.. _`bio/samtools/view`:

SAMTOOLS VIEW
=============


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

Convert or filter SAM/BAM.

**URL**: http://www.htslib.org/doc/samtools-view.html

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule samtools_view:
        input:
            "{sample}.sam",
        output:
            bam="{sample}.bam",
            idx="{sample}.bai",
        log:
            "{sample}.log",
        params:
            extra="",  # optional params string
            region="",  # optional region string
        threads: 2
        wrapper:
            "v3.0.1/bio/samtools/view"

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`, `--write-index`, `-o` or `-O/--output-fmt`).
* The `region` param allows one to specify region to extract as `RNAME[:STARTPOS[-ENDPOS]]` (e.g. `chr1`, `chr2:10000000`, `chr3:1000-2000`, `'*'`).


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

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

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

* SAM/BAM/CRAM file

**Output:**

* SAM/BAM/CRAM file
* SAM/BAM/CRAM index file (optional)




Authors
-------

* Johannes Köster
* Filipe G. Vieira
* Lance Parsons


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.samtools import get_samtools_opts

    samtools_opts = get_samtools_opts(snakemake)
    extra = snakemake.params.get("extra", "")
    region = snakemake.params.get("region", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)


    shell("samtools view {samtools_opts} {extra} {snakemake.input[0]} {region} {log}")


.. |nl| raw:: html

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