==============
2020-04-18
New features:
- Negative indices for ``StepVector`` (thanks to shouldsee for the original PR).
- ``htseq-count-barcodes`` counts features in barcoded SAM/BAM files, e.g. 10X Genomics
single cell outputs. It supports cell barcodes, which result in different columns of
the output count table, and unique molecular identifiers.
- ``htseq-count`` has new option ``-n`` for multicore parallel processing
- ``htseq-count`` has new option ``-d`` for separating output columns by arbitrary character
(defalt TAB, ``,`` is also common)
- ``htseq-count`` has new option ``-c`` for output into a file instead of stdout
- ``htseq-count`` has new option ``--append-output`` for output into a file by appending to
any existing test (e.g. a header with the feature attribute names and sample names)
- ``htseq-count`` has two new values for option ``--nonunique``, namely ``fraction``, which
will count an N-multimapper as 1/N for each feature, and ``random``, which will assign
the alignment to a random one of its N-multimapped features. This feature was added by
ewallace (thank you!).
- ``htseq-qa`` got refactored and now accepts an options ``--primary-only`` which ignores
non-primary alignments in SAM/BAM files. This means that the final number of alignments
scored is equal to the number of reads even when multimapped reads are present.
Testing improvements:
- Extensive testing and installation changes for Mac OSX 10.14 and later versions
- Testing Python 2.7, 3.6, 3.7, and 3.8 on OSX
- Testing and deployment now uses conda environments
Numerous bugfixes and doc improvements.
This is the **last** version of ``HTSEQ`` supporting Python 2.7, as it is unmaintained since Jan 1st, 2020. ``HTSeq`` will support Python 3.5+ from the next version.