.. _`bio/deeptools/alignmentsieve`:

DEEPTOOLS ALIGNMENT-SIEVE
=========================


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

filters/shift alignments in a BAM/CRAM file according the the specified parameters.  It can optionally output to BEDPE format.


**URL**: https://deeptools.readthedocs.io/en/develop/content/tools/alignmentSieve.html

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_deeptools_alignment_sieve:
        input:
            aln="a.bam",
        output:
            "filtered.bam",
        threads: 1
        log:
            "logs/deeptools.log",
        params:
            extra="",
        wrapper:
            "v3.0.1/bio/deeptools/alignmentsieve"

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
-----

Input/output formats are automatically detected.

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

* ``deeptools=3.5.4``

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

* ``aln``: Path to BAM/CRAM formatted alignments. Bam filesm ust be indexed.

**Output:**

* Path to filtered bam alignments or bedpe intervals.



Params
------

* ``extra``: Optional arguments for `alignmentSieve.py`




Authors
-------

* Thibault Dayris


Code
----

.. code-block:: python

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2023, Thibault Dayris"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    from snakemake.shell import shell


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

    blacklist = snakemake.input.get("blacklist", "")
    if blacklist:
        extra += f" --blackListFileName {blacklist} "

    out_file = snakemake.output[0]
    if out_file.endswith(".bed"):
        extra += " --BED "

    shell(
        "alignmentSieve "
        "{extra} "
        "--numberOfProcessors {snakemake.threads} "
        "--bam {snakemake.input.aln} "
        "--outFile {out_file} "
        "{log} "
    )


.. |nl| raw:: html

   <br>