pysam-0.12.0

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.

pysam-0.11.2.2

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

pysam-0.11.2

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

pysam-0.11.1

Bugfix release to improve backwards compatibility:

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

pysam-0.11.0

This release wraps the latest versions of htslib/samtools/bcftools and
implements a few bugfixes.

• [#413] Wrap HTSlib/Samtools/BCFtools 1.4
• [#422] Fix missing pysam.sort.usage() message
• [#411] Fix BGZfile initialization bug
• [#412] Add seek support for BGZFile
• [#395] Make BGZfile iterable
• [#433] Correct getQueryEnd
• [#419] Export SAM enums such as pysam.CMATCH
• [#415] Fix access by tid in AlignmentFile.fetch()
• [#405] Writing SAM now outputs a header by default.
• [#332] split infer_query_length(always) into infer_query_length and infer_read_length

pysam-0.10.0

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.

pysam-0.9.1.4

This release is (almost) identical to 0.9.1 but aims to improve installation by querying htslib configuration directly.

Many thanks @jmarshall

This release also fixes a bug when parsing tags following CL tags in SAM/BAM headers.

pysam-0.9.1.3

This release is identical but aims to improve installation on systems without cython.

pysam-0.9.1.2

This release is identical to pysam 0.9.1 in functionality, but aims to improve installation without libcurl.

pysam-0.9.1.1

This release is functionally equivalent to 0.9.1, but aims to resolve installation issues on systems without cython.