Version history
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)
- 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
Version 0.5.2
2011-06-24
- added the ‘–maxqual’ option to htseq-qa
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):
- 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 with chrom_vector. These now contain
dicts of dicts of ChromVector objects rather than StepVector 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 and memmap, 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, += for GenomicArrayOfSets adds an element to the sets.
- Instead of get_steps, now use steps.
- new parser class VCF_Reader and record class VariantCall
- new parser class BAM_Reader, to add BAM support (including indexed random access)
(requires PySam to be installed)
- new documentation page A detailed use case: TSS plots
- 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)
- 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
Version 0.3.7
2010-03-12
First version that was uploaded to PyPI