.. _`bio/lofreq/indelqual`:

LOFREQ INDELQUAL
================


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

Insert indel qualities into BAM file (required for indel predictions)

**URL**: https://csb5.github.io/lofreq/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule lofreq_uniform_indelqual:
        input:
            bam="data/{sample}.bam",
        output:
            "out/indelqual/{sample}.uindel.bam"
        log:
            "logs/{sample}.uindel.log"
        params:
            extra="-u 15"
        threads: 8
        wrapper:
            "v3.0.4/bio/lofreq/indelqual"

    rule lofreq_dindel_indelqual:
        input:
            bam="data/{sample}.bam",
            ref="data/hg38_chr21.fa"
        output:
            "out/indelqual/{sample}.dindel.bam"
        log:
            "logs/{sample}.dindel.log"
        params:
            extra="--dindel"
        threads: 8
        wrapper:
            "v3.0.4/bio/lofreq/indelqual"

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

* ``samtools=1.18``
* ``lofreq=2.1.5``

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

* bam file that will have variants called
* reference genome of bam (optional unless --dindel specified)

**Output:**

* bam file with indel qualities added




Authors
-------

* Tobin Groth


Code
----

.. code-block:: python

    __author__ = "Tobin Groth"
    __copyright__ = "Copyright 2023, Tobin Groth"
    __email__ = "tobingroth1@gmail.com"
    __license__ = "MIT"


    import os
    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    extra = snakemake.params.get("extra", "")
    if len(snakemake.output) != 1:
        raise ValueError("Expecting only one output file!")

    ref = snakemake.input.get("ref", "")
    if "--dindel" in extra and not ref:
        raise ValueError("Reference required if --dindel option specified")

    if ref:
        ref = f"--ref {ref}"

    shell(
        "lofreq indelqual "
        " {snakemake.input.bam}"
        " {ref}"
        " -o {snakemake.output[0]}"
        " {extra}"
        " {log}"
    )


.. |nl| raw:: html

   <br>