[mira_announce] MIRA 2.9.28x1

Dear all,

I have just put version 2.9.28x1 at
   http://www.chevreux.org/tmp/mira_2.9.28x1_dev_linux-gnu_x86_64.tar.bz2

Several new features that were requested have been implemented (improved EST 
assembly, non-IUPAC consensus, improved info and log files) as well as the 
usual bunch of bug squashing and steady improvements on the way to version 3. 
Please consult the change file below (a bit terse, I admit) as well as the 
documentation that comes along with the package.

Please note: the 2.9 series should currently NOT be used for production
assembly. It is meant as testing version for 454 and Solexa assembly/mapping
as well as different flavours of hybrid assemblies (454/Sanger, Sanger/Solexa,
454/Solexa, Sanger/454/Solexa).

Versions only with numbers (e.g. 2.9.5) are versions that are generally made
available to a broader audience on the download website. They normally go
through a range of assembly projects as quick check whether things work as
intended.

Versions that contain the 'x' character (e.g. 2.9.28x1) are intermediate
development versions or versions made available to fix a quirk. These are not
as well tested as the versions for the general audience but should work as
intended.

Regards,
  Bastien


Changes since 2.9.26x3:

******************************************************************************
***************************  Development version  ****************************
******************************************************************************


2.9.28x1
--------
- new file in *_info directory: <projectname>_info_assembly.txt. This file
  gives basic information on how the assembly went (assembled reads, contig
  sizes, N50/N90/N95, coverage, qualities, possible problems)
- convert_project now dumps the same info as above on CAF input
- for EST assemblies: -job=est now uses per default a poly-AT clipping that
  preserves the poly-A/T signal
- for EST assemblies: renamed -GE:ess to -GE:esps
- for EST assemblies: added -job=esps[1-3]
- made tagsnp working again (for testing)


2.9.27x2
--------
- new parameter to force consensus to be A, C, G or T and not a IUPAC
  code (-CO:fnicpst) 
- enhanced handling of partly masked reads.
- implemented alternative SKIM repeat threshold calculation to deal with
  highly repetitive eukaryotes (temp. fix, needs revisiting later)
- temporarily took out default -SK:mnr again


2.9.27x1
--------
- fixed bug in ACE output which was introduced in 26x6
- fixed small bug when "--job=mapping" was used (introduced in 2924x3)
- activated SKIM routines to mask nasty repeats, added -SK:mnr:rt
- massively reduced disk usage as MIRA can now remove unused log files and the
  complete log directory on request (added -OUT:rrol:rld)
- started documentation for log files written by MIRA


2.9.26x6
--------
- fixed bug in output of read and consensus tag comments in ACE files
- fixed bug in output of BS lines of ACE files
- added error messages naming the faultive read during loading of CAF files
- added -AS:urdcm:urdufrd:urdrdct
- while building contigs using backbones, MIRA now tries to guess memory usage
  and uses preallocation to reduce memory footprint. Though the guesstimate
  may be wrong a few times which then leads to increased memory usage.
- added tag type MRMr (MIRA Repeat Marker)
- SKIM now honours "MRMr" and "FPaS" tags in reads and does not use these
  stretches to find potential overlaps.
- SKIM now adapts dynamically hashes it needs to save to non-ACGT bases
  occuring in sequences. This leads to slightly improved detection of possible
  overlaps in sequences with "N" or other IUPAC codes


2.9.26x5
--------
- fixed bug that was introduced in 26x2 where sometimes during a mapping
  assembly, all contig positions were tagged as unsure.
- fixed bug that -FN:xtii could not be set for sequencing types other than
  Sanger.
- fixed bug: quality clip and clip of masked bases were performed for all
  sequencing technologies even when only one requested it.


2.9.26x4
--------
- added log file for clippings on load
- fixed bug for minimum left clip function
- fixed small bug in "make install"
- testing new workaround for linking on MacOS X (10.5) *sigh*

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