.. _`bio/bedtools/bamtobed`:

BAMTOBED
========


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

Conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.


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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bamtobed:
        input:
            "{sample}.bam",
        output:
            "{sample}.bed",
        log:
            "logs/bamtobed/{sample}.log",
        params:
            extra="-bedpe",  # optional parameters
        wrapper:
            "v3.0.1/bio/bedtools/bamtobed"

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
-----

* This program/wrapper does not handle multi-threading.


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

* ``bedtools=2.31.1``

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

* BAM file, this must be the first file in the input file list

**Output:**

* BED file, this must be the first file in the output file list



Params
------

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




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __license__ = "MIT"


    from snakemake.shell import shell


    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    extra = snakemake.params.get("extra", "")


    shell(
        "(bamToBed"
        " {extra}"
        " -i {snakemake.input[0]}"
        " > {snakemake.output[0]}"
        ") {log}"
    )


.. |nl| raw:: html

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