HadrienG / InSilicoSeq

:rocket: A sequencing simulator
https://insilicoseq.readthedocs.io
MIT License
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Bump pysam from 0.15.4 to 0.16.0 #176

Closed dependabot-preview[bot] closed 4 years ago

dependabot-preview[bot] commented 4 years ago

Bumps pysam from 0.15.4 to 0.16.0.

Release notes

Sourced from pysam's releases.

pysam-v0.16.0

This release wraps htslib/bcftools version 1.10.2 and samtools version 1.10. The following bugs reported against pysam are fixed due to this:

  • #447 Writing out QNAME longer than 251 characters corrupts BAM
  • [#640, #734, #843] Setting VariantRecord pos or stop raises error
  • [#738, #919] FastxFile truncates concatenated plain gzip compressed files

Additional bugfixes:

  • #840 Pileup doesn't work on python3 when index_filename is used
  • #886 FastqProxy raises ValueError when instantiated from python
  • #904 VariantFile.fetch() throws ValueError on files with no records
  • #909 Fix incorrect quoting in VariantFile contig records
  • [#915, #916] Implement pileup() for unindexed files and/or SAM files

Backwards incompatible changes:

  • The samtools import command was removed in samtools 1.10, so pysam no longer exports a samimport function. Use pysam.view() instead.

Many thanks to @jmarshall who has done most of the heavy lifting.

Commits
  • d20cad0 Merge pull request #925 from pysam-developers/pysam-0.16-release-candidate
  • 2282e99 Remove comment pertaining to removed "samimport" function [minor]
  • 7b3f6b2 Additional release notes entries
  • 4a08780 {AH} update release notes
  • e07342b {AH} bump version to 0.16.0
  • cbfdb2d Merge pull request #910 from scanisius/fix-vcf-meta-quoting
  • 95d0557 Merge branch 'graingert-patch-2'
  • 3453826 {AH} FastqProxy raises ValueError when instantiated from python
  • a7cb367 Merge branch 'patch-2' of https://github.com/graingert/pysam into graingert-p...
  • 31183d7 Merge pull request #905 from jmarshall/htstrio-1.10
  • Additional commits viewable in compare view


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codecov[bot] commented 4 years ago

Codecov Report

Merging #176 into dev will not change coverage. The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##              dev     #176   +/-   ##
=======================================
  Coverage   88.43%   88.43%           
=======================================
  Files          10       10           
  Lines         830      830           
=======================================
  Hits          734      734           
  Misses         96       96           

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dependabot-preview[bot] commented 4 years ago

Superseded by #179.