dev3.9.17
---------
- improvement: mira now increases stack size to allow for full length
  alignments of reads >= 15kb
- change: results in FASTA format now splitted into strain specific result
  files
- bugfix: cause for rare premature stop of assembly found and fixed
- bugfix: calculation of number of strains now corrrect
- bugfix: calculation of digital normalisation coverage estimates could be
  wrong for reads lateron determined to be chimeric


dev3.9.16
---------
- change of parameter parsing: "1" and "0" are not allowed anymore for boolean
  parameters. To make up for it, "y", "n", "t", "f" are now allowed shortcuts
- change of parameter parsing: -MI:somrnl:sonfs moved to new section
  -NAG_AND_WARN section: -NW:somrnl:sonfs
- change of parameter parsing: new section -HASHSTATISTICS. Moved several
  parameters from -SKIM to -HASHSTATISTICS
- new parameter: -CL:search_phix174:filter_phix174 to automatically search for
  and filter PhiX174 from Illumina data. Defaults: search only in genome mode,
  search and filter in EST mode
- new parameter -SK:fcem for EST/RNASeq assembly of very skewed distributions
- output: debris file in info directory now contains reason for read being
  pushed to debris
- new functionality: lossless digital normalisaton
- mira: slightly adapted contig naming scheming when using digital
  normalisation
- mira: computation of hash statistics a bit faster
- mira: hash statistics analysis now partly multithreaded
- mira: uses less memory for high-coverage genes in EST/RNASeq projects
- mira: now knows about Nextera adaptors
- mira: increased speed on very large projects with tens of millions of reads
- mira: improved output of parameters, now does not output "san" if sanger is
  not used.
- convert_project: new option -Q for default read quality. Also does not stop
  when missing quality files
- convert_project: new to-target "samnbb". In reference assemblies, leaves out
  the backbone (reference) sequence. Enhances compatibility for conversion to
  BAM.
- convert_project: SAM output now uses "255" as mapping quality instead of
  "50"
- convert_project: bugfix for correctly guessing to and from filetypes from
  filenames
- bugfix: annotations in GenBank files were sometimes garbled
- bugfix: parsing of -AS:mrpc did not work in the long version
- bugfix: repeat resolving of very deep repeats involving indels sometimes did
  not resolve repeats correctly
- bugfix: writing MAF checkpoint files for mapping assemblies
- bugfix: fixed "*sigh*" error in mapping assemblies which struck especially
  in deep mappings and when the reference was very different from mapped
  reads.
- bugfix: erroneous overcall editing in mapping assemblies
- potential bugfix for "would extend AS_skim_edges" error
- more readable error messages


dev3.9.15
---------
- further improvement of EST/RNASeq assembly: more probably reconstructs the
  most frequent splice variant as full transcript and less frequent variants
  as partial transcripts. Further reduction of intron assembly.
- bugfix of problem which led to abort of assembly process.


dev3.9.14
---------
- preprocessing and assembly algorithm improvement for MiSeq data
- improvement: avoidance of intron sequence improved for EST / RNASeq assembly
- improvement: adjustments to default parametrisation for EST / RNASeq
  assemblies lead to better results
- improvement: hybrid assembly of long and short reads (e.g. 454 & Illumina)
  now finds more contig joins
- mirabait: new output type "txt" for list of matching read names
- workaround: convert_project & mirabait now also work (like mira) when
  computer locale is broken.
- bugfix: dump of replay data did not work as intended for mapping
  assemblies.

dev3.9.13
---------
- ooops, forgot to include new file in source

dev3.9.12
---------
- fixed bug which led to stops of the assembly process
- fixed bug which led to segmentation faults in rare cases when mapping
  against a single, short backbone sequence.


