffer []byte) (*BbiBlockDecoder, error)

func (*BbiBlockDecoder) Decode 

func (reader *BbiBlockDecoder) Decode() <-chan BbiBlockDecoderType

func (*BbiBlockDecoder) Import 

func (reader *BbiBlockDecoder) Import(sequence []float64, binsize int) error

type BbiBlockDecoderType 

type BbiBlockDecoderType struct {
	Idx   int
	From  int
	To    int
	Value float64
	Error error
}

type BbiBlockEncoder 

type BbiBlockEncoder struct {
	ItemsPerSlot int
	// contains filtered or unexported fields
}

func NewBbiBlockEncoder 

func NewBbiBlockEncoder(itemsPerSlot int) (*BbiBlockEncoder, error)

func (*BbiBlockEncoder) EncodeBlock 

func (writer *BbiBlockEncoder) EncodeBlock(chromid int, sequence []float64, binsize, reductionLevel int, fixedStep bool) <-chan BbiBlockEncoderType

type BbiBlockEncoderType 

type BbiBlockEncoderType struct {
	From  int
	To    int
	Block []byte
	Error error
}

type BbiDataHeader 

type BbiDataHeader struct {
	ChromId   uint32
	Start     uint32
	End       uint32
	Step      uint32
	Span      uint32
	Type      byte
	Reserved  byte
	ItemCount uint16
}

func (*BbiDataHeader) ReadBuffer 

func (header *BbiDataHeader) ReadBuffer(buffer []byte)

func (*BbiDataHeader) WriteBuffer 

func (header *BbiDataHeader) WriteBuffer(buffer []byte)

type BbiHeader 

type BbiHeader struct {
	Magic             uint32
	Version           uint16
	ZoomLevels        uint16
	CtOffset          uint64
	DataOffset        uint64
	IndexOffset       uint64
	FieldCould        uint16
	DefinedFieldCount uint16
	SqlOffset         uint64
	SummaryOffset     uint64
	UncompressBufSize uint32
	ExtensionOffset   uint64
	NBasesCovered     uint64
	MinVal            uint64
	MaxVal            uint64
	SumData           uint64
	SumSquared        uint64
	ZoomHeaders       []BbiHeaderZoom
	NBlocks           uint64
	// offset positions
	PtrCtOffset          int64
	PtrDataOffset        int64
	PtrIndexOffset       int64
	PtrSqlOffset         int64
	PtrSummaryOffset     int64
	PtrUncompressBufSize int64
	PtrExtensionOffset   int64
}

func NewBbiHeader 

func NewBbiHeader() *BbiHeader

func (*BbiHeader) Read 

func (header *BbiHeader) Read(file io.ReadSeeker) error

func (header *BbiHeader) Read(file *os.File) error {

func (*BbiHeader) Write 

func (header *BbiHeader) Write(file io.WriteSeeker) error

func (*BbiHeader) WriteNBlocks 

func (header *BbiHeader) WriteNBlocks(file io.WriteSeeker) error

func (*BbiHeader) WriteOffsets 

func (header *BbiHeader) WriteOffsets(file io.WriteSeeker) error

func (*BbiHeader) WriteUncompressBufSize 

func (header *BbiHeader) WriteUncompressBufSize(file io.WriteSeeker) error

type BbiHeaderZoom 

type BbiHeaderZoom struct {
	ReductionLevel uint32
	Reserved       uint32
	DataOffset     uint64
	IndexOffset    uint64
	NBlocks        uint32
	PtrDataOffset  int64
	PtrIndexOffset int64
}

func (*BbiHeaderZoom) Read 

func (zoomHeader *BbiHeaderZoom) Read(file io.ReadSeeker) error

func (*BbiHeaderZoom) Write 

func (zoomHeader *BbiHeaderZoom) Write(file io.WriteSeeker) error

func (*BbiHeaderZoom) WriteNBlocks 

func (zoomHeader *BbiHeaderZoom) WriteNBlocks(file io.WriteSeeker) error

func (*BbiHeaderZoom) WriteOffsets 

func (zoomHeader *BbiHeaderZoom) WriteOffsets(file io.WriteSeeker) error

type BbiQueryType 

type BbiQueryType struct {
	BbiSummaryRecord
	Error error
}

func NewBbiQueryType 

func NewBbiQueryType() *BbiQueryType

type BbiReader 

type BbiReader struct {
	Header    BbiHeader
	ChromData BData
	Index     RTree
	IndexZoom []RTree
	Fptr      io.ReadSeeker
	// contains filtered or unexported fields
}

func NewBbiReader 

func NewBbiReader(f io.ReadSeeker) *BbiReader

func (*BbiReader) Close 

func (bwf *BbiReader) Close() error

func (*BbiReader) Genome 

func (bwf *BbiReader) Genome() ([]string, []int)

func (*BbiReader) InitIndex 

func (bwf *BbiReader) InitIndex() error

func (*BbiReader) Query 

func (bwf *BbiReader) Query(idx, from, to, binsize int) <-chan *BbiQueryType

func (*BbiReader) QueryBedBin 

func (bwf *BbiReader) QueryBedBin(idx, from, to, binsize int) <-chan *BedBbiQueryType

