Version history¶
Version 2.0.2¶
2022-07-03
Bugfix release. All users are encouraged to upgrade.
Scripts:
htseq-count
had silently adopted a new logic to handle a corner case where read 1 was missing but read 2 was present. This has now been reverted to ensure exact compatibility withHTSeq<=0.13.5
.
Version 2.0.1¶
2022-03-25
Maintenance version. Users are not required to upgrade.
CI:
- Updated docker CI requirements.
Version 2.0.0¶
2022-03-22
Major release. All users are encouraged to upgrade.
Publication:
- New paper describing HTSeq 2.0 in [Bioinformatics](https://doi.org/10.1093/bioinformatics/btac166). Please cite the new paper to help us maintain HTSeq!
API features:
- Support for StretchVector, a data structure for “island-of-data” sparsity
- Added BigWig_Reader
- Added I/O functions for
GenomicArray
to/from bedGraph and BigWig files make_feature_genomicarrayofsets
now supports multiple primary attributesmake_feature_genomicarrayofsets
can now add chromosome info as an additional attribute- Improved context manager support (
with
statement) for parsers - Support for
pathlib.Path
objects
Scripts:
- Refactoring of
htseq-count
for readability - Added exon-level counting to
htseq-count
- Added output formats to
htseq-count
: loom, h5ad, mtx files - The above all apply to
htseq-count-barcodes
as well. - Added
--with-header
option tohtseq-count
.
Documentation:
- Modernized template of docs
- Added tutorial on High C analysis
- Added step by step explanation of
htseq-count
logic - Improved API documentation on a number of interfaces
- Improved docstrings throughout
Tests/Infrastructure:
- Better testing infra (e.g.
test.sh
) - Many more unit tests
Bug fixes:
- Fixed a bug with templates SAM files
- Fixed a bug about
ChromVector
steps. - Fixed a bug about file opening (thanks @mruffalo)
- Fixed a bug about ambiguous reads (thanks @Mashin6)
- Fixed a typo in the docs (thanks @Tejindersingh1)
- Improved style of code and documentation
Version 0.13.5¶
2020-12-29
Maintenance and small feature release
- Refactored CI to use Github actions.
- Improved docs and fixed docs building bugs
- Reader classes (e.g. FastaReader, BAM_Reader) can be used with
with
(as context managers) - Fixed a few bugs in
htseq-count
Version 0.12.3¶
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 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.
Version 0.11.2¶
2019-01-07
Bugfix release for htseq-count
:
- fixed bug and changed how to use output SAM files via
-o
: you now have to specify the option once per input/output file
Version 0.11.1¶
2019-01-03
Bugfix release for htseq-count
:
- fixed bug and changed how to use of additional attributes via
--additional-attr
Version 0.11.0¶
2018-08-01
htseq-count
ignores secondary and supplementary alignments by default- bugfix in the SAM output of
htseq-count
- optional argument name in reverse complement function
- better linting of Cython files
Version 0.10.0¶
2018-05-08
- flush output of
htseq-count
(thanks dcroote) - pass memmap_dir to ChromVector.create (thanks wkopp)
BAM_Reader
supportscheck_sq
for PacBio reads (thanks jbloom)- a number of Bugfixes
Version 0.9.1¶
2017-07-26
Bugfix release for htseq-count
:
--secondary-alignments
andsupplementary-alignments
should now work for some corner cases of unmapped reads
Version 0.9.0¶
2017-07-11
This release adds a few options to htseq-count
:
--secondary-alignments
handles secondary alignments coming from the same read--supplementary-alignments
handles supplementary alignments (aka chimeric reads)
Raw but fast iterators for FASTA and FASTQ files have been added.
Support for the SAM CIGAR flags =
and X
(sequence match and mismatch) has been added.
Sequence
objects can now be pickled/serialized.
Binaries for linux and OSX are now provided on PyPI.
Automation of the release process has been greatly extended, including OSX continuous integration builds.
Several bugs have been fixed, and some parts of the code have been linted or modernized.
