Whatshap

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

* Providing a reference FASTA (with ``--reference`` or ``-r``)
is now mandatory even for ``whatshap haplotag``. It was already
mandatory for ``whatshap phase``. In both cases, this is to prevent
accidentally getting bad results because allele detection through
realignment (which usually performs better) is only possible if a
reference is provided. Use ``--no-reference`` explicitly to fall
back to the less accurate algorithm.
* :issue:`394`: Fixed ``whatshap phase`` option ``--recombination--list``
not working.
* :issue:`371`: ``whatshap split`` crashed when attempting to split
reads in a FASTQ file by haplotype.
* :pr:`377`: Speed-up of about 20-30% for ``whatshap polyphase`` via
some optimizations in the read clustering algorithm.
* Removed the deprecated ``--pigz`` option for ``whatshap split``

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

* :pr:`362`: ``whatshap polyphase`` received extensive algorithmic updates. The compatiblity with
different data sets (species and sequencing technology) has been improved. The wall-clock time
has been reduced by about 20-30%, depending on the input data.

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

* :issue:`353`: Fix incorrect HS tags in ``whatshap polyphase``
* :issue:`356`: Fixed crash when reading VCF variants without ``GT`` fields (happens in GVCFs).
* :pr:`352`: ``whatshap haplotag`` has gained option ``--output-threads`` for setting the
number of compression threads, significantly reducing wall-clock time. Also, if output
is sent to a pipe, uncompressed BAM is written. Thanks to cjw85.

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

* :issue:`208`: Fix ``phase --merge-reads``. This option has never worked correctly and just led to
``whatshap phase`` taking a very long time and in some cases even crashing. With the fix, the
option should work as intended, but we have not evaluated how much it improves phasing results.
* :issue:`337`: Add ``--skip-missing-contigs`` option to ``whatshap haplotag``
* :pr:`335`: Add option ``--ignore-sample-name`` to ``whatshap compare`` (thanks to Pontus Höjer)
* :issue:`342`: Fix ``whatshap compare`` crashing on VCFs with genotypes with an unknown allele
(where ``GT`` is ``1|.`` or similar).
* :issue:`343`: ``whatshap stats`` now reads the chromosome lengths (for N50 computation) from
the VCF header, no need to use ``--chr-lengths``.

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

* :issue:`223`: Fix ``haplotag --ignore-linked-reads`` not working
* :issue:`241`: Fix some ``polyphase`` problems.
* :issue:`249`: Fix crash in the ``haplotag`` command on reading a VCF with the
``PS`` tag set to ``.``.
* :issue:`251`: Allow ``haplotag`` to correctly write to standard output.
* :issue:`207`: Allow multiple ``--chromosome`` arguments to ``stats``.
* The file created with ``--output-read-list`` was not correctly tab-separated.
* :issue:`248`: Remove ``phase --full-genotyping`` option. Instead, use ``whatshap genotype``
followed by ``whatshap phase``.
* :issue:`289`: Fix parsing of GVCFs (with dots in the ALT column)
* :pr:`265`: ``polyphase`` can now work in parallel

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

WhatsHap has not seen a release in over a year although development has continued. To make up for
it, we decided to leave `ZeroVer <https://0ver.org/>`_ behind and set the version number to 1.0.

* WhatsHap has gained initial support for phasing polyploid samples! While this feature may not be
quite ready for production use, we encourage you to test it by using the ``whatshap polyphase``
subcommand and to report any issues you find back to us. See also the pre-print at
<https://doi.org/10.1101/2020.02.04.933523> for details.
* :issue:`51`: Reading and writing VCF files is now significantly faster because we switched
to a different library for that task (``pysam.VariantFile``).
* The switch to ``pysam.VariantFile`` also makes WhatsHap stricter in which VCF files it accepts.
We have tried to give sensible error messages in these cases, but please report any remaining
issues.
* ``.bcf`` files can now be read and written.
* :issue:`110`: ``.vcf.gz`` output files are now compressed with bgzip so that they can be
indexed with tabix.
* Providing an indexed reference FASTA is now mandatory (with ``-r`` or ``--reference``). It
is possible to bypass this by using ``--no-reference``, but that will disable realignment and
therefore give worse phasing results on error-prone reads (PacBio, Nanopore).
* :issue:`187`: Implemented a ``--regions`` option for the ``haplotag`` subcommand.
* Implemented a ``--discard-unknown-reads`` option for the ``split`` subcommand. Reads that are in
the input reads file (BAM/FASTQ), but are not listed in the haplotag file will be
discarded (by default, they are part of the "untagged" output).
* Fixed :issue:`215`. ``split`` subcommand can now process ``.bam`` files lacking the
``sequence`` field for some/all reads.
* The minimum required Python version for WhatsHap is now 3.6.