dev3.9.11
---------
- several bugfixes in the assembly engine which previously led to an abort of
  the assembly process.
- changes in configure script to ensure better build compatibility on GenToo


dev3.9.10
---------
- improvement: major speed improvement for mapping projects with hybrid
  technologies where one of the technologies is Illumina
- improvement: preprocessing of read now fully multi-threaded
- improvement: now reads faulty GenBank files written by CloneManager
- convert_project: comfort functions. Parameters -f and -t now not mandatory
  anymore but deduced from given file names
- convert_project: now also understands .gbk as filetype for GenBank data
- new/old functionality: reactivated, MAF & CAF files can now be used as again
  as input in manifest files
- change: some warnings caused by internal errors now cause a full MIRA stop
  to hunt down the cause of the problems.
- change: in mapping assemblies, template_size and segment_placement now use
  "infoonly" as default if not given.
- change: MIRA version written to assembly info file
- several internal changes to loading system for future enhancements
- several internal code cleanups
- bugfix: mira -c did not work as described
- bugfix: some reads could sometimes not be correctly aligned, problem
  triggered by many indels in reads (Ion Torrent, 454) of high coverage
  contigs.
- bugfix: -highlyrepetitive in manifest parameters caused a parsing error
- documentation: added "default_qual" in documentation for manifest files

dev3.9.9
--------
- bugfix: MIRA sometimes stopped when building low coverage contigs


dev3.9.8
--------
- bugfix: on machines with heavy load, some files and directories sometimes
  failed to be deleted. Fixed.
- bugfix: mapping of Illumina at contig ends sometimes failed (since 3.9.6)
- bugfix: error causing "gaaah, had doubles" in de-novo assemblies of genomes
  fixed.
- small runtime improvement: some unnecessary steps in the overlap graph
  traversal are now dynamically left out.
- convert_project: new option -S (currently only for Illumina data)
- convert_project: reactivated -i
- unnecessary debug files are now not written anymore to the tmp directory
- new -MI:ef2 flag for switching off experimental code


dev3.9.7
--------
- bugfix: -MI:ef1 did not work


dev3.9.6
--------
- improvement: mapping assemblies with greatly improved alignments for
  non-perfect matches, especially in larger indel regions
- improvement: assembly of repetitive areas in de-novo assemblies, no more
  "repeat coverage peaks"
- improvement: parsing of sequence identifiers in NCBI gi format automatically
  chooses the simple sequence name as read name
- improvement: can now load GFF3 files without sequences (as provided by the
  NCBI)
- improvement: data loading consistency checks added to catch illegal quality
  values >100.
- convert_project: "-t stats" now also outputs consensus tags info file
- slight change in output of info file of consensus tags (added length of tag)
- change: output of wiggle files is now always for the full, padded contig
- change: output of alignments as text or HTML now has lowercase alignments,
  uppercase for bases which do not match the consensus
- documentation: using Illumina data from the SRA
- bugfix: possible segmentation faults removed
- bugfix: -SB:abnc=true led to a problem since 3.9.5, fixed.
- bugfix: MAF parsing got phase information wrong in GFF3 tags
- bugfix: CAF writing phase info from GFF3 tags was not ASCII
- bugfix: creation of SAM files failed when libraries with FR or RF
  orientation were present.
- bugfix: coverage equivalent reads were created too short for coverages >1.


dev3.9.5
--------
- better handling of failing disk operations when memory is tight
- improved assembly of repetitive regions in genome assemblies: faster and
  non-heuristic.
- improved assembly of EST / RNASeq of eukaryotic data: intronic sequences
  should be less frequent.
- major speed improvement in de-novo assemblies higher coverages of Illumina,
  Ion Torrent and 454 data
- better clipping of degenerated Ion Torrent adaptors
- new 454 adaptor clipped
- rename -CL:mkfr to -CL:pmkfr and added automatic adjustments for high
  coverage data.
- better error handling on OSX: user now always gets a specific MIRA error
  message.
- better semantic checking of manifest files (missing reference, no data,
  etc.)
- manifest files: allowing LEFTIES and RIGHTIES in segment placement
- the 3.9.x line now recognises if it was called with parameters from the
  3.4.x line and stops
- parameter -CL:lcc was split into -CL:lccf:lccb
- bugfix: parsing MAF files with Illumina and / or Ion data leads to less used
  memory like as if loaded anew (important for resumed assemblies).
- bugfix: FASTQ loader now stops on illegal FASTQ files
- bugfix: some alignments did don get propper flags, leading to suboptimal
  assembly graphs.