Version 0.8.0¶
2017-06-07
This release adds a few options to htseq-count
:
--nonunique
handles non-uniquely mapped reads--additional-attr
adds an optional column to the output (typically for human-readable gene names)--max-reads-in-buffer
allows increasing the buffer size when working with paired end, coordinate sorted files
Moreover, htseq-count
can now take more than one input file and prints the output with one column per input file.
Finally, parts of the code have been streamlined or modernized, documentation has been moved to readthedocs, and other minor changes.
Version 0.7.2¶
2017-03-24
This release effectively merges the Python2 and Python3 branches.
Enhancements:
pip install HTSeq
works for both Python 2.7 and 3.4+
Version 0.7.0¶
2017-02-07
Enhancements:
- understands SAMtools optional field B (used sometimes in STAR aligner)
- write fasta files in a single line
- better docstrings thanks to SWIG 3
Bugfixes:
- fixed tests and docs in .rst files
Support bumps:
- supports pysam >=0.9.0
New maintainer: Fabio Zanini.
Version 0.6.1¶
2014-02-27
- added parser classes for BED and Wiggle format
Patch versions:
- 0.6.1p1 (2014-04-13)
- Fixed incorrect version tag
- 0.6.1p2 (2014-08-09)
- some improvements to documentation
Version 0.6.0¶
2014-02-26
- Several changes and improvements to htseq-count:
- BAM files can now be read natively. (New option
--format
) - Paired-end SAM files can be used also if sorted by position. No need any mroe to sort by name. (New option
--order
.) - Documentation extended by a FAQ section.
- Default for
--minaqual
is now 10. (was: 0)
- BAM files can now be read natively. (New option
- New chapter in documentation, with more information on counting reads.
- New function
pair_SAM_alignments_with_buffer
to implement pairing for position-sorted SAM files.
Version 0.5.4¶
2013-02-20
Various bugs fixed, including
- GFF_Reader interpreted the constructor’s “end_included” flag in the wrong way, hence the end position of intervals of GFF features was off by 1 base pair before
- htseq-count no longer warns about missing chromosomes, as this warning was often misleading. Also, these reads are no properly included in the “no_feature” count.
- default for “max_qual” in “htseq-qa” is now 41, to accommodate newer Illumina FASTQ files
- BAM_Reader used to incorrectly label single-end reads as paired-end
Patch versions:
- v0.5.4p1 (2013-02-22):
- changed default for GFF_Reader to end_included=True, which is actually the correct style for Ensemble GTF files. Now the behavious should be as it was before.
- v0.5.4p2 (2013-04-18):
- fixed issue blocking proper built on Windows
- v0.5.4p3 (2013-04-29):
- htseq-count now correctly skips over “M0” cigar operations
- v0.5.4p4 (2013-08-28):
- added
.get_original_line()
function toVariantCall
- firex a bug with reads not being read as paired if they were not flagged as proper pair
- added
- v0.5.4p5 (2013-10-02/2013-10-10):
- parsing of GFF attribute field no longer fails on quoted semicolons
- fixed issue with get_line_number_string
Version 0.5.3¶
2011-06-29
- added the ‘–stranded=reverse’ option to htseq-count
Patch versions:
- v0.5.3p1 (2011-07-15):
- fix a bug in pair_sam_Alignment (many thanks for Justin Powell for finding the bug and suggesting a patch)
- v0.5.3p2 (2011-09-15)
- fixed a bug (and a documentation bug) in trim_left/right_end_with_quals
- v0.5.3p3 (2011-09-15)
- p2 was built improperly
- v0.5.3p5 (2012-05-29)
- added ‘to_line’ function to VariantCall objects and ‘meta_info’ function to VCF_Reader objects to print VCF-lines / -headers respectively
- v0.5.3p5b (2012-06-01) - added ‘flag’ field to SAM_Alignment objects and fixed ‘get_sam_line’ function of those
- v0.5.3p6 (2012-06-11) - fixed mix-up between patches p3, p4 and p5
- v0.5.3p7 (2012-06-13) - switched global pysam import to on-demand version
- v0.5.3p9ur1 (2012-08-31) - corrected get_sam_line: tab isntead of space between optional fields
Version 0.5.1¶
2011-05-03
- added steps method to GenomicArray
Patch versions:
- v0.5.1p1 (2011-05-11):
- fixed a bug in step_vector.h causing linkage failure under GCC 4.2
- v0.5.1p2 (2011-05-12):
- fixed pickling
- v0.5.1p3 (2011-05-22):
- fixed quality plot in htseq-qa (top pixel row, for quality score 40, was cut off)
Version 0.5.0¶
2011-04-21
- refactoring of GenomicArray class:
- field
step_vectors
replaced withchrom_vector
. These now contain dicts of dicts ofChromVector
objects rather thanStepVector
ones. chrom_vectors
is now always a dict of dict, even for unstranded GenomicArrays to make it easier to loop over them. (The inner dict has either keys"+"
and"-"
, or just one key,"."
