.. _`bio/samtools/fixmate`:

SAMTOOLS FIXMATE
================


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

Use samtools to correct mate information after BWA mapping.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule samtools_fixmate:
        input:
            "mapped/{input}",
        output:
            "fixed/{input}",
        log:
            "{input}.log",
        message:
            "Fixing mate information in {wildcards.input}"
        threads: 1
        params:
            extra="",
        wrapper:
            "v3.0.1/bio/samtools/fixmate/"

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
-----

* The `extra` param allows for additional program arguments (not `-@/--threads` or `-O/--output-fmt`).
* For more information see, http://www.htslib.org/doc/samtools-fixmate.html


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

* ``samtools=1.18``
* ``snakemake-wrapper-utils=0.6.2``

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

* bam or sam file (.bam,.sam)

**Output:**

* bam or sam file (.bam,.sam)




Authors
-------

* Thibault Dayris
* Filipe G. Vieira


Code
----

.. code-block:: python

    """Snakemake wrapper for samtools fixmate"""

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2019, Dayris Thibault"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    from snakemake.shell import shell
    from snakemake.utils import makedirs
    from snakemake_wrapper_utils.samtools import get_samtools_opts

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

    shell(
        "samtools fixmate {samtools_opts} {extra} {snakemake.input[0]} {snakemake.output[0]} {log}"
    )


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