.. _`bio/samtools/flagstat`:

SAMTOOLS FLAGSTAT
=================


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

Use samtools to create a flagstat file from a bam or sam file.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule samtools_flagstat:
        input:
            "mapped/{sample}.bam",
        output:
            "mapped/{sample}.bam.flagstat",
        log:
            "{sample}.log",
        params:
            extra="",  # optional params string
        wrapper:
            "v3.0.1/bio/samtools/flagstat"

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`).
* For more information see, http://www.htslib.org/doc/samtools-flagstat.html


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

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

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

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

**Output:**

* flagstat file (.flagstat)




Authors
-------

* Christopher Preusch
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Christopher Preusch"
    __copyright__ = "Copyright 2017, Christopher Preusch"
    __email__ = "cpreusch[at]ust.hk"
    __license__ = "MIT"


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

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

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


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