.)- The new
ChromVector
class wraps the actual vector and supports three different storage modes:step
,ndarray
andmemmap
, the latter two being numpy arrays, without and with memory mapping. - The
GenomicArray
constructor now take two new arguments, one for the storage class, one for the memmap directory (if needed). - The
add_value
methods had been replaced with an__iadd__
method, to enable the+=
semantics. - Similarily,
+=
forGenomicArrayOfSets
adds an element to the sets. - Instead of
get_steps
, now usesteps
.
- field
- new parser class
VCF_Reader
and record classVariantCall
- new parser class
BAM_Reader
, to add BAM support (including indexed random access) (requires PySam to be installed) - new documentation page Tutorial: Transcription start sites (TSS)
Fasta_Reader
now allows indexed access to Fasta files (requires Pysam to be installed)- peek function removed
Patch Versions:
- v0.5.0p1 (2011-04-22):
- build was incomplete; fixed
- v0.5.0p2 (2011-04-22):
- build was still faulty; new try
- v0.5.0p3 (2011-04-26)
- fixed regression bug in htseq-count
Version 0.4.7¶
2010-12-22
- added new option
-o
(or--samout
) to htseq-count
Patch versions:
- Version 0.4.7p1 (2011-02-14)
- bug fix: GFF files with empty attribute fiels are now read correctly
- Version 0.4.7p2 (2011-03-13)
- fixed assertion error in pair_SAM_alignment, triggered by incorrect flags
- Version 0.4.7p3 (2011-03-15)
- fixed problem due to SAM_Alignment.peek (by removing the method)
- Version 0.4.7p4 (2011-03-18)
- removed left-over debugging print statement
Version 0.4.6¶
2010-12-09
- pair_SAM_alignments now handles multiple matches properly
- SAM_Alignments now allows access to optional fields via the new methods optional_field and optional_fields
- htseq-count now skips reads that are non-uniquely mapped according to the ‘NH’ optional field
- updated documentation
Patch versions:
- Version 0.4.6p1 (2010-12-17)
- updated htseq-count documentation page
- htseq-count now accepts ‘-’ as SAM file name
- Version 0.4.6p2 (2012-12-21)
- corrected a bug in htseq-count regarding the handling of warnings and added SAM_Reader.peek.
Version 0.4.5¶
2010-08-30
- correction to GenomicArray.get_steps() when called without arguments
- correction to FileOrSequence.get_line_number_string
- removed use of urllib’s quote and unquote in GFF parsing/writing
- GFF_Reader now stores “meta information”
- qa.py now gives progress report
- auto add chrom now also works on read access
- refactored CIGAR parser
- added bool fields to SAM_Alignment for all flag bits
Patch versions:
- Version 0.4.5p1 (2010-10-08)
- correction of a mistake in CIGAR checking, misreading symbol “N”
- Version 0.4.5p2 (2010-10-13)
- Sequence.add_bases_to_count_array and hence htseq-qa now accepts ‘.’ instead of ‘N’ in a fastq file
- Version 0.4.5p3 (2010-10-20)
- fixed error reporting for PE in htseq-count
- Version 0.4.5p4 (2010-10-21)
- fixed another error reporting for PE in htseq-count
- Version 0.4.5p5 (2010-10-28)
- Not only ‘N’ but also ‘S’ was read the wrong way. Fixed.
