Pysam

==============

.. rubric:: 17 November 2021

This release wraps htslib/samtools/bcftools version 1.14.

* [1048] and [1060], clarify documentation of index statistics with CRAM files
* Prevent "retval may be used uninitialised" warning.
* Add new "samples" subcommand to pysam/samtools.py
* Introduce TupleProxyIterator iterator object class

==============

.. rubric:: 30 September 2021

This release wraps htslib/samtools/bcftools version 1.13. Corresponding
to new samtools commands, `pysam.samtools` now has additional functions
`ampliconclip`, `ampliconstats`, `fqimport`, and `version`.

Bugs fixed:

* [447] The maximum QNAME length is fully restored to 254
* [506, 958, 1000] Don't crash the Python interpreter on ``pysam.bcftools.*()`` errors
* [603] count_coverage: ignore reads that have no SEQ field
* [928] Fix ``pysam.bcftools.mpileup()`` segmentation fault
* [983] Add win32/\*.[ch] to MANIFEST.in
* [994] Raise exception in ``get_tid()`` if header could not be parsed
* [995] Choose TBI/CSI in ``tabix_index()`` via both min_shift and csi
* [996] ``AlignmentFile.fetch()`` now works with large chromosomes longer than 2\ :sup:`29` bases
* [1019] Fix Sphinx documentation generation by avoiding Python 2 ``ur'string'`` syntax
* [1035] Improved handling of file iteration errors
* [1038] ``tabix_index()`` no longer leaks file descriptors
* [1040] ``print(aligned_segment)`` now prints the correct TLEN value
(it also now prints RNAME/RNEXT more clearly and prints POS/PNEXT 1-based)
* *setup.py* longer uses ``setup(use_2to3)`` for compatibility with setuptools >= v58.0.0

New facilities:

* [PR 963] Additional VCF classes are exposed to pysam programmers
* [998, PR 1001] Add ``get/set_encoding_error_handler()`` to control UTF-8 conversion
* [PR 1012] Running ``python setup.py sdist`` now automatically runs cythonize
* Running tests with ``pytest`` now automatically runs ``make`` to generate test data

Documentation improvements:

* [726] Clarify get_forward_sequence/get_forward_qualities documentation
* [865] Improved example
* [968] ``get_index_statstics`` parameters
* [986] Clarify ``VariantFile.fetch`` start/stop region parameters are 0-based and half-open.
* [990] Corrected ``PileupColumn.get_query_sequences`` documentation
* [999] Fix documentation for ``AlignmentFile.get_reference_length()``
* [1002] Document the default min_base_quality for ``pileup()``

==============

.. rubric:: 8 June 2020

This release wraps htslib/bcftools version 1.10.2 and samtools version
1.10. The following bugs reported against pysam are fixed due to this:

* [447] Writing out QNAME longer than 251 characters corrupts BAM
* [640, 734, 843] Setting VariantRecord pos or stop raises error
* [738, 919] FastxFile truncates concatenated plain gzip compressed files

Additional bugfixes:

* [840] Pileup doesn't work on python3 when `index_filename` is used
* [886] FastqProxy raises ValueError when instantiated from python
* [904] VariantFile.fetch() throws ValueError on files with no records
* [909] Fix incorrect quoting in VariantFile contig records
* [915, 916] Implement pileup() for unindexed files and/or SAM files

Backwards incompatible changes:

* The `samtools import` command was removed in samtools 1.10, so pysam
no longer exports a `samimport` function. Use `pysam.view()` instead.

==============

Bugfix release. Principal reason for release is to update cython
version in order to fix pip install pysam with python 3.8.

* [879] Fix add_meta function in libcbcf.pyx, so meta-information
lines in header added with this function have double-quoting rules
in accordance to rules specified in VCF4.2 and VCF4.3 specifications
* [863] Force arg to bytes to support non-ASCII encoding
* [875] Bump minimum Cython version
* [868] Prevent segfault on Python 2.7 AlignedSegment.compare(other=None)
* [867] Fix wheel building on TravisCI
* [863] Force arg to bytes to support non-ASCII encoding
* [799] disambiguate interpretation of bcf_read return code
* [841] Fix silent truncation of FASTQ with bad q strings
* [846] Prevent segmentation fault on ID, when handling malformed records
* [829] Run configure with the correct CC/CFLAGS/LDFLAGS env vars

==============

Bugfix release.

* [824] allow reading of UTF-8 encoded text in VCF/BCF files.
* [780] close all filehandles before opening new ones in pysam_dispatch
* [773] do not cache VariantRecord.id to avoid memory leak
* [781] default of multiple_iterators=True is changed to False for
CRAM files.
* [825] fix collections.abc import
* [825] use bcf_hdr_format instead of bcf_hdr_fmt_text, fix memcpy
bug when setting FORMAT fields.
* [804] Use HTSlib's kstring_t, which reallocates and enlarges its
memory as needed, rather than a fixed-size char buffer.
* [814] Build wheels and upload them to PyPI
* [755] Allow passing flags and arguments to index methods
* [763] Strip \0 in header check
* [761] Test Tabix index contents, not the compression

==============

Bugfix release.

* [746] catch pileup itorator out-of-scope segfaults
* [747] fix faixd fetch with region
* [748] increase max_pos to (1<<31)-1
* [645] Add missing macOS stub files in `MANIFEST.in`, SoapZA
* [737] Fix bug in get_aligned_pairs, bkohrn