[mira_announce] MIRA 2.9.28x4

Additionally to the usual bug fixing and addition of some small features, 
Sanger & Solexa, 454 & Solexa as well as Sanger & 454 & Solexa hybrid de-novo 
assemblies are now possible ... as proof-of-concept. But if you've got a 
bacterium and some time to wait for the machine to finish, I'd love to get 
feedback.

http://www.chevreux.org/tmp/mira_2.9.28x4_dev_linux-gnu_x86_64.tar.bz2

2.9.28x4
--------
- first version which allows Solexa de-novo. Albeit *very* slow at the
  moment, do not use for anything else than bacteria (1 week of computation,
  sorry).
- new functionality: MIRA now marks IUPAC positions in the consensus as tag
  "IUPc"
- the info_assembly.txt file now gives info on the number of positions in the
  consensus where sequencing methods disagree.
- bugfix in clipping: when reads have no ancillary data (and this no good left
  clip), the clipping of bad quality stretches could lead to the complete read
  being clipped if the bad quality on the left was long enough
- bugfix: for 454 data, -CO:mrpg and -CO:mgqrt were not honoured but some
  fixed values used instead.
- bugfix: average total coverage of contigs was wrongly reported in statistics
  and furthermore only as integer, not as double
- bugfix: -OUT:sssip:stsip could not be set for sequencing technologies other
  than Sanger.

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