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1 | 1 | .. An online version of the release history can be found here: |
2 | 2 | .. http://pysam.readthedocs.io/en/latest/release.html |
3 | 3 |
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| 4 | +Release 0.24.0 |
| 5 | +============== |
| 6 | + |
| 7 | +.. rubric:: xx November 2025 |
| 8 | + |
| 9 | +This pysam release wraps htslib and samtools version 1.22.1 and |
| 10 | +bcftools version 1.22 (PR #1343) and now requires Cython 3. |
| 11 | + |
| 12 | +It has been tested with Python versions 3.8 through 3.14, and wheels are |
| 13 | +available via PyPI_ for all of those Python versions. Wheels are built for |
| 14 | +macOS and Linux (manylinux_2_28 and musllinux_1_2) on both ARM and x86-64. |
| 15 | + |
| 16 | +The final pysam release that supported Python 3.6 and 3.7 was v0.23.0. |
| 17 | +v0.24.x is expected to be the last release series supporting Python 3.8. |
| 18 | + |
| 19 | +Bugs fixed: |
| 20 | + |
| 21 | +* Remove :attr:`.AlignedSegment.modified_bases`'s limitation of only five |
| 22 | + modification types in MM/ML fields. (#1348, reported by Leszek Pryszcz) |
| 23 | + |
| 24 | +* Suppressed TestBinaryCompatibility test cases on platforms where we |
| 25 | + have not calculated the expected sizes. Also fixed the capturing of |
| 26 | + :func:`pysam.samtools.calmd() <.samtools.command>` output, particularly |
| 27 | + on 32-bit i386. (#1367, reported by Étienne Mollier for Debian) |
| 28 | + |
| 29 | +New functionality: |
| 30 | + |
| 31 | +* Updated pysam/libchtslib.pxd declarations to the HTSlib 1.22.1 API. |
| 32 | + This is the first comprehensive update that these Cython HTSlib API |
| 33 | + declarations have received. (PR #1362) |
| 34 | + |
| 35 | +Documentation improvements: |
| 36 | + |
| 37 | +* New documentation for VariantRecordSample et al FIXME |
| 38 | + (PR #1358, PR #1359, PR #1361, thanks to Tim Dunn) |
| 39 | + |
| 40 | +* Clarified :attr:`.AlignedSegment.query_alignment_length` et al |
| 41 | + behaviour for unmapped reads. (#1319, reported by Sam Chorlton) |
| 42 | + |
| 43 | + |
4 | 44 | Release 0.23.3 |
5 | 45 | ============== |
6 | 46 |
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