Releases: htseq/htseq
Releases · htseq/htseq
0.12.3
First release since migration to the new Github organization htseq
.
Binaries for Linux and OSX are provided on PyPI: https://pypi.org/project/HTSeq/#files.
As usual, installation with pip is recommended.
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 processinghtseq-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 stdouthtseq-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
, namelyfraction
, which
will count an N-multimapper as 1/N for each feature, andrandom
, 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.