.. _history: *************** Version history *************** 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 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) - 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 to ``VariantCall`` - firex a bug with reads not being read as paired if they were not flagged as proper pair * 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 0.5.2 ============= 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): - 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 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 :ref:`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 Version 0.3.7 ============= 2010-03-12 First version that was uploaded to PyPI