Whatshap

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* :pr:`521`: Added ``haplotagphase`` command. The command adds phase information to variants
based on haplotagged reads.
Contributed by Nikolai Karpov (nkkarpov) and Mitchell Robert Vollger (mrvollger).
* :issue:`516`: Added ``--use-supplementary`` option to ``phase``. Use this to use supplementary
alignments for phasing (previously, supplementary alignments would be ignored).
Contributed by Nikolai Karpov (nkkarpov).

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* :issue:`496`: Fixed a segmentation fault in ``polyphase``.
* :issue:`498`: Fixed a numeric overflow in the scoring phase of ``polyphase``.
It could occur for variants with extremely high coverages (i.e. >200X).
* :issue:`472`: Fixed various warnings and assertion violations when running
``polyphase``.
* :issue:`214`: Added support for ploidies greater than two to ``whatshap
split``.
* Added another algorithm for diploid phasing, which is a heuristic version of
the default algorithm. Since it has not been tested extensively, we recommend
the old algorithm for productive use, especially for pedigree phasing. Main
benefit is support for higher coverages and/or larger pedigrees at the cost
of not solving the underlying MEC model to optimality anymore. The heuristic
is accessible via the parameter ``--algorithm=heuristic``.

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* We added *k*-merald, a new method for allele detection
based on *k*-mer alignment. Instead of using a fixed cost value,
*k*-merald derives *k*-mer mismatch penalties using the error profiles
generated by ``whatshap learn``. *k*-merald is available as an alternative
to the edit-distance-based allele detection.
* WhatsHap can now be used to generate sequencing error profiles for a
specific technology using ``whatshap learn``.
* :issue:`470`: Avoid ZeroDivisionError in ``whatshap stats`` when there
are no heterozygous or no phased variants.
* :issue:`485`: Fixed a KeyError: 'parse_vcf' in ``whatshap polyphase`` when a
full chromosome is skipped.

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* :issue:`346`: Phasing of indels (and other non-SNVs) is now enabled by
default. This previously required specifying the ``--indels`` option,
which not all users knew about and were thus unnecessarily getting
suboptimal phasing results. The option is now ignored and leads to a
warning. An ``--only-snvs`` option was added that restores the old behavior.
This change applies to the following subcommands: ``phase``, ``haplotype``,
``polyphase``, ``polyphasegenetic``.

Since this is a backwards incompatible change (when not using ``--indels``
already), the major version has been increased.
* :issue:`425`: Haplotagging CRAM files should now work in more cases with
``haplotag``.
* :issue:`427`: ``polyphase`` did not phase indels, even if explicitly told.
* :pr:`432`: ``polyphase`` can use existing phasing information in VCF when
using the ``--use-prephasing`` flag. Still very experimental.
* :issue:`439`: ``polyphasegenetic`` now handles pedigree information more
robustly and properly detects available ILP solvers.
* :issue:`449`: Fixed runtime issues for ploidies above 4, if no pre-phasing
is used.
* :pr:`450`: ``polyphase`` now supports multi-allelic variants.
* :issue:`457`: ``haplotag`` now also tags alignments marked as duplicate.
* :issue:`466`: Inconsistent runtime measurements now lead to a warning and
no longer to a crash.
* This is the last WhatsHap release to support Python 3.7.

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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).