[mira_announce] MIRA 2.9.29x4

Dear all,

http://www.chevreux.org/tmp/mira_2.9.29x4_dev_linux-gnu_x86_64.tar.bz2

It turns out that 2.9.29x2 still had a few quirks, these should now be fixed. 
In addition, I've implemented some strategies to reduce administrative 
overhead of reads, leading to some sizable RAM savings for large assemblies 
(5 to 10 million reads).

If no severe problems are reported, it'll make an official appearance on the 
web site in one or two weeks.

Regards,
  Bastien


2.9.29x4
--------
- the cutback strategy for 454 reads introduced in 2929x1 has been eased a
  bit: paired-end reads do not get cut back and if read lengths would fall
  below the minumum required length, they don't get cut back neither.
- bugfix: the bad sequence search was not performed if the minimum left clip
  was set to "no"
- MACHINE_TYPE, PROGRAM_ID and STRAIN are now read from TRACEINFO XML files.
- fixed a couple of bugs that led to an abort of MIRA when writing SNP files.
  Bug struck only on very rare boundary cases.


2.9.29x3
--------
- implemented a couple of memory reduction strategies for the read
  objects. This reduces overhead of every read by almost 30% (264 instead of
  368) and additionally saves memory of cached values (strain, basecaller,
  machine type, paths etc.). This should also reduce memory fragmentation a
  bit.
  In a typical 454 project with 1 million reads, this amounts to 208-400 MB
  savings of RAM.
- miramem now knows about 454 Titanium reads
- convert_project has new command line parameter: -r

Other related posts: