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
#999 Fix documentation for AlignmentFile.get_reference_length()
#1002 Document the default min_base_quality for pileup()
Notes and comments:
Apologies for the hiatus in releases. A big thank you to @jmarshall who has been doing a lot of the work of maintaining pysam in the last year. The delay in getting out releases has been entirely down to me. We have now automated the release process using Github actions. With less overhead, we should be able to release more timely again.
The priorities in the near future are to:
track htslib releases and release pysam in a timely manner.
remove python2 compatibility from pysam. This will simplify quite a bit of code within pysam.
review and triage the many open issues and pull requests. Many thanks to the whole community for submissions and apologies in the delay on acting on them.
The medium term priority is to review the pysam API in order to arrive at a 1.0 release with a consistent API.
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Bumps pysam from 0.16.0.1 to 0.17.0.
Release notes
Sourced from pysam's releases.
Commits
7d1a70e
restrict publish actionsf770bb8
Merge pull request #1049 from pysam-developers/release-0.17.03a6a5bb
only publish to pytest for tagged branchc978f17
update release notesccd7738
set version to 0.17.0647c4a3
update release notes (thanks to@jmarshall
)c6913a9
Upload sdist artifact from the linux CI job2422ebd
add test-pypi upload,26d412b7
add test-pypi upload5b77b1d
try osx builds, 4Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
@dependabot rebase
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