rNA (1.0)

  * rNA now can be compiled (with CYGWIN) and used in Windows(tm) environment.
  * bugfix: auto-k in --create doesn't work well
  * renaming: --filter-for-assembly was changed in --filter (shortly!)

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>

rNA (0.9.11)

  * bugfix: corrected output with not found reads when using --gap
  * renaming: parameter --min-phred-value-CLC is now renamed in --min-phread-value-mott
  * improvement: --query2 is no longer required for --filter-for-assembly

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>

rNA (0.9.10)

  * improvement: --reference options is not required for filter-for-assembly module  
  * bugfix: --print-all not works
  * improvement: filter-for-assembly default output is set to "sanger"-like; added --preserve-encoding to preserve input encoding

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>

rNA (0.9.9)

  * improvement: added -fno-stack-protector compile option
  * mrNA: new RMA version (communication improvement)
  * rNA: added gapped search (insertion in the reference)
  * rNA: k value in create phase is autodetected by default
  * improvement: fixed space allocation when loading FASTA files
  * bugfix: rNA --filter-for-assembly dosn't accept --min-mean-quality parameter
  * bugfix: trimming mean quality calculated slightly worse

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>

rNA (0.9.8)

  * bugfix: CRLF problem with fasta files
  * bugfix: problem with output for --filter-for-assembly (in unpaired files, read 2)
  * improvement: --force-* options now work in --filter-for-assembly

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>

rNA (0.9.7)

  * improvement: now "--output -" can be used to redirect to standard output
  * --filter-for-assembly bugfix: output FASTQ format version (sanger/illumina) now is the same of the input
  * improvement for mrNA: .inf file creation and control
  * improvement: removed useless variable Mask::type
  * added: proper pair information to --gui-output
  * bugfix: illumina 1.8+ autodetect now works
  * bigfix: minor correction to mrNA
  * added: --nobalancing option for mrNA

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>

rNA (0.9.6)

  * added --insert-size-{min,max} parameter for "proper pair" bam property
  * added "proper pair" information to --gui-output
  * maximum allowed read size is set to 300bp
  * illumina format version detection improved
  * bugfix for mrNA

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>

rNA (0.9.5)

  * --min-size option introduce in filter-for-assembly

 -- Francesco Vezzi <vezzi@appliedgenomics.org>

  * Changed output format for GUI

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>

rNA (0.9.4)
  * bugfix: insertion (with --indels options) are now handled correctly
  * added: --indels-max options to change maximum allowed indels bases (default: 5)

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>

rNA (0.9.3)

  * delta and indels searches are no more mutually exclusive
  * SAM output bug with paired reads and Delta option active fixed
  * parameter --filter-for-assembly now works

 -- Francesco Vezzi <vezzi@appliedgenomics.org>

rNA (0.9.2)

  * AUTHORS, README, COPYING, and ChangeLog files are installed in standard directory
  * added --version option (GNU standard)

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>

rNA (0.9.1)

  * SAM output bug on standard FASTQ fixed.

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>

rNA (0.9)

  * First stable release.

 -- Cristian Del Fabbro <delfabbro@appliedgenomics.org>
