Whatshap

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

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.

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* Add option ``--plot-sum-of-blocksizes`` to ``whatshap compare``.
* Fix in ``whatshap stats``: sometimes returned wrong N50 values if the end
position of the last block of a chromosome was larger than the starting position
of the first block of the next chromosome.
* :issue:`173`: The ``haplotag`` command should now be able to properly write
CRAM files.
* :issue:`177`: Option ``--ignore-read-groups`` did not work when phased blocks
(VCF) were provided as input.
* :issue:`122`: Add ``--ignore-read-groups`` and ``--samples`` options to ``haplotag``.
* Integration of the HapChat algorithm as an alternative MEC solver, available
through ``whatshap phase --algorithm=hapchat``. Contributed by the HapChat
team, see https://doi.org/10.1186/s12859-018-2253-8.
* This is the last release of WhatsHap to support Python 3.4.

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* :issue:`140`: Haplotagging now works when chromosomes are missing in the VCF.
* Added option ``--merge-reads``, which is helpful for high coverage data.
* When phasing pedigrees, ensure that haplotypes are ordered as
paternal_allele|maternal_allele in the output VCF. This seems to be a common
convention and also used by 1000G.
* Test cases now use pytest instead of nose (which is discontinued).

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* :issue:`167`: Fix the ``haplotag`` command. It would tag reads incorrectly.
* :issue:`154`: Use barcode information in BX tags when running ``haplotag``
on 10x Genomics linked read data.
* :issue:`153`: Allow combination of ``--ped`` and ``--samples`` to only work
on a subset of samples in a pedigree. Added ``--use-ped-samples`` to only
phase samples mentioned in PED file (while ignoring other samples in input VCF).

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* New subcommand ``genotype`` for haplotype-aware genotyping
(see https://doi.org/10.1101/293944 for details on the method).
* Support CRAM files in addition to BAM.
* :issue:`133`:
No longer create BAM/CRAM index if it does not exist. This is safer when running multiple
WhatsHap instances in parallel. From now on, you need to create the index yourself
(for example with ``samtools index``) before running WhatsHap.
* :issue:`152`: Reads marked as “duplicate” in the input BAM/CRAM file are now ignored.
* :issue:`157`: Adapt to changed interface in Pysam 0.14.
* :issue:`158`: Handle read groups with missing sample (SM) tag correctly.

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

* Fix compilation problem by distinguishing gcc and clang.