.. _`bio/fgbio/filterconsensusreads`:

FGBIO FILTERCONSENSUSREADS
==========================


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

Filters consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule FilterConsensusReads:
        input:
            "mapped/{sample}.bam"
        output:
            "mapped/{sample}.filtered.bam"
        params:
            extra="",
            min_base_quality=2,
            min_reads=[2, 2, 2],
            ref="genome.fasta"
        log:
            "logs/fgbio/filterconsensusreads/{sample}.log"
        threads: 1
        wrapper:
            "v3.0.1/bio/fgbio/filterconsensusreads"

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
-----

* min_base_quality: a single value (Int). Mask (make N) consensus bases with quality less than this threshold. (default: 5)
* min_reads: n array of Ints, max length 3, min length 1. Number of reads that need to support a UMI. For filtering bam files processed with CallMolecularConsensusReads one value is required. 3 values can be provided for bam files processed with CallDuplexConsensusReads, if fewer than 3 are provided the last value will be repeated, the first value is for the final consensus sequence and the two last for each strands consensus.
* For more information see, http://fulcrumgenomics.github.io/fgbio/tools/latest/FilterConsensusReads.html


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

* ``fgbio=2.1.0``

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

* bam file
* vcf files
* reference genome

**Output:**

* filtered bam file




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2019, Patrik Smeds"
    __email__ = "patrik.smeds@gmail.com"
    __license__ = "MIT"


    from snakemake.shell import shell

    shell.executable("bash")

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

    extra_params = snakemake.params.get("extra", "")

    min_base_quality = snakemake.params.get("min_base_quality", None)
    if not isinstance(min_base_quality, int):
        raise ValueError("min_base_quality needs to be provided as an Int!")

    min_reads = snakemake.params.get("min_reads", None)
    if not isinstance(min_reads, list) or not (1 <= len(min_reads) <= 3):
        raise ValueError(
            "min_reads needs to be provided as list of Ints, min length 1, max length 3!"
        )

    ref = snakemake.params.get("ref", None)
    if ref is None:
        raise ValueError("A reference needs to be provided!")

    bam_input = snakemake.input[0]

    if not isinstance(bam_input, str) and len(snakemake.input) != 1:
        raise ValueError("Input bam should be one bam file: " + str(bam_input) + "!")

    bam_output = snakemake.output[0]

    if not isinstance(bam_output, str) and len(snakemake.output) != 1:
        raise ValueError("Output should be one bam file: " + str(bam_output) + "!")

    shell(
        "fgbio FilterConsensusReads"
        " -i {bam_input}"
        " -o {bam_output}"
        " -r {ref}"
        " --min-reads {min_reads}"
        " --min-base-quality {min_base_quality}"
        " {extra_params}"
        " {log}"
    )


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