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jmarshall committed Apr 23, 2024
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.. An online version of the release history can be found here:
.. http://pysam.readthedocs.io/en/latest/release.html

Release 0.22.1
==============

.. rubric:: 24 April 2024

Bugfix release, which still wraps htslib/samtools/bcftools 1.18.

Bugs fixed:

* Preserve all header field tags defined in the SAM specification (notably TP)
in :meth:`.AlignmentHeader.from_dict` and :meth:`.AlignmentHeader.to_dict`
(#1237, PR #1238, thanks to Tim Fennell and Nils Homer)

* Adjust HTSlib's Makefile so that ``make distclean`` no longer tries to
rebuild the htscodecs configury (PR #1247, reported by Nicola Soranzo)

* Add missing :attr:`.AlignedSegment.is_mapped` etc properties to type stubs
(PR #1273, thanks to Matt Stone)

* Reinstate S3 support in pre-built Linux wheels: support for this protocol
was inadvertently omitted from the pre-built 0.22.0 wheels on Linux
(#1249, #1257, #1277, etc varying circumstances; likely it is this that
was reported by Mathew Baines, Daisie Huang, Benjamin Sargsyan, et al)

* Fix off-by-one NamedTupleProxy, :meth:`.asBed`, etc array bounds check
(#1279, reported by Dan Bolser)

* Make pysam's klib headers compatible with C++ (reported by Martin Grigorov)


Release 0.22.0
==============

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