Reproduce bedtools methods

[noamteyssier]

• intersect
• window
• closest
• coverage
• map
• genomecov
• merge
• cluster
• complement
• shift
• subtract
• slop
• flank
• sort
• random
• shuffle
• sample
• spacing
• unionbedg

[mrvollger]

I don't know if you are going for every subcommand but if so I would like to see this one as well:

bedtools unionbedg

Tool:    bedtools unionbedg (aka unionBedGraphs)
Version: v2.31.0
Summary: Combines multiple BedGraph files into a single file,
         allowing coverage comparisons between them.

Usage:   bedtools unionbedg [OPTIONS] -i FILE1 FILE2 .. FILEn
         Assumes that each BedGraph file is sorted by chrom/start
         and that the intervals in each are non-overlapping.

Options:
        -header         Print a header line.
                        (chrom/start/end + names of each file).

        -names          A list of names (one/file) to describe each file in -i.
                        These names will be printed in the header line.

        -g              Use genome file to calculate empty regions.
                        - STRING.

        -empty          Report empty regions (i.e., start/end intervals w/o
                        values in all files).
                        - Requires the '-g FILE' parameter.

        -filler TEXT    Use TEXT when representing intervals having no value.
                        - Default is '0', but you can use 'N/A' or any text.

        -examples       Show detailed usage examples.

Error: missing BedGraph file names (-i) to combine.

[noamteyssier]

Sure - seems easy enough. I'll add this to the list

[noamteyssier]

@mrvollger

I took a stab at unionbedg and it's available in the gia-2.0 branch of the repo if you'd like to try it out.
I don't have the additional arguments implemented but should be easy to fill in later.