Whatshap

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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.

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* Fix compilation problem by distinguishing gcc and clang.

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* Added ``--full-genotyping`` to (re-)genotype the given variants based on the reads
* Added option ``whatshap compare --switch-error-bed`` to write BED file with switch
error positions
* Added ``whatshap compare --plot-blocksizes`` to plot histogroms of block sizes
* Added option ``--longest-block-tsv`` to output position-wise stats on longest joint
haplotype block
* Added option ``whatshap compare --tsv-multiway`` to write results of multi-way
comparison to tab-separated file
* Added option --chromosome to whatshap stats
* ``whatshap compare`` can now compute the block-wise Hamming distance
* ``whatshap stats`` can now compute an N50 for the phased blocks
* Fixed compilation issues on OS X (clang)
* Detect unsorted VCFs and chromosome name mismatches between BAM and VCF
* Fix crash when whatshap compare encounteres unphased VCFs
* Expanded documentation.