dev3.9.4
--------
- bugfix: FASTQ input in Illumina-64 format was broken
- bugfix & improvement: SAM format from convert_project now more compatible to
  SAM specification
- bugfix: bugs leading to error message trackingunused != countingunused
- bugfix: loading of gzip packed FASTQ with a name ending in .gz did not work
- first speed improvements in contig cleanup routines when mapping Ion data,
  more to come in next versions
- further improvements for binary compatibility to older Linux kernels, errors
  of BOOST induced problems with locale settings should now be a thing of the
  past
- minor updates to the documentation
- new ./configure option "--enable-native" for processor specific optimised
  code


dev3.9.3
--------
- fixed ./configure to produce a fully statically linked binary on OSX
- bugfix: CAF files were not read correctly (bug due to MIRA now also saving
  placement code in CAF)
- fixed segfault for some projects when doing "convert_project -t asnp"
- fix: building without EdIt broke on some systems
- mira now advertises the resume option in "mira -h"
- improvement: distributed binary packages now compatible again to older
  kernels (down to 2.6.15)
- improvement: saving of snapshots is now much more error resistant, a working
  snapshot should always be present on disk
- improvement: SNP and feature analysis now only writes "X" as amino acid if a
  SNP leads to a codon change which resolves to a different AA.
- improvement: quicker SNP and feature analysis in intergenic regions
- improvement: parsing of MAF files with lots of tags a lot faster (50% and
  more)
- change: *_info_featuresequences.txt and *_info_featureanalysis.txt now
  include an additional column "FType" (FeatureType)


dev3.9.2
--------
- fixed possible segfault (only hit when assembling de-novo with more than one
  strain)
- fixed parsing error in manifest files when loading data from pacbio
- improved configure script for compiling on a wider variety of platforms and
  with different versions of gcc and BOOST libraries
- MIRA resume: added "-r"
- binary package for Linux: fixed issue where older Linux kernels needed to
  have 'export LC_ALL=C' or else they would not start.


dev3.9.0 & dev3.9.1
-------------------
The 3.9 line of MIRA is the development line of MIRA which will ultimately
lead to MIRA 4. It's the result of 10 months of work since the last 3.4.x
versions and much has changed. A lot behind the scenes, but also interesting
things for everyone, most notably in speed and quality terms. The most
important changes for users: the interface. Please absolutely do consult the
section on manifest files in the documentation!

Improvements made to simplify life:
- flexibilised parametrisation to easily define input data and assembly job:
  the "manifest" configuration files allow using concepts of read groups as
  well as segment orientation & segment placement
- SAM output via convert_project, simplifies interaction with outside world
  (gap5, tablet etc.pp)
- full GFF3 input and output compatibility, using Sequence Ontology,
  translation to and from gap4/gap5
- CASAVA 1.8 read naming for the new Illumina read name scheme
- new sequencing "technology" TEXT for unspecified data, i.e., from databases
  like NCBI etc.

Speed improvements:
- faster contig handling routines, improves de-novo assembly times with Ion
  Torrent or 454 / Solexa hybrid by 30%
- faster mapping routines, allows MIRA to more or less gracefully handle
  projects with several thousand reference sequences. Useful for mapping
  against EST / RNASeq assemblies.
- faster handling of deep coverage RNASeq and genome data (to be improved
  still)
- faster kmer counting & smaller footprint in RAM and on disk
- faster checking of template restrictions
- optimized: faster data reading, does not need to count reads beforehand
  anymore
- other improvements left and right which add up ;-)

Assembly quality improvements:
- new "fire & forget" mode of MIRA which basically should reduce misassemblies
  in result files to zero: earlier version of MIRA would dump out
  misassemblied contigs (with markers pointing at the misassembly), now
  contigs dumped out do not contain any misassembly (at least none which MIRA
  could discover).
- improved assembly quality for ultra-high coverage Solexa RNASeq data contigs
  (new parameter -CL:rkm)

Documentation
- rewritten in large parts for manifest files
- started to update walkthrough for newer public data sets.

Bugfixes affecting users:
- orientation in CAF consensus tags
- expat building on newer Linux systems, e.g. (K)Ubuntu 11.10
- GenBank parsing of Vector NTI and DDBJ variants now working
- clearer error messages for users when parsing GenBank
- gap5 compatibility: CAF input allows for more weird characters in names

convert_project:
- -N for sorting reads, not only contigs
- new output targets: sam (obvious), gcwig (WIG file of GC content) and fcov
  (statistics for genome coverage respectively gene expression levels)

Other internal changes:
- lots of reshuffled/reworked code
- improved gcc warnings
- improved build environment, now out-of-the box building on more Linux
  distros
- better and simplified code due to transitioning to C++11
- new MAF format v2
