Pysam

==============

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

==============

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

==============

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

==============

This release wraps htslib/samtools/bcftools version 1.9.

* [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

==============

This is mostly 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

==============

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.