.. _`bio/samtools/calmd`:

SAMTOOLS CALMD
==============


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

Calculates MD and NM tags.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule samtools_calmd:
        input:
            aln="{sample}.bam",  # Can be 'sam', 'bam', or 'cram'
            ref="genome.fasta",
        output:
            "{sample}.calmd.bam",
        log:
            "{sample}.calmd.log",
        params:
            extra="-E",  # optional params string
        threads: 2
        wrapper:
            "v3.0.1/bio/samtools/calmd"

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


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

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




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2020, Filipe G. Vieira"
    __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
    )
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)

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


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