func (*BbiReader) QueryBedRaw 

func (bwf *BbiReader) QueryBedRaw(idx, from, to int) <-chan *BedBbiBlockDecoderType

func (*BbiReader) QueryRaw 

func (bwf *BbiReader) QueryRaw(idx, from, to int) <-chan *BbiBlockDecoderType

func (*BbiReader) ReadIndex 

func (bwf *BbiReader) ReadIndex(f io.ReadSeeker) error

func (*BbiReader) WriteIndex 

func (bwf *BbiReader) WriteIndex(f io.WriteSeeker) error

type BbiSummaryRecord 

type BbiSummaryRecord struct {
	ChromId    int
	From       int
	To         int
	Valid      int
	Min        float64
	Max        float64
	Sum        float64
	SumSquares float64
}

func NewBbiSummaryRecord 

func NewBbiSummaryRecord() BbiSummaryRecord

func (*BbiSummaryRecord) AddRecord 

func (record *BbiSummaryRecord) AddRecord(x BbiSummaryRecord)

func (*BbiSummaryRecord) AddValue 

func (record *BbiSummaryRecord) AddValue(x float64)

type BbiZoomBlockDecoder 

type BbiZoomBlockDecoder struct {
	Buffer []byte
}

func NewBbiZoomBlockDecoder 

func NewBbiZoomBlockDecoder(buffer []byte) *BbiZoomBlockDecoder

func (*BbiZoomBlockDecoder) Decode 

func (reader *BbiZoomBlockDecoder) Decode() <-chan BbiZoomBlockDecoderType

type BbiZoomBlockDecoderType 

type BbiZoomBlockDecoderType struct {
	BbiSummaryRecord
	Error error
}

type BbiZoomRecord 

type BbiZoomRecord struct {
	ChromId    uint32
	Start      uint32
	End        uint32
	Valid      uint32
	Min        float32
	Max        float32
	Sum        float32
	SumSquares float32
}

func (*BbiZoomRecord) Read 

func (record *BbiZoomRecord) Read(reader io.Reader) error

func (BbiZoomRecord) Write 

func (record BbiZoomRecord) Write(writer io.Writer) error

type BedBbiBlockDecoder 

type BedBbiBlockDecoder struct {
	//Header BedBbiDataHeader
	Buffer []byte
}

func NewBedBbiBlockDecoder 

func NewBedBbiBlockDecoder(buffer []byte) (*BedBbiBlockDecoder, error)

func (*BedBbiBlockDecoder) Decode 

func (reader *BedBbiBlockDecoder) Decode() <-chan *BedBbiBlockDecoderType

type BedBbiBlockDecoderType 

type BedBbiBlockDecoderType struct {
	Idx   int
	From  int
	To    int
	Value string
	Error error
}

type BedBbiDataHeader 

type BedBbiDataHeader struct {
	ChromId uint32
	Start   uint32
	End     uint32
}

type BedBbiQueryType 

type BedBbiQueryType struct {
	*BedBbiSummaryRecord
	Error error
}

func NewBedBbiQueryType 

func NewBedBbiQueryType() *BedBbiQueryType

type BedBbiSummaryRecord 

type BedBbiSummaryRecord struct {
	ChromId int
	From    int
	To      int
	Valid   int
	Sum     float64
}

func NewBedBbiSummaryRecord 

func NewBedBbiSummaryRecord() *BedBbiSummaryRecord

func (*BedBbiSummaryRecord) AddRecord 

func (record *BedBbiSummaryRecord) AddRecord(x BbiSummaryRecord)

func (*BedBbiSummaryRecord) AddValue 

func (record *BedBbiSummaryRecord) AddValue(x float64)

type BigBedReader 

type BigBedReader struct {
	Reader *BbiReader
	Genome Genome
}

func NewBigBedReader 

func NewBigBedReader(b *BbiReader) *BigBedReader

func (*BigBedReader) Binsizes 

func (bw *BigBedReader) Binsizes() []int

func (*BigBedReader) Format 

func (bb *BigBedReader) Format(e *BedBbiBlockDecoderType) string

func (*BigBedReader) GetBinsize 

func (bw *BigBedReader) GetBinsize(length int, width int) int

func (*BigBedReader) Iter 

func (bb *BigBedReader) Iter() <-chan *BedBbiBlockDecoderType

func (*BigBedReader) Query 

func (bw *BigBedReader) Query(chr string, start int, end int, width int) (<-chan *BedBbiQueryType, error)

func (*BigBedReader) QueryBin 

func (bw *BigBedReader) QueryBin(chr string, start int, end int, binsize int) (<-chan *BedBbiQueryType, error)

func (*BigBedReader) QueryRaw 

func (bw *BigBedReader) QueryRaw(chr string, start int, end int) (<-chan *BedBbiBlockDecoderType, error)

type BigWigReader 

type BigWigReader struct {
	Reader *BbiReader
	Genome Genome
}

func NewBigWigReader 

func NewBigWigReader(b *BbiReader) *BigWigReader

func (*BigWigReader) Binsizes 

func (bw *BigWigReader) Binsizes() []int

func (*BigWigReader) GetBinsize 

func (bw *BigWigReader) GetBinsize(length int, width int) int

func (*BigWigReader) Query 

func (bw *BigWigReader) Query(chr string, start int, end int, width int) (<-chan *BbiQueryType, error)

func (*BigWigReader) QueryBin 

func (bw *BigWigReader) QueryBin(chr string, start int, end int, binsize int) (<-chan *BbiQueryType, error)

