.. _`bio/samtools/index`:

SAMTOOLS INDEX
==============


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

Index bam file with samtools.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule samtools_index:
        input:
            "mapped/{sample}.sorted.bam",
        output:
            "mapped/{sample}.sorted.bam.bai",
        log:
            "logs/samtools_index/{sample}.log",
        params:
            extra="",  # optional params string
        threads: 4  # This value - 1 will be sent to -@
        wrapper:
            "v3.0.1/bio/samtools/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.
* For more information see, http://www.htslib.org/doc/samtools-index.html


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

* ``samtools=1.18``

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

* bam file

**Output:**

* bam file index (.bai)




Authors
-------

* Johannes Köster
* 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

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

    # Samtools takes additional threads through its option -@
    # One thread for samtools merge
    # Other threads are *additional* threads passed to the '-@' argument
    threads = "" if snakemake.threads <= 1 else " -@ {} ".format(snakemake.threads - 1)

    shell(
        "samtools index {threads} {extra} {snakemake.input[0]} {snakemake.output[0]} {log}"
    )


.. |nl| raw:: html

   <br>