.. _`bio/bamtools/split`:

BAMTOOLS SPLIT
==============


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

Split bam file into sub files, default by reference

**URL**: https://github.com/pezmaster31/bamtools

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bamtools_split:
        input:
            "mapped/{sample}.bam",
        output:
            "mapped/{sample}.REF_xx.bam",
        params:
            extra="-reference",
        log:
            "logs/bamtoos_split/{sample}.log",
        wrapper:
            "v3.0.1/bio/bamtools/split"

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
-----

A complete usage documentation is available here: https://raw.githubusercontent.com/wiki/pezmaster31/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf

This tool/wrapper does not handle multi threading


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

* ``bamtools=2.5.2``

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

* bam file, this must be the only file in input.

**Output:**

* multiple bam file multiple formats.



Params
------

* ``extra``: Optional parameters




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2021, Patrik Smeds"
    __email__ = "patrik.smeds@scilifelab.uu.se"
    __license__ = "MIT"


    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=False, stderr=True)

    extra = snakemake.params.get("extra", "")

    if len(snakemake.input) != 1:
        raise ValueError("One bam input file expected, got: " + str(len(snakemake.input)))

    shell("bamtools split -in {snakemake.input} {extra} {log}")


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