.. _vcf:

Reading VCF
===========

.. contents:: Table of contents:
   :local:

The :func:`sgkit.io.vcf.vcf_to_zarr` function converts one or more VCF files to Zarr files stored in
sgkit's Xarray data representation.

Highlights
----------

* Reads bgzip-compressed VCF and BCF files.
* Large VCF files can be partitioned into regions using a Tabix (``.tbi``) or CSI (``.csi``)
  index, and each region is processed in parallel using `Dask <https://dask.org/>`_.
* VCF parsing is performed by `cyvcf2 <https://github.com/brentp/cyvcf2>`_,
  a Cython wrapper around `htslib <https://github.com/samtools/htslib>`_,
  the industry-standard VCF library.
* Control over Zarr chunk sizes allows VCFs with a large number of samples
  to be converted efficiently.
* Input and output files can reside on local filesystems, Amazon S3, or
  Google Cloud Storage.
* Support for polyploid and mixed-ploidy genotypes.

Installation
------------

VCF support is an "extra" feature within sgkit and requires additional
dependencies, notably ``cyvcf2``.

To install sgkit with VCF support using pip (there is no conda package)::

    $ pip install 'sgkit[vcf]'

There are `installation instructions for cyvcf2 <https://github.com/brentp/cyvcf2#installation>`_,
which may be helpful if you encounter errors during installation.

.. warning::
   Reading VCFs is not supported on Windows, since ``cyvcf2`` and ``htslib`` do
   not `currently work on Windows <https://github.com/brentp/cyvcf2/issues/90>`_.
   As a workaround, consider using scikit-allel's ``vcf_to_zarr`` function
   to write a VCF in Zarr format, followed by :func:`sgkit.read_vcfzarr` to
   read the VCF as a :class:`xarray.Dataset`.

Usage
-----

To convert a single VCF or BCF file to Zarr, just specify the input and output file names::

    >>> import sgkit as sg
    >>> from sgkit.io.vcf import vcf_to_zarr
    >>> vcf_to_zarr("CEUTrio.20.21.gatk3.4.g.vcf.bgz", "output.zarr")
    >>> ds = sg.load_dataset("output.zarr")
    >>> ds
    <xarray.Dataset>
    Dimensions:               (alleles: 4, ploidy: 2, samples: 1, variants: 19910)
    Dimensions without coordinates: alleles, ploidy, samples, variants
    Data variables:
        call_genotype         (variants, samples, ploidy) int8 dask.array<chunksize=(10000, 1, 2), meta=np.ndarray>
        call_genotype_mask    (variants, samples, ploidy) bool dask.array<chunksize=(10000, 1, 2), meta=np.ndarray>
        call_genotype_phased  (variants, samples) bool dask.array<chunksize=(10000, 1), meta=np.ndarray>
        sample_id             (samples) <U7 dask.array<chunksize=(1,), meta=np.ndarray>
        variant_allele        (variants, alleles) object dask.array<chunksize=(10000, 4), meta=np.ndarray>
        variant_contig        (variants) int8 dask.array<chunksize=(10000,), meta=np.ndarray>
        variant_id            (variants) object dask.array<chunksize=(10000,), meta=np.ndarray>
        variant_id_mask       (variants) bool dask.array<chunksize=(10000,), meta=np.ndarray>
        variant_position      (variants) int32 dask.array<chunksize=(10000,), meta=np.ndarray>
    Attributes:
        contigs:                    ['20', '21']
        max_variant_allele_length:  48
        max_variant_id_length:      1

The :func:`sgkit.io.vcf.vcf_to_zarr` function can accept multiple files, and furthermore, each of these
files can be partitioned to enable parallel processing.

Multiple files
--------------

If there are multiple files, then pass a list::

    >>> from sgkit.io.vcf import vcf_to_zarr
    >>> vcf_to_zarr(["CEUTrio.20.gatk3.4.g.vcf.bgz", "CEUTrio.21.gatk3.4.g.vcf.bgz"], "output.zarr")

Processing multiple inputs is more work than a single file, since behind the scenes each input is
converted to a separate temporary Zarr file on disk, then these files are concatenated and rechunked
to form the final output Zarr file.

