Whatshap

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* :pr:`379`: Added the ability to do polyploid phasing with pedigree information.
This is implemented in a new ``polyphasegenetic`` subcommand.
* :issue:`143`: ``whatshap stats`` now outputs the fraction of heterozygous variants that are phased.
* :pr:`410`: ``haplotag`` gained support for tagging data with ploidy greater
than two (use option ``--ploidy``).
* :issue:`400`: Fixed artificial overinflation of block length stats in ``whatshap stats``.
* :pr:`418`: Fixed problem in ``stats`` where NaN values caused ValuError
* :pr:`416`: Clarified in the docs what ``stats`` considers as "phased".
* :issue:`207`: Enable comma-separated chromosomes as argument to ``whatshap stats``.
* :pr:`412`: Changed ``stats`` to compute all length statistics on split blocks
* :pr:`399`: Formatted ``stats`` output so that long values are right-aligned with all other values.

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* :pr:`384`: Fixed how interleaved phase blocks in ``whatshap stats`` are split
when computing NG50 values. This allows NG50 values to be larger than before.
Thanks to pontushojer.
* :pr:`385`: Speed up ``whatshap stats`` when used with ``--chromosomes`` by avoiding to
read in the entire VCF. Thanks to pontushojer.
* :pr:`387`: ``whatshap haplotag`` got some optimizations and is now about 20% faster.
Thanks to pontushojer.
* :issue:`397`: Fixed ``whatshap haplotag`` to include reads not assigned to a contig
(unmapped) in the output (unless the ``--region`` option is used).

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* 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``

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* :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.

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* :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.

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* :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``.