.. _`bio/bcftools/reheader`:

BCFTOOLS REHEADER
=================


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

Change header or sample names of vcf/bcf file.

**URL**: http://www.htslib.org/doc/bcftools.html#reheader

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bcftools_reheader:
        input:
            vcf="a.bcf",
            ## new header, can be omitted if "samples" is set
            header="header.txt",
            ## file containing new sample names, can be omitted if "header" is set
            samples="samples.tsv",
        output:
            "a.reheader.bcf",
        log:
            "a.reheader.log",
        params:
            uncompressed_bcf=False,
            extra="",  # optional parameters for bcftools reheader
            view_extra="",  # optional parameters for bcftools view
        threads: 2
        wrapper:
            "v3.0.1//bio/bcftools/reheader"


    use rule bcftools_reheader as bcftools_reheader_map with:
        input:
            vcf="a.bcf",
            header="header.txt",
            samples="samples_map.tsv",
        output:
            "a.reheader_map.bcf",
        log:
            "a.reheader_map.log",

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

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

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

* VCF/BCF file
* ``header``: new header (optional if "samples" is set)
* ``samples``: new sample names (optional if "header" is set)

**Output:**

* VCF/BCF file with new header



Params
------

* ``uncompressed_bcf``: specify that a BCF output should be uncompressed (ignored otherwise).

* ``extra``: additional program arguments (not `--threads`, `-o/--output`, `-O/--output-type`, or `-T/--temp-prefix`)




Authors
-------

* Jan Forster
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Jan Forster"
    __copyright__ = "Copyright 2020, Jan Forster"
    __email__ = "j.forster@dkfz.de"
    __license__ = "MIT"


    import tempfile
    from pathlib import Path
    from snakemake.shell import shell
    from snakemake_wrapper_utils.bcftools import get_bcftools_opts


    bcftools_opts = get_bcftools_opts(
        snakemake, parse_ref=False, parse_samples=False, parse_memory=False
    )
    extra = snakemake.params.get("extra", "")
    view_extra = snakemake.params.get("view_extra", "")
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)


    ## Extract arguments
    header = snakemake.input.get("header", "")
    if header:
        header = f"--header {header}"

    samples = snakemake.input.get("samples", "")
    if samples:
        samples = f"--samples {samples}"


    with tempfile.TemporaryDirectory() as tmpdir:
        tmp_prefix = Path(tmpdir) / "bcftools_reheader."

        shell(
            "(bcftools reheader"
            " --threads {snakemake.threads}"
            " {header}"
            " {samples}"
            " {extra}"
            " --temp-prefix {tmp_prefix}"
            " {snakemake.input[0]}"
            "| bcftools view"
            " {bcftools_opts}"
            " {view_extra}"
            ") {log}"
        )


.. |nl| raw:: html

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