Merge pull request #1091 from pysam-developers/v0.19.0.x

V0.19.0.x

.github/workflows/release.yaml

@@ -3,7 +3,7 @@ name: Publish pysam wheels to PyPI and TestPyPI
 on:
   push:
     branches:
-      - v[0-9]+.[0-9]+.x
+      - v[0-9]+.[0-9]+.[0-9].x
     tags:
       - v*
   release:

NEWS

@@ -5,6 +5,120 @@ http://pysam.readthedocs.io/en/latest/release.html
 Release notes
 =============
 
+Release 0.19.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.15.
+
+* [#1085] Improve getopt()/getopt_long() resetting when running samtools/bcftools commands
+
+* [#1078] Support BAM_CPAD in get_aligned_pairs
+
+* [#1063] Run flake8 and fix some linting issues
+
+* [#1088] Add AlignedSegment is_mapped/mate_is_mapped/is_forward/mate_is_forward properties
+
+* Write an absent AlignedSegment.qual as all-bytes-0xff
+
+* Fix BGZFile.read() behaviour near or at EOF
+
+* First API for the htslib modified bases interface
+
+Release 0.18.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.14.
+
+* [#1048] and [#1060], clarify documentation of index statistics with CRAM files
+* Prevent "retval may be used uninitialised" warning.
+* Add new "samples" subcommand to pysam/samtools.py
+* Introduce TupleProxyIterator iterator object class
+
+Release 0.17.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.13. Corresponding
+to new samtools commands, `pysam.samtools` now has additional functions
+`ampliconclip`, `ampliconstats`, `fqimport`, and `version`.
+
+Bugs fixed:
+
+* [#447] The maximum QNAME length is fully restored to 254
+* [#506, #958, #1000] Don't crash the Python interpreter on ``pysam.bcftools.*()`` errors
+* [#603] count_coverage: ignore reads that have no SEQ field
+* [#928] Fix ``pysam.bcftools.mpileup()`` segmentation fault
+* [#983] Add win32/\*.[ch] to MANIFEST.in
+* [#994] Raise exception in ``get_tid()`` if header could not be parsed
+* [#995] Choose TBI/CSI in ``tabix_index()`` via both min_shift and csi
+* [#996] ``AlignmentFile.fetch()`` now works with large chromosomes longer than 2\ :sup:`29` bases
+* [#1019] Fix Sphinx documentation generation by avoiding Python 2 ``ur'string'`` syntax
+* [#1035] Improved handling of file iteration errors
+* [#1038] ``tabix_index()`` no longer leaks file descriptors
+* [#1040] ``print(aligned_segment)`` now prints the correct TLEN value
+  (it also now prints RNAME/RNEXT more clearly and prints POS/PNEXT 1-based)
+* *setup.py* longer uses ``setup(use_2to3)`` for compatibility with setuptools >= v58.0.0
+
+New facilities:
+
+* [PR #963] Additional VCF classes are exposed to pysam programmers
+* [#998, PR #1001] Add ``get/set_encoding_error_handler()`` to control UTF-8 conversion
+* [PR #1012] Running ``python setup.py sdist`` now automatically runs cythonize
+* Running tests with ``pytest`` now automatically runs ``make`` to generate test data
+
+Documentation improvements:
+
+* [#726] Clarify get_forward_sequence/get_forward_qualities documentation
+* [#865] Improved example
+* [#968] ``get_index_statstics`` parameters
+* [#986] Clarify ``VariantFile.fetch`` start/stop region parameters are 0-based and half-open.
+* [#990] Corrected ``PileupColumn.get_query_sequences`` documentation
+* [#999] Fix documentation for ``AlignmentFile.get_reference_length()``
+* [#1002] Document the default min_base_quality for ``pileup()``
+
+
+Release 0.16.0
+==============
+
+This release wraps htslib/bcftools version 1.10.2 and samtools version
+1.10. The following bugs reported against pysam are fixed due to this:
+
+* [#447] Writing out QNAME longer than 251 characters corrupts BAM
+* [#640, #734, #843] Setting VariantRecord pos or stop raises error
+* [#738, #919] FastxFile truncates concatenated plain gzip compressed files
+
+Additional bugfixes:
+
+* [#840] Pileup doesn't work on python3 when `index_filename` is used
+* [#886] FastqProxy raises ValueError when instantiated from python
+* [#904] VariantFile.fetch() throws ValueError on files with no records
+* [#909] Fix incorrect quoting in VariantFile contig records
+* [#915, #916] Implement pileup() for unindexed files and/or SAM files
+
+Backwards incompatible changes:
+
+* The `samtools import` command was removed in samtools 1.10, so pysam
+  no longer exports a `samimport` function. Use `pysam.view()` instead.
+
+
+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 vars
+
 Release 0.15.3
 ==============
 

doc/release.rst

@@ -2,6 +2,25 @@
 Release notes
 =============
 
+Release 0.19.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.15.
+
+* [#1085] Improve getopt()/getopt_long() resetting when running samtools/bcftools commands
+
+* [#1078] Support BAM_CPAD in get_aligned_pairs
+
+* [#1063] Run flake8 and fix some linting issues
+
+* [#1088] Add AlignedSegment is_mapped/mate_is_mapped/is_forward/mate_is_forward properties
+
+* Write an absent AlignedSegment.qual as all-bytes-0xff
+
+* Fix BGZFile.read() behaviour near or at EOF
+
+* First API for the htslib modified bases interface
+
 Release 0.18.0
 ==============
 

pysam/version.py

@@ -1,5 +1,5 @@
 # pysam versioning information
-__version__ = "0.18.0"
+__version__ = "0.19.0"
 
 __samtools_version__ = "1.15"
 __bcftools_version__ = "1.15"