QueryBin: * Query with binsize

func (*BigWigReader) QueryRaw 

func (bw *BigWigReader) QueryRaw(chr string, start int, end int) (<-chan *BbiBlockDecoderType, error)

type Chromo 

type Chromo struct {
	Idx    int
	Name   string
	Length int
}

type Genome 

type Genome struct {
	Chrs    []Chromo
	Chr2Idx map[string]int
}

type RTree 

type RTree struct {
	BlockSize     uint32
	NItems        uint64
	ChrIdxStart   uint32
	BaseStart     uint32
	ChrIdxEnd     uint32
	BaseEnd       uint32
	IdxSize       uint64
	NItemsPerSlot uint32
	Root          *RVertex
	PtrIdxSize    int64
}

func NewRTree 

func NewRTree() *RTree

func (*RTree) BuildTree 

func (tree *RTree) BuildTree(leaves []*RVertex) error

func (*RTree) Read 

func (tree *RTree) Read(file io.ReadSeeker) error

func (*RTree) Write 

func (tree *RTree) Write(file io.WriteSeeker) error

func (*RTree) WriteSize 

func (tree *RTree) WriteSize(file io.WriteSeeker) error

type RTreeTraverser 

type RTreeTraverser struct {
	Tree *RTree
}

func NewRTreeTraverser 

func NewRTreeTraverser(tree *RTree) RTreeTraverser

func (RTreeTraverser) QueryVertices 

func (traverser RTreeTraverser) QueryVertices(idx, from, to int) <-chan RTreeTraverserType

type RTreeTraverserType 

type RTreeTraverserType struct {
	Vertex *RVertex
	Idx    int
}

type RVertex 

type RVertex struct {
	IsLeaf      uint8
	NChildren   uint16
	ChrIdxStart []uint32
	BaseStart   []uint32
	ChrIdxEnd   []uint32
	BaseEnd     []uint32
	DataOffset  []uint64
	Sizes       []uint64
	Children    []*RVertex
	// positions of DataOffset and Sizes values in file
	PtrDataOffset []int64
	PtrSizes      []int64
}

func (*RVertex) Read 

func (vertex *RVertex) Read(file io.ReadSeeker) error
TODO MV BbiFile to BbiWriteSeeker

func (vertex *RVertex) WriteBlock(bwf *BbiWriteSeeker, i int, block []byte) error {
	var err error
	if bwf.Header.UncompressBufSize != 0 {
		// update header.UncompressBufSize if block length
		// exceeds size
		if uint32(len(block)) > bwf.Header.UncompressBufSize {
			bwf.Header.UncompressBufSize = uint32(len(block))
			if err = bwf.Header.WriteUncompressBufSize(bwf.Fptr); err != nil {
				return err
			}
		}
		if block, err = compressSlice(block); err != nil {
			return err
		}
	}
	// get current offset and update DataOffset[i]
	if offset, err := bwf.Fptr.Seek(0, 1); err != nil {
		return err
	} else {
		vertex.DataOffset[i] = uint64(offset)
		// write updated value to the required position in the file
		if vertex.PtrDataOffset[i] != 0 {
			if err = fileWriteAt(bwf.Fptr, binary.LittleEndian, int64(vertex.PtrDataOffset[i]), vertex.DataOffset[i]); err != nil {
				return err
			}
		}
	}
	// write data
	if err = binary.Write(bwf.Fptr, binary.LittleEndian, block); err != nil {
		return err
	}
	// update size of the data block
	vertex.Sizes[i] = uint64(len(block))
	// write it to the required position in the file
	if vertex.PtrSizes[i] != 0 {
		if err = fileWriteAt(bwf.Fptr, binary.LittleEndian, int64(vertex.PtrSizes[i]), vertex.Sizes[i]); err != nil {
			return err
		}
	}
	return nil
}

func (*RVertex) ReadBlockFromReader 

func (vertex *RVertex) ReadBlockFromReader(bwf *BbiReader, i int) ([]byte, error)

func (*RVertex) Write 

func (vertex *RVertex) Write(file io.WriteSeeker) error

type RVertexGenerator 

type RVertexGenerator struct {
	BlockSize    int
	ItemsPerSlot int
	Channel      chan RVertexGeneratorType
}

func NewRVertexGenerator 

func NewRVertexGenerator(blockSize, itemsPerSlot int) (*RVertexGenerator, error)

func (*RVertexGenerator) Generate 

func (generator *RVertexGenerator) Generate(idx int, sequence []float64, binsize, reductionLevel int, fixedStep bool) <-chan RVertexGeneratorType

type RVertexGeneratorType 

type RVertexGeneratorType struct {
	Vertex *RVertex
	Blocks [][]byte
}

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