.. _`bio/gatk/collectreadcounts`:

GATK COLLECTREADCOUNTS
======================


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

Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval. 


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/360037592671-CollectReadCounts

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule collectreadcounts:
        input:
            bam=["mapped/a.bam"],
            intervals=["a.interval_list"],
        output:
            counts="a.counts.hdf5",
        log:
            "logs/gatk/collectreadcounts.log",
        params:
            extra="",  # optional
            java_opts="",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/collectreadcounts"

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

* ``gatk4=4.4.0.0``
* ``snakemake-wrapper-utils=0.6.2``

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

* ``bam``: BAM/SAM/CRAM file containing reads
* ``intervals``: one or more genomic intervals over which to operate

**Output:**

* ``counts``: output file for read counts, `tsv` or `hdf5`



Params
------

* ``mergingRule``: interval merging rule for abutting intervals (default, OVERLAPPING_ONLY)

* ``java_opts``: additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).

* ``extra``: additional program arguments.




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2023, Patrik Smed"
    __email__ = "patrik.smeds@gmail.com"
    __license__ = "MIT"


    import tempfile
    from snakemake.shell import shell
    from snakemake_wrapper_utils.java import get_java_opts


    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)

    mergingRule = snakemake.params.get("mergingRule", "OVERLAPPING_ONLY")

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "gatk --java-options '{java_opts}' CollectReadCounts"
            " -I {snakemake.input.bam}"
            " -L {snakemake.input.intervals}"
            " --interval-merging-rule {mergingRule}"
            " {extra}"
            " --tmp-dir {tmpdir}"
            " --output {snakemake.output.counts}"
            " {log}"
        )


.. |nl| raw:: html

   <br>