rQuant version 2.0 (May 24, 2011)
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New features:
- The optimisation of the transcript and profile variables has been
newly implemented. The optimisation problems are now solved via
coordinate descent and the analytical solution, making the
calculations much faster than in the old releases and making rQuant
independent of a commercial solving software.
- The profile functions are now modelled with piecewise linear
functions instead of piecewise constant functions.

Bug fixes:
- ParseGFF.py: assertion for a GFF file without 9 columns


rQuant version 1.2 (May 18, 2011)
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New features:
- transcripts from overlapping loci are merged for quantitation
- additional option allowing genome annotation to be in AGS format

Other changes:
- ParseGFF.py: now also parses multiple mappings of parent IDs of GFF
features


rQuant version 1.1 (March 11, 2011)
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New features:
- tool ReadStats: generates a statistic about the read alignments and
the covered genes

Other changes:
- prctiles.m: replaced function by own implementation
- ParseGFF.py: now also parses non-coding transcripts; exons
coordinates always in ascending order (for both strands)

Bug fixes:
- get_reads: fixed a memory leak and segmentation faults
- sanitise_genes.m: adapted to closed intervals in gene structure from
ParseGFF.py
- rquant_core.m: corrected initialisation of transcript length bins


rQuant version 1.0 (December 17, 2010)
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This is the first release of the quantitation tool rQuant, which
determines abundances of multiple transcripts per gene locus from
RNA-Seq measurements.
Please also visit http://fml.mpg.de/raetsch/suppl/rquant for more
information about this software.
