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API Reference

Public

Internal

BED.Reader — Method
BED.Reader(input::IO; index=nothing)
BED.Reader(input::AbstractString; index=:auto)

Create a data reader of the BED file format.

The first argument specifies the data source. When it is a filepath that ends with .bgz, it is considered to be block compression file format (BGZF) and the function will try to find a tabix index file (<filename>.tbi) and read it if any. See http://www.htslib.org/doc/tabix.html for bgzip and tabix tools.

Arguments

  • input: data source
  • index: path to a tabix file
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BED.Record — Method
BED.Record(str::AbstractString)

Create a BED record object from str.

This function verifies and indexes fields for accessors.

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BED.Record — Method
BED.Record(data::Vector{UInt8})

Create a BED record object from data.

This function verifies and indexes fields for accessors. Note that the ownership of data is transferred to a new record object.

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BED.Writer — Type
BED.Writer(output::IO)

Create a data writer of the BED file format.

Arguments:

  • output: data sink
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BED.blockcount — Method
blockcount(record::Record)::Int

Get the number of blocks (exons) in record.

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BED.blocksizes — Method
blocksizes(record::Record)::Vector{Int}

Get the block (exon) sizes of record.

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BED.blockstarts — Method
blockstarts(record::Record)::Vector{Int}

Get the block (exon) starts of record.

Note that the first base is numbered 1.

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BED.chrom — Method
chrom(record::Record)::String

Get the chromosome name of record.

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BED.chromstart — Method
chromstart(record::Record)::Int

Get the starting position of record.

Note that the first base is numbered 1.

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BED.name — Method
name(record::Record)::String

Get the name of record.

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BED.score — Method
score(record::Record)::Int

Get the score between 0 and 1000.

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BED.strand — Method
strand(record::Record)::GenomicFeatures.Strand

Get the strand of record.

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BED.thickend — Method
thickend(record::Record)::Int

Get the end position at which record is drawn thickly.

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BED.thickstart — Method
thickstart(record::Record)::Int

Get the starting position at which record is drawn thickly.

Note that the first base is numbered 1.

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Base.read! — Method
read!(rdr::Reader, rec::Record)

Read a Record into rec; overwriting or adding to existing field values. It is assumed that rec is already initialized or empty.

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