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
  • 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)
  • 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 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)
    • 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