Htseq

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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

=============

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

=============

2010-04-07

First "official" release, i.e., uploaded to PyPI and announced at SeqAnswers

=============

2010-03-12

First version that was uploaded to PyPI