- Cython had some odd way handling properties overloading attributes, which caused issues with ‘Alignment.read’. Worked around.
- Version 0.4.5p6 (2010-11-02)
- write_to_fastq should not break lines. Fixed.
- Version 0.4.5p7 (2010-11-16)
- added fallback to distutils in case setuptools in unavailable
- fixed documentation of ‘-a’ option to htseq-count
Version 0.4.4¶
2010-05-19
- StepVectors (and hence also GenomicArrays) now notice if, when setting the value of a step, this value is equal to an adjacent step and merge the steps.
- GenomicArray’s constructor now allows the special value
"auto"
for its first arguments in order to start without chromosomes and automatically add them when first encountered.
Patch versions:
- Version 0.4.4p1 (2010-05-26):
- minor change to make it run on Python 2.5 again
- changed ‘str’ to ‘bytes’ at various places, now compiles with Cython 0.12 (but no longer with Cython 0.11 and Python 2.5)
- Version 0.4.4p2 (2010-06-05):
- change to SAM parser: if flag “query unmapped is set” but RNAME is not “*”, a warning (rather than an error) is issued
- Version 0.4.4p3 (2010-06-25)
- again removed an “except sth as e”
- Version 0.4.4p4 (2010-07-12)
- dto.
- Version 0.4.4p5 (2010-07-13)
- rebuilt with Cython 0.12.1 (previous one was accidently built with Cython 0.11.1, causing it to fail with Python 2.5)
- Version 0.4.4p6 (2010-07-21)
- fixed bug in error reporting in count.py
- losened GFF attribute parsing
- changed “mio” to “millions” in qa output
- improved error reporting in GFF parser
- made SAM parsing more tolerant
Version 0.4.3¶
2010-05-01
New argument to constructer of GFF_Reader: end_include
- Version 0.4.3-p1 (2010-05-04): version number was messed up; fixed
- Version 0.4.3-p2 (2010-05-15): fixed ‘-q’ option in htseq-count
- Version 0.4.3-p3 (2010-05-15): parse_GFF_attribute_string can now deal with empty fields; score treated as float, not int
- Version 0.4.3-p3 (2010-05-15): - parse_GFF_attribute_string can now deal with empty fields; score treated as float, not int - fixed bug in SAM_Reader: can now deal with SAM files with 11 columns - SAM_Alignment._tags is now a list of strings
- Version 0.4.3-p4 (2010-05-16): bumped version number again just to make sure
Version 0.4.2¶
2010-04-19
Bug fixes to htseq-count and pair_SAM_alignments. Bumped version number to avoid confusion.
- Version 0.4.2-p1 (2010-04-20): there was still a bug left in htseq-count, fixed.
- Version 0.4.2-p2 (2010-04-26): bug fix: adapter trimming failed if the adapter was completely included in the sequence
- Version 0.4.2-p3
- Version 0.4.2-p4 (2010-04-29): bug fix: error in warning when htseq-count encountered an unknown chromosome
- Version 0.4.2-p5 (2010-04-30): bug fixes: error in warning when PE positions are mismatched, and misleading error when calling get_steps with unstranded interval in a stranded array
Version 0.4.1¶
2010-04-19
Bug fixes:
- Fixed bug in
htseq-count
: CIGAR strings with gaps were not correctly handled - Fixed bug in Tour (last section, on counting): An wrong indent, and accidental
change to the
exons
variable invalidated data. - SolexaExportReader no longer complains about multiplexing (indexing) not being supported.
- Mention link to example data in Tour.
- Fix installation instructions. (
--user
does not work for Python 2.5.)
Enhancements:
- Paired-end support for SAM_Alignment.
- “_as_pos” attributes for GenomicInterval
Version 0.4.0¶
2010-04-07
First “official” release, i.e., uploaded to PyPI and announced at SeqAnswers