.. _`bio/bamtools/filter`:

BAMTOOLS FILTER
===============


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

Filters BAM files. 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:
        input:
            "{sample}.bam"
        output:
            "filtered/{sample}.bam"
        params:
            # optional parameters
            tags = [ "NM:<4", "MQ:>=10" ],    # list of key:value pair strings
            min_size = "-2000",
            max_size = "2000",
            min_length = "10",
            max_length = "20",
            # to add more optional parameters (see bamtools filter --help):
            additional_params = "-mapQuality \">=0\" -isMapped \"true\""
        log:
            "logs/bamtools/filtered/{sample}.log"
        wrapper:
            "v3.0.1/bio/bamtools/filter"

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
------

* ``tags``: filtering tags

* ``min_size``: minimum insert size

* ``max_size``: maximum insert size

* ``min_length``: minimum read length

* ``max_length``: maximum read length

* ``additional_params``: Other filtering and optional parameters




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)

    # extract arguments
    params = ""
    extra_limits = ""
    tags = snakemake.params.get("tags")
    min_size = snakemake.params.get("min_size")
    max_size = snakemake.params.get("max_size")
    min_length = snakemake.params.get("min_length")
    max_length = snakemake.params.get("max_length")
    additional_params = snakemake.params.get("additional_params")

    if tags and tags is not None:
        params = params + " " + " ".join(map('-tag "{}"'.format, tags))

    if min_size and min_size is not None:
        params = params + ' -insertSize ">=' + min_size + '"'
        if max_size and max_size is not None:
            extra_limits = extra_limits + ' -insertSize "<=' + max_size + '"'
    else:
        if max_size and max_size is not None:
            params = params + ' -insertSize "<=' + max_size + '"'

    if min_length and min_length is not None:
        params = params + ' -length ">=' + min_length + '"'
        if max_length and max_length is not None:
            extra_limits = extra_limits + ' -length "<=' + max_length + '"'
    else:
        if max_length and max_length is not None:
            params = params + ' -length "<=' + max_length + '"'

    if additional_params and additional_params is not None:
        params = params + " " + additional_params

    if extra_limits:
        params = params + " | bamtools filter" + extra_limits

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


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