Whatshap

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* Use ``PS`` tag instead of ``HP`` tag by default to store phasing information.
This applies to the ``phase`` and ``hapcut2vcf`` subcommands. ``PS`` is also
used by other tools and standard according to the VCF specification.
* Incorporated genotype likelihoods into our phasing framework. On request
(by using option ``--distrust-genotypes``), genotypes can now be changed at a cost
corresponding to their input genotype likelihoods. The changed genotypes are
written to the output VCF. The behavior of ``--distrust-genotypes`` can be
fine-tuned by the added options ``--include-homozygous``, ``--default-gq``,
``--gl-regularizer``, and ``--changed-genotype-list``.
* Correctly handle cases when processing VCFs with two or more disjoint
families.

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* Speed up allele detection
* Add an ``unphase`` subcommand which removes all phasing from a VCF file
(``HP`` and ``PS`` tags, pipe notation).
* Add option ``--tag=`` to the ``phase`` subcommand, which allows to choose
whether ReadBackedPhasing-compatible ``HP`` tags or standard ``PS`` tags are
used to describe phasing in the output VCF.
* Manage versions with `versioneer <https://github.com/warner/python-versioneer>`_.
This means that ``whatshap --version`` and the program version in the VCF header
will include the Git commit hash, such as ``whatshap 0.11+50.g1b7af7a``.
* Add subcommand "haplotag" to tag reads in a BAM file with their haplotype.
* Fix a bug where re-alignment around variants at the very end of a chromosome
would lead to an AssertionError.

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* When phasing a pedigree, blocks that are not connected by reads but
can be phased based on genotypes will be connected per default. This
behavior can be turned off using option ``--no-genetic-haplotyping``.
* Implemented allele detection through re-alignment: To detect which allele of a
variant is seen in a read, the query is aligned to the two haplotypes at that
position. This results in better quality phasing, especially for
low-quality reads (PacBio). Enabled if ``--reference`` is provided. Current
limitation: No score for the allele is computed.
* As a side-effect of the new allele detection, we can now also phase
insertions, deletions, MNPs and "complex" variants.
* Added option ``--chromosome`` to only work on specifed chromosomes.
* Use constant recombination rate per default, allows to use ``--ped``
without using ``--genmap``.
* ``whatshap`` has become a command with subcommands. From now on, you need
to run ``whatshap phase`` to phase VCFs.
* Add a ``stats`` subcommand that prints statistics about phased VCFs.

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* Use ``--ped`` to phase pedigrees with the PedMEC algorithm
* Phase all samples in a multi-sample VCF
* Drop support for Python 3.2 - we require at least Python 3.3 now

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* This is the first release available via PyPI (and that can therefore be
installed via ``pip install whatshap``)

January 2016
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* Trio phasing implemented in a branch

September 2015
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* pWhatsHap implemented (in a branch)

April 2015
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* Create haplotype-specific BAM files

February 2015
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* Smart read selection

January 2015
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* Ability to read multiple BAM files and merge them on the fly

December 2014
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* Logo
* Unit tests

November 2014
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* Cython wrapper for C++ code done
* Ability to write a phased VCF (using HP tags).

June 2014
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* Repository for WhatsHap refactoring created

April 2014
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* The WhatsHap algorithm is introduced at RECOMB