[mira_talk] MIRA 3 release candidate 4

From: Bastien Chevreux <bach@xxxxxxxxxxxx>
To: mira_announce@xxxxxxxxxxxxx
Date: Sun, 4 Oct 2009 15:25:55 +0200
Dear all,

MIRA 3 release candidate 4 is available from 
  http://sourceforge.net/projects/mira-assembler/files/

I initially didn't plan for a rc4, but rc3 had too many smaller and larger 
bugs and/or annoying things that I wanted to iron out before going to version 
3.

One big highlight for rc4 is that it now compiles again on Apple Mac OSX, 
thanks to Liam Elbourne and Peter Stockwell who found out that some Apple 
libraries collided with MIRA libraries.

List of changes since RC3:
- MIRA now also compiles again on Apple Mac OSX (yay!)
- scripts added to distribution: fixACE4consed.tcl, fastaselect.tcl and
  fasta2frag.tcl
- new clipping: clip lowercases (-LR:llc). Made for 454 data, but can be used
  with other sequencing types, too.
- MIRA now switches off automatic memory management when system information
  cannot be gathered
- change to get SKIM working on 31 base hashes also on 32 bit machines where
  the compiler knows 64 bit data types
- slightly changed messages for STDOUT log when writing cluster info to disk
- added option "-r f" to convert_project
- convert_project can now convert from and to MAF
- changed -GE:gbmf to -GE:kpmf (sorry for the inconvenience)
- miraSearchESTSNPs does not load "me_stepX.par" files anymore (it parses the
  command line like normal mira now)
- default parameters for miraSearchESTSNPs have been chaged in step 1 and
  2. Notably, the automatic editor is switched of in step 1, but switched on
  in step 2. Furthermore, both steps change from single pass/multi-loop
  (-AS:nop=1:rbl=...) to multipass/multi-loop (-AS:nop=...:rbl=...) setup
- fixed bug in automatic memory management where RAM allocated was actually
  less than minimum asked for and could lead to disastrous assembly results
- fixed bug that prevented recalculation of contig consensus when loading CAF
- fixed bug in contig building where in rare cases a missed alignement led
  to MIRA stopping
- fixed bug that led to extremely long run times and suboptimal contigs in
  rare cases
- fixed bug that led to MIRA stopping in rare cases during mapping of Solexa
  reads
- fixed bug that led to MIRA missing internal functionality of merging short
  reads after loading contigs from CAF or MAF
- fixed segmentation fault in parsing the "--job" parameter when only "est"
  was given
- fixed bug that led MIRA want to load a file named ".maf" when trying to load
  a CAF format.
- fixed bug where loading of sequences in CAF failed as MIRA thought there was
  no data in the file
- added logfile to replay eventual errors during contig building

Regards,
  Bastien


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[mira_talk] MIRA 3 release candidate 4

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