bigWig

Documentation

Index

• type BbiHeader
• type BigWig
  • func Read(filename string) BigWig
• type TotalSummaryBlock
• type ZoomHeader

Types

type BbiHeader

type BbiHeader struct {
	Magic                uint32 // magic bytes at the beginning of file. Must match constant above to be a valid bigWig.
	Version              uint16 // Specifies the wig version. This package was built following specs for bigWig version 4.
	ZoomLevels           uint16 // Number of zoom levels built into the file.
	ChromosomeTreeOffset uint64 // Offset in file to chromosome B+ tree index.
	FullDataOffset       uint64 // Offset to the main dta. Points to the dataCount.
	FullIndexOffset      uint64 // Offset to R tree index of items.
	FieldCount           uint16 // Number of fields in a BED file. For bigWig, this should always be zero.
	DefinedFieldCount    uint16 // Number of fields that are predefined BED files. this should also be zero for bigWig files.
	AutoSqlOffset        uint64 // From specs: Offset to zero-terminated string with .as spec. Used for bigBed, not used in bigWig.
	TotalSummaryOffset   uint64 // Offset to overall file summary data block.
	UncompressBufferSize uint32 // Maximum size of decompression buffer needed (nonzero on compressed files).
	ExtensionOffset      uint64 // Offset to header extension 0 if no such extension.
}

BbiHeader represents the bbi header of the bigWig data file and contains metadata and offset values for file navigation.

type BigWig

type BigWig struct {
	BbiHeader         BbiHeader         // Contains high-level information about file and offsets to various parts of the file.
	ZoomHeaders       []ZoomHeader      // One for each zoom level built into the file, as specified in the BbiHeader.
	TotalSummaryBlock TotalSummaryBlock // Statistical summary of the entire file.
}

BigWig represents the data of a BigWig file in a data structure.

func Read

func Read(filename string) BigWig

Read parses a BigWig struct from an input filename.

type TotalSummaryBlock

type TotalSummaryBlock struct {
	BasesCovered uint64  // Number of bases for which there is data.
	MinVal       float64 // Minimum value in the file.
	MaxVal       float64 // Maximum value in the file.
	SumData      float64 // Sum of all values in the file.
	SumSquares   float64 // Sum of all squares of values in the file.
}

TotalSummaryBlock provides an overall statistical summary of the file contents. Mean and standard deviation values can be quickly calculated from these values.

type ZoomHeader

type ZoomHeader struct {
	ReductionLevel uint32 // Number of bases summarized in each reduction level.
	Reserved       uint32 // Reserved for future expansion. 0 in bigWig.
	DataOffset     uint64 // Position of zoomed data in file.
	IndexOffset    uint64 // Position of zoomed data index in file.
}

ZoomHeader immediately follows the BbiHeader in the file, one for each of the ZoomLevels, as specified in the BbiHeader.