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This release is the same as v0.15.0 release on pypi, I was not aware that v0.15.0 had been release on github.

Release notes:
Release 0.15.0.1

This release wraps htslib/samtools/bcftools version 1.9.0.

  • [#673] permit dash in chromosome name of region string
  • [#656] Support text when opening a SAM file for writing
  • [#658] return None in get_forward_sequence if sequence not in record
  • [#683] allow lower case bases in MD tags
  • Ensure that = and X CIGAR ops are treated the same as M

@kyleabeauchamp kyleabeauchamp released this Jul 26, 2018 · 4 commits to master since this release

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This release wraps htslib (and friends) versions 1.9.

@AndreasHeger AndreasHeger released this Mar 20, 2018 · 30 commits to master since this release

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Release 0.14.1

This is predominantly a bugfix release, though bcftools has now also been
upgraded to 1.7.0.

  • [#621] Add a warning to count_coverage when an alignment has an
    empty QUAL field
  • [#635] Speed-up of AlignedSegment.find_intro()
  • treat border case of all bases in pileup column below quality score
  • [#634] Fix access to pileup reference_sequence

@AndreasHeger AndreasHeger released this Feb 9, 2018 · 62 commits to master since this release

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This release wraps htslib/samtools versions 1.7.0.

  • SAM/BAM/CRAM headers are now managed by a separate AlignmentHeader
    class.

  • AlignmentFile.header.as_dict() returns an ordered dictionary.

  • Use "stop" instead of "end" to ensure consistency to
    VariantFile. The end designations have been kept for backwards
    compatibility.

  • [#611] and [#293] CRAM repeated fetch now works, each iterator
    reloads index if multiple_iterators=True

  • [#608] pysam now wraps htslib 1.7 and samtools 1.7.

  • [#580] reference_name and next_reference_name can now be set to "*"
    (will be converted to None to indicate an unmapped location)

  • [#302] providing no coordinate to count_coverage will not count from
    start/end of contig.

  • [#325] @sq records will be automatically added to header if they are
    absent from text section of header.

  • [#529] add get_forward_sequence() and get_forward_qualities()
    methods

  • [#577] add from_string() and to_dict()/from_dict() methods to
    AlignedSegment. Rename tostring() to to_string() throughout for
    consistency

  • [#589] return None from build_alignment_sequence if no MD tag is set

  • [#528] add PileupColumn.len method

Backwards incompatible changes:

  • AlignmentFile.header now returns an AlignmentHeader object. Use
    AlignmentFile.header.to_dict() to get the dictionary as
    previously. Most dictionary accessor methods (keys(), values(),
    getitem, ...) have been implemented to ensure some level of
    backwards compatibility when only reading.

    The rationale for this change is to have consistency between
    AlignmentFile and VariantFile.

  • AlignmentFile and FastaFile now raise IOError instead of OSError

Medium term we plan to have a 1.0 release. The pysam
interface has grown over the years and the API is cluttered with
deprecated names (Samfile, getrname(), gettid(), ...). To work towards
this, the next release (0.15.0) will yield DeprecationWarnings
for any parts of the API that are considered obsolete and will not be
in 1.0. Once 1.0 has been reached, we will use semantic versioning.

@AndreasHeger AndreasHeger released this Nov 4, 2017 · 184 commits to master since this release

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This release wraps htslib/samtools/bcftools versions 1.6.0 and
contains a series of bugfixes.

  • [#544] reading header from remote TabixFiles now works.
  • [#531] add missing tag types H and A. A python float will now be
    added as 'f' type instead of 'd' type.
  • [#543] use FastaFile instead of Fastafile in pileup.
  • [#546] set is_modified flag in setAttribute so updated attributes
    are output.
  • [#537] allow tabix index files to be created in a custom location.
  • [#530] add get_index_statistics() method

@AndreasHeger AndreasHeger released this Sep 7, 2017 · 223 commits to master since this release

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Bugfix release resolving an issue with a missing config.h file in bcftools.

