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pysam-v0.16.0

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@AndreasHeger AndreasHeger released this 07 Jun 20:42
· 402 commits to master since this release
d20cad0

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.