In the single file case, the input VCF is converted to the output Zarr file in a single sequential
pass with no need for intermediate temporary files. For small files this is fine, but for very large
files it's a good idea to partition them so the conversion runs faster.

Partitioning
------------

Partitioning a large VCF file involves breaking it into a number of roughly equal-sized parts that can
be processed in parallel. The parts are specified using genomic regions that follow the regions format
used in `bcftools <http://samtools.github.io/bcftools/bcftools.html>`_: ``chr:beg-end``,
where positions are 1-based and inclusive.

All files to be partitioned must have either a Tabix (``.tbi``) or CSI (``.csi``) index. If both are present
for a particular file, then Tabix is used for finding partitions.

The :func:`sgkit.io.vcf.partition_into_regions` function will create a list of region strings for a VCF
file, given a desired number of parts to split the file into:

    >>> from sgkit.io.vcf import partition_into_regions
    >>> partition_into_regions("CEUTrio.20.21.gatk3.4.g.vcf.bgz", num_parts=10)
    ['20:1-10108928', '20:10108929-10207232', '20:10207233-', '21:1-10027008', '21:10027009-10043392', '21:10043393-10108928', '21:10108929-10141696', '21:10141697-10174464', '21:10174465-10190848', '21:10190849-10207232', '21:10207233-']

It's important to note that the number of regions returned may not be exactly the number of parts
requested: it may be more or less. However, it is guaranteed that the regions will be contiguous and
will cover the whole VCF file.

The region strings are passed to ``vcf_to_zarr`` so it can process the parts in parallel:

    >>> from sgkit.io.vcf import partition_into_regions, vcf_to_zarr
    >>> regions = partition_into_regions("CEUTrio.20.21.gatk3.4.g.vcf.bgz", num_parts=10)
    >>> vcf_to_zarr("CEUTrio.20.21.gatk3.4.g.vcf.bgz", "output.zarr", regions=regions)

It's also possible to produce parts that have an approximate target size (in bytes). This is useful
if you are partitioning multiple files, and want all the parts to be roughly the same size.

    >>> from sgkit.io.vcf import partition_into_regions, vcf_to_zarr
    >>> inputs = ["CEUTrio.20.gatk3.4.g.vcf.bgz", "CEUTrio.21.gatk3.4.g.vcf.bgz"]
    >>> regions = [partition_into_regions(input, target_part_size=100_000) for input in inputs]
    >>> vcf_to_zarr(inputs, "output.zarr", regions=regions)

The same result can be obtained more simply by specifying ``target_part_size`` in the call to
``vcf_to_zarr``:

    >>> from sgkit.io.vcf import vcf_to_zarr
    >>> inputs = ["CEUTrio.20.gatk3.4.g.vcf.bgz", "CEUTrio.21.gatk3.4.g.vcf.bgz"]
    >>> vcf_to_zarr(inputs, "output.zarr", target_part_size=100_000)

As a special case, ``None`` is used to represent a single partition.

    >>> from sgkit.io.vcf import partition_into_regions
    >>> partition_into_regions("CEUTrio.20.21.gatk3.4.g.vcf.bgz", num_parts=1)
    None

Chunk sizes
-----------

One key advantage of using Zarr as a storage format is its ability to store
large files in chunks, making it straightforward to process the data in
parallel.

You can control the chunk *length* (in the variants dimension) and *width*
(in the samples dimension) by setting the ``chunk_length`` and ``chunk_width``
parameters to :func:`sgkit.io.vcf.vcf_to_zarr`.

Due to the way that VCF files are parsed, all of the sample data for a given
chunk of variants are loaded into memory at one time. In other words,
``chunk_length`` is honored at read time, whereas ``chunk_width`` is honored
at write time. For files with very large numbers of samples, this can
exceed working memory. The solution is to also set ``temp_chunk_length`` to be a
smaller number (than ``chunk_length``), so that fewer variants are loaded
into memory at one time, while still having the desired output chunk sizes
(``chunk_length`` and ``chunk_width``). Note that ``temp_chunk_length`` must
divide ``chunk_length`` evenly.

