pysam-v0.15.4

Release 0.15.4

Bugfix release. Principal reason for release is to update cython
version in order to fix pip install pysam with python 3.8.

• [#879] Fix add_meta function in libcbcf.pyx, so meta-information
  lines in header added with this function have double-quoting rules
  in accordance to rules specified in VCF4.2 and VCF4.3 specifications
• [#863] Force arg to bytes to support non-ASCII encoding
• [#875] Bump minimum Cython version
• [#868] Prevent segfault on Python 2.7 AlignedSegment.compare(other=None)
• [#867] Fix wheel building on TravisCI
• [#863] Force arg to bytes to support non-ASCII encoding
• [#799] disambiguate interpretation of bcf_read return code
• [#841] Fix silent truncation of FASTQ with bad q strings
• [#846] Prevent segmentation fault on ID, when handling malformed records
• [#829] Run configure with the correct CC/CFLAGS/LDFLAGS env va

pysam-v0.15.3

Release 0.15.3

Bugfix release.

• [#824] allow reading of UTF-8 encoded text in VCF/BCF files.
• [#780] close all filehandles before opening new ones in pysam_dispatch
• [#773] do not cache VariantRecord.id to avoid memory leak
• [#781] default of multiple_iterators=True is changed to False for
  CRAM files.
• [#825] fix collections.abc import
• [#825] use bcf_hdr_format instead of bcf_hdr_fmt_text, fix memcpy
  bug when setting FORMAT fields.
• [#804] Use HTSlib's kstring_t, which reallocates and enlarges its
  memory as needed, rather than a fixed-size char buffer.
• [#814] Build wheels and upload them to PyPI
• [#755] Allow passing flags and arguments to index methods
• [#763] Strip \0 in header check
• [#761] Test Tabix index contents, not the compression

pysam-0.15.2

Bugfix release.

• [#746] catch pileup itorator out-of-scope segfaults
• [#747] fix faixd fetch with region
• [#748] increase max_pos to (1<<31)-1
• [#645] Add missing macOS stub files in MANIFEST.in, @SoapZA
• [#737] Fix bug in get_aligned_pairs, @bkohrn

pysam-0.15.1

Release 0.15.1

Bugfix release.

• [#716] raise ValueError if tid is out of range when writing
• [#697] release version using cython 0.28.5 for python 3.7
  compatibility

pysam-0.15.0.1

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

0.15.0

This release wraps htslib (and friends) versions 1.9.

pysam-0.14.1

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

pysam-0.14

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.

pysam-0.13.0

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

pysam-0.12.0.1

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