.. _`bio/samtools/mpileup`:

SAMTOOLS MPILEUP
================


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

Generate pileup using samtools.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule mpilup:
        input:
            # single or list of bam files
            bam="mapped/{sample}.bam",
            reference_genome="genome.fasta",
        output:
            "mpileup/{sample}.mpileup.gz",
        log:
            "logs/samtools/mpileup/{sample}.log",
        params:
            extra="-d 10000",  # optional
        wrapper:
            "v3.0.1/bio/samtools/mpileup"

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


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

* ``samtools=1.18``
* ``pigz=2.8``




Authors
-------

* Patrik Smeds
* Filipe G. Vieira


Code
----

.. code-block:: python

    """Snakemake wrapper for running mpileup."""

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


    from snakemake.shell import shell

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

    if not snakemake.output[0].endswith(".gz"):
        raise Exception(
            'output file will be compressed and therefore filename should end with ".gz"'
        )

    shell(
        "(samtools mpileup {extra} -f {snakemake.input.reference_genome} {snakemake.input.bam} | pigz > {snakemake.output}) {log}"
    )


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