.. _`bio/bgzip`:

BGZIP
=====


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

Block compression/decompression utility

**URL**: https://github.com/samtools/htslib

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bgzip:
        input:
            "{prefix}.vcf",
        output:
            "{prefix}.vcf.gz",
        params:
            extra="", # optional
        threads: 1
        log:
            "logs/bgzip/{prefix}.log",
        wrapper:
            "v3.0.1/bio/bgzip"

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

* ``htslib=1.18``

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

* file to be compressed or decompressed

**Output:**

* compressed or decompressed output




Authors
-------

* William Rowell


Code
----

.. code-block:: python

    __author__ = "William Rowell"
    __copyright__ = "Copyright 2020, William Rowell"
    __email__ = "wrowell@pacb.com"
    __license__ = "MIT"


    from snakemake.shell import shell

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

    shell(
        """
        (bgzip -c {extra} --threads {snakemake.threads} \
            {snakemake.input} > {snakemake.output}) {log}
        """
    )


.. |nl| raw:: html

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