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pysam-0.8.2

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@AndreasHeger AndreasHeger released this 17 Feb 20:29
· 1674 commits to master since this release
  • Pysam now wraps htslib 1.2.1 and samtools version 1.2
  • Added CRAM file support to pysam
  • New alignment info interface.
    • opt() and setTag are deprecated, use get_tag() and set_tag()
      instead.
    • added has_tag()
    • tags is deprecated, use get_tags() and set_tags() instead.
  • FastqFile is now FastxFile to reflect that the latter permits
    iteration over both fastq- and fasta-formatted files.
  • A Cython wrapper for htslib VCF/BCF reader/writer. The wrapper
    provides a nearly complete Pythonic interface to VCF/BCF metadata
    with reading and writing capability. However, the interface is still
    incomplete and preliminary and lacks capability to mutate the
    resulting data.