Change file for MIRA 2.8.3
==========================


2.8.3
-----
- fixed bug in XML traceinfo routines: XML elements with uppercase letters
  were not recognised (backport from the 2.9 development line)


2.8.2
-----
- polishing of the MIRA build process, added flex version check, added
  --enable-static flag to ./configure


2.8.1
-----
- fixed bug that prevented mapping assemblies against backbones to be fast
  (backported from 2.9.3)
- bugfix when loading CAF: some attributes were not reset, leading some reads
  having attributes of preceding reads in CAF file (backported from 2.9.2)


2.8.0
-----
- replace tcl dependency in compile process with perl dependency


2.6.x -> 2.7.x -> 2.8.0rc2
--------------------------

The 2.8.x series of MIRA is an intermediate step towards MIRA 3.0. However,
two major highlights (beside the usual stream of small improvements and
bugfixes) justify a new production release:

1) Important speedups in a few central places (Reads, Contigs). Additionally,
   the all-against-all read comparison algorithm (SKIM) has been speeded-up by
   a factor of >60 (for large number of reads).
2) MIRA is going Open Source! More specifically, MIRA is being put under the
   GPL (version 2) as I kindly received the authorisation from both the DKFZ
   Heidelberg (Deutsches Krebsforschungszentrum, German Cancer Research
   Center) and from Thomas Pfisterer (the author of the EdIt part in MIRA) to
   release the code.

Please note that the 2.8 line does still not officially support assembly of
454 data. These routines are still under development and will be made
available in the 2.9 development line.

Important notice: a few parameter switches were changed since the 2.6.x
releases, existing parameter files may have to be changed. Please consult the
documentation for the new names of the parameters.



Changes in detail:
==================

2.7.8
-----
- Major bugfix: assembling with more than one strain without backbone produced
  less than sub-optimal solutions.


2.7.7
-----
- internal changes
- fixed error in assembly class in handling bases tagged as SIOx within a
  strain. (had only minor repercussion in assemblies)
- fixed bug in skim output: permbans were not updated correctly for the
  summary. (had no effect whatsover on assemblies, just in the printed skim
  summary of the MIRA log)


2.7.6
-----
- smaller internal changes (removed deprecated strstream constructs, removed
  old code)
- also put EdIt and other code from Thomas under GPL
- fixed bug when loading backbones sequences that have no sequence
- fixed bug when assembling with more than one backbone sequence (introduced
  in 2.7.5)
- added -AS:bdq
- brought documentation up-to-date


2.7.5
-----
- Larger internal changes. Reduced memory footprint for alignment checks:
  results are now temporarily written to disks instead of being kept in
  memory. Useful when working with millions of reads.
- speedups in contig: moved some redundant costly internal checks
  into versions compiled only for special bughunting
- removed -SK:im:mc
- added -SK:bph:hss:mhim
- new log file containing SKIM raw hash hit numbers in log directory
- new log file containing simple readpool info in log directory
- squashed a small bug in alignment code that sneaked in in 2.7.2
- switched miraEST on again (switched off in 2.7.4). SNP analysis still the
  old one though.
- the pathfinder object is now faster for backbone assembly.
- put MIRA code under GPL


2.7.4
-----
- added -454:c454cq (not public yet)
- change: MIRA now writes files into three direcorties below the starting
  directory: <projectname>_log, <projectname>_info and
  <projectname>_results. This helps to keep things a bit cleaner in the
  directory.
- due to the above: temporarily switched off miraEST (also wrt the fact that
  SNP analysis is going to undergo a major rehaul)
- speeded up endgame (coping with remaining singlets) of assemblies that have
  a large number of reads.
- *major* speedup of SKIM (all against all comparison)
  routine. E.g. SKIMming of 53,000 reads now takes a minute instead of 62
  minutes.
- reduced memory footprint for SKIM: results are now written to disks instead
  of being kept in memory. Useful when working with millions of reads.

2.7.3
-----
- first trial version that assembles 454 consensus data (not real 454 data
  yet)
- changed pathfinder strategy. Now uses a less aggressive way of determining
  next read to add. Should improve all "difficult" assemblies with many
  repeats a bit
- reworked/changed all existing -454 parameters
- Change: there is no more default source for the reads to be loaded. It now
  must be explicitly set, either via -GE:lj or the quickswitches like -fasta
  etc.
- Name change: main assembly 'loops' are now called assembly 'passes' for
  better distinction to PRMB break loops. Renamed -AS:nol:sel:sdllo to
  -AS:nop:sep:sdlpo, -SB:sbuil to -SB:sbuip, -DP:feil:leil to -DP:feip:leip
- MIRA now writes clear parameter parsing error messages (if needed) on
  startup

2.7.2
-----
- speedups in assembly & output: moved some redundant costly internal checks
  into versions compiled only for special bughunting
- changed consensus quality computation (faster). Results are mostly the same
  or a tad higher than for the old routines (a tad lower for quality values <=
  10 or so).


2.7.1
-----
- fixed small bug in handling of tags for alignments


2.7.0
-----
- initial takeover from 2.6.0

