.. _`bio/samtools/stats`:

SAMTOOLS STATS
==============


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

Generate stats using samtools.

**URL**: http://www.htslib.org/doc/samtools-stats.html

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule samtools_stats:
        input:
            bam="mapped/{sample}.bam",
            bed="design.bed",  #Optional input, specify target regions
        output:
            "samtools_stats/{sample}.txt",
        params:
            extra="",  # Optional: extra arguments.
            region="xx:1000000-2000000",  # Optional: region string.
        log:
            "logs/samtools_stats/{sample}.log",
        wrapper:
            "v3.0.1/bio/samtools/stats"

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
---------------------

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

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

* SAM/BAM/CRAM file

**Output:**

* statistics file



Params
------

* ``extra``: additional program arguments (not `-@/--threads`).




Authors
-------

* Julian de Ruiter
* Filipe G. Vieira


Code
----

.. code-block:: python

    """Snakemake wrapper for trimming paired-end reads using cutadapt."""

    __author__ = "Julian de Ruiter"
    __copyright__ = "Copyright 2017, Julian de Ruiter"
    __email__ = "julianderuiter@gmail.com"
    __license__ = "MIT"


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


    bed = snakemake.input.get("bed", "")
    if bed:
        bed = f"-t {bed}"

    samtools_opts = get_samtools_opts(
        snakemake, parse_write_index=False, parse_output=False, parse_output_format=False
    )


    extra = snakemake.params.get("extra", "")
    region = snakemake.params.get("region", "")
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)


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


.. |nl| raw:: html

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