.. _`bio/bamtools/filter_json`:

BAMTOOLS FILTER WITH JSON
=========================


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

Filters BAM files with JSON-script for filtering parameters and rules. For more information about bamtools see `bamtools documentation <http://stab.st-andrews.ac.uk/wiki/index.php/Bamtools>`_

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bamtools_filter_json:
        input:
            "{sample}.bam"
        output:
            "filtered/{sample}.bam"
        params:
            json="filtering-rules.json",
            region="" # optional parameter for defining a specific region, e.g. "chr1:500..chr3:750"
        log:
            "logs/bamtools/filtered/{sample}.log"
        wrapper:
            "v3.0.1/bio/bamtools/filter_json"

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 files (.bam), must be in first position

**Output:**

* bam file (.bam), must be in first position



Params
------

* ``json``: Path to filter file, json formatted.

* ``region``: see documentation for more information about multiple formats.




Authors
-------

* Antonie Vietor


Code
----

.. code-block:: python

    __author__ = "Antonie Vietor"
    __copyright__ = "Copyright 2020, Antonie Vietor"
    __email__ = "antonie.v@gmx.de"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    region = snakemake.params.get("region")
    region_param = ""

    if region and region is not None:
        region_param = ' -region "' + region + '"'

    shell(
        "(bamtools filter"
        " -in {snakemake.input[0]}"
        " -out {snakemake.output[0]}"
        + region_param
        + " -script {snakemake.params.json}) {log}"
    )


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