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pysam-0.9.1

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@AndreasHeger AndreasHeger released this 14 Jun 21:00
· 1123 commits to master since this release

This is a bugfix release addressing some installation problems
in pysam 0.9.0, in particular:

  • patch included htslib to work with older libcurl versions, fixes #262.
  • do not require cython for python 3 install, fixes #260
  • FastaFile does not accept filepath_index any more, see #270
  • add AlignedSegment.get_cigar_stats method.
  • py3 bugfix in VariantFile.subset_samples, fixes #272
  • add missing sysconfig import, fixes #278
  • do not redirect stdout, but instead write to a separately
    created file. This should resolve issues when pysam is used
    in notebooks or other environments that redirect stdout.
  • wrap htslib-1.3.1, samtools-1.3.1 and bcftools-1.3.1
  • use bgzf throughout instead of gzip
  • allow specifying a fasta reference for CRAM file when opening
    for both read and write, fixes #280