.. _`bio/bcftools/index`:

BCFTOOLS INDEX
==============


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

Index vcf/bcf file.

**URL**: http://www.htslib.org/doc/bcftools.html#index

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bcftools_index:
        input:
            "a.bcf",
        output:
            "a.bcf.csi",
        log:
            "index/a.log",
        params:
            extra="",  # optional parameters for bcftools index
        wrapper:
            "v3.0.1/bio/bcftools/index"

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`, `-o/--output`).


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

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




Authors
-------

* Jan Forster
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2016, Johannes Köster"
    __email__ = "koester@jimmy.harvard.edu"
    __license__ = "MIT"


    from snakemake.shell import shell
    from snakemake_wrapper_utils.bcftools import get_bcftools_opts


    bcftools_opts = get_bcftools_opts(
        snakemake, parse_ref=False, parse_output_format=False, parse_memory=False
    )
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)


    if "--tbi" in extra or "--csi" in extra:
        raise ValueError(
            "You have specified index format (`--tbi/--csi`) in `params.extra`; this is automatically infered from the first output file."
        )

    if snakemake.output[0].endswith(".tbi"):
        extra += " --tbi"
    elif snakemake.output[0].endswith(".csi"):
        extra += " --csi"
    else:
        raise ValueError("invalid index file format ('.tbi', '.csi').")


    shell("bcftools index {bcftools_opts} {extra} {snakemake.input[0]} {log}")


.. |nl| raw:: html

   <br>