Cloud storage
-------------

VCF files can be read from various file systems including cloud stores. However,
since different underlying libraries are used in different functions, there are
slight differences in configuration that are outlined here.

The :func:`sgkit.io.vcf.partition_into_regions` function uses `fsspec <https://filesystem-spec.readthedocs.io/en/latest/>`_
to read VCF metadata and their indexes. Therefore, to access files stored on Amazon S3 or Google Cloud Storage
install the ``s3fs`` or ``gcsfs`` Python packages, and use ``s3://`` or ``gs://`` URLs.

You can also pass ``storage_options`` to :func:`sgkit.io.vcf.partition_into_regions` to configure the ``fsspec`` backend.
This provides a way to pass any credentials or other necessary arguments needed to ``s3fs`` or ``gcsfs``.

The :func:`sgkit.io.vcf.vcf_to_zarr` function does *not* use ``fsspec``, since it
relies on ``htslib`` for file handling, and therefore has its own way of accessing
cloud storage. You can access files stored on Amazon S3 or Google Cloud Storage
using ``s3://`` or ``gs://`` URLs. Setting credentials or other options is
typically achieved using environment variables for the underlying cloud store.

Low-level operation
-------------------

Calling :func:`sgkit.io.vcf.vcf_to_zarr` runs a two-step operation:

1. Write the output for each input region to a separate temporary Zarr store
2. Concatenate and rechunk the temporary stores into the final output Zarr store

Each step is run as a Dask computation, which means you can use any Dask configuration
mechanisms to control aspects of the computation.

For example, you can set the Dask scheduler to run on a cluster. In this case you
would set the temporary Zarr store to be a cloud storage URL (by setting ``tempdir``) so
that all workers can access the store (both for reading and writing).

For debugging, or for more control over the steps, consider using
:func:`sgkit.io.vcf.vcf_to_zarrs` followed by :func:`sgkit.io.vcf.zarrs_to_dataset`,
then saving the dataset using Xarray's :meth:`xarray.Dataset.to_zarr` method.

Polyploid and mixed-ploidy VCF
------------------------------

The :func:`sgkit.io.vcf.vcf_to_zarr` function can be used to convert polyploid VCF
data to Zarr files stored in sgkit's Xarray data representation by specifying the
ploidy of the dataset using the ``ploidy`` parameter.

By default, sgkit expects VCF files to have a consistent ploidy level across all samples
and variants.
Manual specification of ploidy is necessary because, within the VCF standard,
ploidy is indicated by the length of each genotype call and hence it may not be
consistent throughout the entire VCF file.

If a genotype call of lower than specified ploidy is encountered it will be treated
as an incomplete genotype.
For example, if a VCF is being processed assuming a ploidy of four (i.e. tetraploid)
then the diploid genotype ``0/1`` will be treated as the incomplete tetraploid
genotype ``0/1/./.``.

If a genotype call of higher than specified ploidy is encountered an exception is raised.
This exception can be avoided using the ``truncate_calls`` parameter in which case the
additional alleles will be skipped.

Conversion of mixed-ploidy VCF files is also supported by :func:`sgkit.io.vcf.vcf_to_zarr`
by use of the ``mixed_ploidy`` parameter.
In this case ``ploidy`` specifies the maximum allowed ploidy and lower ploidy
genotype calls within the VCF file will be preserved within the resulting dataset.

Note that many statistical genetics methods available for diploid data are not generalized
to polyploid and or mixed-ploidy data.
Therefore, some methods available in sgkit may only be applicable to diploid or fixed-ploidy
datasets.

Methods that are generalized to polyploid and mixed-ploidy data may make assumptions
such as polysomic inheritance and hence it is necessary to understand the type of polyploidy
present within any given dataset.