.. _`bio/bedtools/merge`:

MERGEBED
========


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/bedtools/merge?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/bedtools/merge

Merge entries in one or multiple BED/BAM/VCF/GFF files with bedtools.

**URL**: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bedtools_merge:
        input:
            # Multiple bed-files can be added as list
            "A.bed"
        output:
            "A.merged.bed"
        params:
            ## Add optional parameters
            extra="-c 1 -o count" ## In this example, we want to count how many input lines we merged per output line
        log:
            "logs/merge/A.log"
        wrapper:
            "v3.0.1/bio/bedtools/merge"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Notes
-----

* Warning: If multiple files are provided in input, then this wrapper requires exactly 3 threads. Else, it requires exactly one thread.

Software dependencies
---------------------

* ``bedtools=2.31.1``

Input/Output
------------
**Input:**

* Path or list of paths to interval(s) file(s) (BED/GFF/VCF/BAM)

**Output:**

* Path to merged interval(s) file.



Params
------

* ``extra``: additional program arguments (except for `-i`)




Authors
-------

* Jan Forster


Code
----

.. code-block:: python

    __author__ = "Jan Forster, Felix Mölder"
    __copyright__ = "Copyright 2019, Jan Forster"
    __email__ = "j.forster@dkfz.de, felix.moelder@uni-due.de"
    __license__ = "MIT"

    from snakemake.shell import shell

    ## Extract arguments
    extra = snakemake.params.get("extra", "")

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    if len(snakemake.input) > 1:
        if all(f.endswith(".gz") for f in snakemake.input):
            cat = "zcat"
        elif all(not f.endswith(".gz") for f in snakemake.input):
            cat = "cat"
        else:
            raise ValueError("Input files must be all compressed or uncompressed.")
        shell(
            "({cat} {snakemake.input} | "
            "sort -k1,1 -k2,2n | "
            "bedtools merge {extra} "
            "-i stdin > {snakemake.output}) "
            " {log}"
        )
    else:
        shell(
            "( bedtools merge"
            " {extra}"
            " -i {snakemake.input}"
            " > {snakemake.output})"
            " {log}"
        )


.. |nl| raw:: html

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