.. _`bio/fgbio/setmateinformation`:

FGBIO SETMATEINFORMATION
========================


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

Adds and/or fixes mate information on paired-end reads. Sets the MQ (mate mapping quality), MC (mate cigar string), ensures all mate-related flag fields are set correctly, and that the mate reference and mate start position are correct.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule SetMateInfo:
        input:
            "mapped/a.bam"
        output:
            "mapped/{sample}.mi.bam"
        params: ""
        log:
            "logs/fgbio/set_mate_info/{sample}.log"
        wrapper:
            "v3.0.4/bio/fgbio/setmateinformation"

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.


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

* ``fgbio=2.1.0``




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2018, Patrik Smeds"
    __email__ = "patrik.smeds@gmail.com"
    __license__ = "MIT"


    from snakemake.shell import shell

    shell.executable("bash")

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

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

    bam_input = snakemake.input[0]

    if not isinstance(bam_input, str) and len(snakemake.input) != 1:
        raise ValueError("Input bam should be one bam file: " + str(bam_input) + "!")

    output_file = snakemake.output[0]

    if not isinstance(output_file, str) and len(snakemake.output) != 1:
        raise ValueError("Output should be one bam file: " + str(output_file) + "!")

    shell(
        "fgbio SetMateInformation"
        " -i {bam_input}"
        " -o {output_file}"
        " {extra_params}"
        " {log}"
    )


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