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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 0.23.0 |
| 5 | +============== |
| 6 | + |
| 7 | +.. rubric:: 5 February 2025 |
| 8 | + |
| 9 | +This pysam release wraps htslib/samtools/bcftools 1.21 (PR #1310). |
| 10 | + |
| 11 | +It has been tested with Python versions 3.6 through 3.13, and wheels are |
| 12 | +available via PyPI_ for all of those Python versions. Python versions 3.6 |
| 13 | +through 3.8 are end-of-life; particularly if you use pysam with one of |
| 14 | +these versions, please vote in the version survey at issue #1230. |
| 15 | + |
| 16 | +This is expected to be the last release supporting Python 3.6 and 3.7. |
| 17 | + |
| 18 | +Bugs fixed: |
| 19 | + |
| 20 | +* Fix :func:`pysam.samtools.command(save_stdout=filename) <.samtools.command>` |
| 21 | + redirection of output to a file. (#677, reported by Haowen Zhang and analysed |
| 22 | + by Youri Hoogstrate) |
| 23 | + |
| 24 | +* Reinstate HTTPS/S3/GCS support in pre-built Linux wheels when used on Debian |
| 25 | + and Ubuntu: these wheels now work around the discrepancy between Red Hat and |
| 26 | + Debian CA Certificate file locations. (#1257, #1268, reported by Daisie Huang |
| 27 | + and Li Tai Fang) |
| 28 | + |
| 29 | +* Calling :meth:`.VariantHeader.new_record` repeatedly with the same |
| 30 | + :obj:`samples` object now sets GT correctly every time. (#1308, reported |
| 31 | + by Arthur Gymer) |
| 32 | + |
| 33 | +* Correct the exception produced when :meth:`.AlignedSegment.set_tags` is |
| 34 | + used with an invalid value type. (#1233, PR #1235, reported by Weisheng Wu |
| 35 | + and Marcus Stoiber) |
| 36 | + |
| 37 | +* Many type hinting corrections. (#1298, #1316, PR #1296, PR #1306, PR #1313, |
| 38 | + PR #1315, thanks to Victor Epain, Arthur Gymer, @mshunjan, and Matt Stone) |
| 39 | + |
| 40 | +* The undocumented :func:`!pysam.samtools.import_` alias for invoking |
| 41 | + ``samtools import`` has been removed; |
| 42 | + use :func:`pysam.samtools.fqimport() <.samtools.command>` instead. |
| 43 | + |
| 44 | +* Corrections to several test data files to account for HTSlib 1.20 and later's |
| 45 | + improved validity checking. (#1291, reported by David Seifert; etc) |
| 46 | + |
| 47 | +New functionality: |
| 48 | + |
| 49 | +* :meth:`.AlignedSegment.get_aligned_pairs` now optionally returns the |
| 50 | + associated CIGAR operator in each position tuple. (#1292, PR #1294, |
| 51 | + thanks to Lara Fuhrmann and Ivan Blagoev Topolsky) |
| 52 | + |
| 53 | +* New :meth:`AlignmentFile.flush() <.HTSFile.flush>` and |
| 54 | + :meth:`VariantFile.flush() <.HTSFile.flush>` methods for flushing buffered |
| 55 | + output to streams. (#1299, requested by @blex-max) |
| 56 | + |
| 57 | +* Improved :class:`str() <str>` for :class:`.AlignedSegment` now displays |
| 58 | + reference sequence names when they are available and uses ``#N`` only when |
| 59 | + necessary. (#1318, requested by Liu) |
| 60 | + |
| 61 | +* Implement :func:`repr` for :class:`.AlignedSegment` so that it displays the |
| 62 | + most useful fields. (PR #1267, thanks to Marcel Martin) |
| 63 | + |
| 64 | +* Pysam's tests can now run in parallel. (#1284, reported by Yuri Victorovich) |
| 65 | + |
| 66 | +Documentation improvements: |
| 67 | + |
| 68 | +* More complete documentation of invoking SAMtools and BCFtools subcommands |
| 69 | + via Pysam. (#1096, #1241, PR #1261, PR #1275, #1323, et al, reported by |
| 70 | + Seung-been "Steven" Lee, Robert Baldwin, Michael Hall, Indraniel Das, |
| 71 | + and @shokrofont) |
| 72 | + |
| 73 | +* Use the Pysam names for CIGAR operators rather than internal C names. |
| 74 | + (#1255, reported by Ilya Shlyakhter) |
| 75 | + |
| 76 | +* Mention :meth:`AlignmentFile.fetch("*") <.AlignmentFile.fetch>` in the |
| 77 | + FAQ entry on fetching unmapped reads. (#424, reported by Ben Weisburd) |
| 78 | + |
| 79 | + |
4 | 80 | Release 0.22.1 |
5 | 81 | ============== |
6 | 82 |
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