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smithlabcode / ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data
http://doi.org/djv4
GNU General Public License v3.0
28 stars 8 forks source link

Bump pysam from 0.18.0 to 0.19.0 #118

Closed dependabot[bot] closed 2 years ago

dependabot[bot] commented 2 years ago

Bumps pysam from 0.18.0 to 0.19.0.

Release notes

Sourced from pysam's releases.

pysam-v0.19.0

Release 0.19.0

This release wraps htslib/samtools/bcftools version 1.15.

  • #1085 Improve getopt()/getopt_long() resetting when running samtools/bcftools commands

  • #1078 Support BAM_CPAD in get_aligned_pairs

  • #1063 Run flake8 and fix some linting issues

  • #1088 Add AlignedSegment is_mapped/mate_is_mapped/is_forward/mate_is_forward properties

  • Write an absent AlignedSegment.qual as all-bytes-0xff

  • Fix BGZFile.read() behaviour near or at EOF

  • First API for the htslib modified bases interfac

Changelog

Sourced from pysam's changelog.

Release 0.19.0

This release wraps htslib/samtools/bcftools version 1.15.

  • #1085 Improve getopt()/getopt_long() resetting when running samtools/bcftools commands

  • #1078 Support BAM_CPAD in get_aligned_pairs

  • #1063 Run flake8 and fix some linting issues

  • #1088 Add AlignedSegment is_mapped/mate_is_mapped/is_forward/mate_is_forward properties

  • Write an absent AlignedSegment.qual as all-bytes-0xff

  • Fix BGZFile.read() behaviour near or at EOF

  • First API for the htslib modified bases interface

Commits
  • bc1e4de Merge pull request #1091 from pysam-developers/v0.19.0.x
  • d00f38b update ci regex to three levels
  • 7282066 update release notes
  • 1c41e65 change version to 0.19.0
  • 2a5e55e Merge pull request #1008 from marcelm/type-hints
  • d94fe42 Merge pull request #1071 from odidev/aarch64_wheel
  • beb2633 Merge pull request #1085 from jmarshall/optreset
  • ef06e42 Merge pull request #1078 from terrycojones/handle-cpad
  • 460a431 Make CIGAR 'P' (padding in the reference) operations return None (not '*') fo...
  • f29f932 Re-import samtools/bcftools to apply getopt() resetting improvements
  • Additional commits viewable in compare view


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