@AndreasHeger AndreasHeger released this Aug 24, 2017 · 225 commits to master since this release

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This release wraps htslib/samtools/bcftools versions 1.5.0 and
contains a series of bugfixes.

  • [#473] A new FastxRecord class that can be instantiated from class and
    modified in-place. Replaces PersistentFastqProxy.
  • [#521] In AligmentFile, Simplify file detection logic and allow remote index files
    • Removed attempts to guess data and index file names; this is magic left
      to htslib.
    • Removed file existence check prior to opening files with htslib
    • Better error checking after opening files that raise the appropriate
      error (IOError for when errno is set, ValueError otherwise for backward
      compatibility).
    • Report IO errors when loading an index by name.
    • Allow remote indices (tested using S3 signed URLs).
    • Document filepath_index and make it an alias for index_filename.
    • Added a require_index parameter to AlignmentFile
  • [#526] handle unset ref when creating new records
  • [#513] fix bcf_translate to skip deleted FORMAT fields to avoid
    segfaults
  • [#516] expose IO errors via IOError exceptions
  • [#487] add tabix line_skip, remove 'pileup' preset
  • add FastxRecord, replaces PersistentFastqProxy (still present for
    backwards compatibility)
  • [#496] upgrade to htslib/samtools/bcftools versions 1.5
  • add start/stop to AlignmentFile.fetch() to be consistent with
    VariantFile.fetch(). "end" is kept for backwards compatibility.

Upcoming changes:

In the next release we are plannig to separate the header information
from AlignmentFile into a separate class AlignmentHeader. This layout
is similar to VariantFile/VariantHeader. With this change we will
ensure that an AlignedSegment record will be linked to a header so
that chromosome names can be automatically translated from the numeric
representation. As a consequence, the way new AlignedSegment records
are created will need to change as the constructor requires a header::

header = pysam.AlignmentHeader(
    reference_names=["chr1", "chr2"],
    reference_lengths=[1000, 1000])
    
read = pysam.AlignedSegment(header)

This will affect all code that instantiates AlignedSegment objects
directly. We have not yet merged to allow users to provide feed-back.
The pull-request is here: #518
Please comment on github.

@AndreasHeger AndreasHeger released this Jun 11, 2017 · 285 commits to master since this release

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Bugfix release to address two issues:

  • Changes in 0.11.2.1 broke the GTF/GFF3 parser. Corrected and
    more tests have been added.
  • [#479] Correct VariantRecord edge cases described in issue

@AndreasHeger AndreasHeger released this May 12, 2017 · 301 commits to master since this release

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This release wraps htslib/samtools/bcfools versions 1.4.1 in response
to a security fix in these libraries. Additionaly the following
issues have been fixed:

  • [#452] add GFF3 support for tabix parsers
  • [#461] Multiple fixes related to VariantRecordInfo and handling of INFO/END
  • [#447] limit query name to 251 characters (only partially addresses issue)

VariantFile and related object fixes

  • Restore VariantFile.__dealloc__
  • Correct handling of bcf_str_missing in bcf_array_to_object and
    bcf_object_to_array
  • Added update() and pop() methods to some dict-like proxy objects
  • scalar INFO entries could not be set again after being deleted
  • VariantRecordInfo.delitem now allows unset flags to be deleted without
    raising a KeyError
  • Multiple other fixes for VariantRecordInfo methods
  • INFO/END is now accessible only via VariantRecord.stop and
    VariantRecord.rlen. Even if present behind the scenes, it is no longer
    accessible via VariantRecordInfo.
  • Add argument to issue a warning instead of an exception if input appears
    to be truncated

Other features and fixes:

  • Make AlignmentFile __dealloc__ and close more
    stringent
  • Add argument AlignmentFile to issue a warning instead of an
    exception if input appears to be truncated

@AndreasHeger AndreasHeger released this Apr 23, 2017 · 333 commits to master since this release

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Bugfix release to improve backwards compatibility:

  • [#440] add deprecated 'always' option to infer_query_length for backwards compatibility.