.. _`bio/samtools/depth`:

SAMTOOLS DEPTH
==============


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

Compute the read depth at each position or region using samtools.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule samtools_depth:
        input:
            bams=["mapped/A.bam", "mapped/B.bam"],
            bed="regionToCalcDepth.bed",  # optional
        output:
            "depth.txt",
        log:
            "depth.log",
        params:
            # optional bed file passed to -b
            extra="",  # optional additional parameters as string
        wrapper:
            "v3.0.1/bio/samtools/depth"

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


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

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




Authors
-------

* Dayne Filer
* Filipe G. Vieira


Code
----

.. code-block:: python

    """Snakemake wrapper for running samtools depth."""

    __author__ = "Dayne L Filer"
    __copyright__ = "Copyright 2020, Dayne L Filer"
    __email__ = "dayne.filer@gmail.com"
    __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_format=False
    )
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    # check for optional bed file
    bed = snakemake.input.get("bed", "")
    if bed:
        bed = "-b " + bed

    shell("samtools depth {samtools_opts} {extra} {bed} {snakemake.input.bams} {log}")


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