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@AndreasHeger AndreasHeger released this 22 Jan 21:02
· 972 commits to master since this release
v0.10.0
f749181

This release implements further functionality in the VariantFile API
and includes several bugfixes:

  • treat special case -c option in samtools view outputs to stdout even
    if -o given, fixes #315
  • permit reading BAM files with CSI index, closes #370
  • raise Error if query name exceeds maximum length, fixes #373
  • new method to compute hash value for AlignedSegment
  • AlignmentFile, VariantFile and TabixFile all inherit from HTSFile
  • Avoid segfault by detecting out of range reference_id and
    next_reference in AlignedSegment.tostring
  • Issue #355: Implement streams using file descriptors for VariantFile
  • upgrade to htslib 1.3.2
  • fix compilation with musl libc
  • Issue #316, #360: Rename all Cython modules to have lib as a prefix
  • Issue #332, hardclipped bases in cigar included by
    pysam.AlignedSegment.infer_query_length()
  • Added support for Python 3.6 filename encoding protocol
  • Issue #371, fix incorrect parsing of scalar INFO and FORMAT fields in VariantRecord
  • Issue #331, fix failure in VariantFile.reset() method
  • Issue #314, add VariantHeader.new_record(), VariantFile.new_record() and
    VariantRecord.copy() methods to create new VariantRecord objects
  • Added VariantRecordFilter.add() method to allow setting new VariantRecord filters
  • Preliminary (potentially unsafe) support for removing and altering header metadata
  • Many minor fixes and improvements to VariantFile and related objects

Please note that all internal cython extensions now have a lib prefix. Any user cython extensions
using cimport to import pysam definitions will need changes.

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