Reference

BEDTools

Julia bindings to BEDTools, the suite of tools for genomic intervals, from BEDTools_jll.

BEDTools is a program rather than a library, so the bindings are its commands. BEDTools.Bindings has a builder for the command of every subcommand, generated from its help, which checks its options; BEDTools.lines runs a command and returns its output. BEDTools.sort, BEDTools.intersect, BEDTools.bed12tobed6 and BEDTools.genomecov run the subcommands that are used most. Its main use is as a reference implementation, to validate Julia packages against BEDTools.

BEDToolsError(arguments, message)

The error of a call of bedtools that failed: its arguments, and what BEDTools wrote to standard error. It keeps the arguments rather than the command, whose environment would show every environment variable.

BEDTools.bed12tobed6(path; options...)::Vector{String}

The blocks of the BED12 records of path, each as a BED6 record, as bedtools bed12tobed6 -i path prints them. options are those of BEDTools.Bindings.bed12tobed6.

BEDTools.command(arguments...)::Cmd

The bedtools command of BEDTools_jll with arguments, as on the command line, such as BEDTools.command("sort", "-i", path). It checks nothing, for what the help of a subcommand doesn't describe; the builders of BEDTools.Bindings check their options.

BEDTools.genomecov(path, genome; options...)::Vector{String}

The coverage of the intervals of path over the genome of the file genome, as bedtools genomecov -i path -g genome prints it. options are those of BEDTools.Bindings.genomecov, such as bg = true for a BedGraph.

BEDTools.intersect(a, b; options...)::Vector{String}

The output of bedtools intersect -a a -b b, for the interval files a and b. options are those of BEDTools.Bindings.intersect: wa = true, wb = true prints each pair of overlapping intervals, and v = true the intervals of a that overlap none of b.

BEDTools.is_available()::Bool

Whether BEDTools_jll provides BEDTools for this platform.

BEDTools.lines(command::Cmd)::Vector{String}

Run command, such as one of BEDTools.Bindings or BEDTools.command, and return the lines that it writes to standard output. If it fails, a BEDToolsError gives its arguments and what it wrote to standard error.

So BEDTools.lines(BEDTools.Bindings.merge(i = "features.bed", d = 10)) runs bedtools merge -i features.bed -d 10.

BEDTools.sort(path; options...)::Vector{String}

The lines of the BED, GFF or VCF file path, sorted by sequence and start position, as bedtools sort -i path prints them. options are those of BEDTools.Bindings.sort, such as sizeA = true for -sizeA.

BEDTools.version()::VersionNumber

The version of the bedtools of BEDTools_jll.