2018-01-17
- version 1.07

2017-08-09
- maximum sequence length increased to 10Mb

2016-11-09
- added option --config in exonhunter and prepare evidence

2016-11-08
- bug fix in filter add_strand, previously strand not added at the end
  of transcript (i.e last exon)

2016-09-02
- gtf2transcript allows some rows without support

2014-10-21
- New version of rpsblast, different format of species option in repeatmasker

2014-01-14
- New filter mark_bad_frame; filter add_stop_codon and others now
  check frames more carefully.

2013-10-23
- gtf2transcript now correctly uses frames for incomplete transcripts.

2011-05-01
- New option prefer_first_ORF to filter add_CDS

2011-03-19
- Blatp parser adds transcript id based on blat alignments. This improves
  process of adding introns in filter-gtf.
- Filter find_pseudogenes now can mark pseudogene rows as bad.
- New filter split_nonsense_transcripts.
- New option check_info to add_start_codon and add_stop_codon

2010-11-03
- version 1.06
- program none in prepare-evidence now can copy gtf file to ehtemp directory.

2010-08-23
- Updates to documentation.
- bug fix in filter add_CDS, add_start_codon and add_stop_codon in filter-gtf 
  (problem with reverse strand)

2010-08-18
- Added support for blat (EST and protein alignment to the genome) as well as limited
  experimental support for exonerate 

2010-05-09
- Added options start_codons and stop_codons to filters add_start/stop_site,
  add_start/stop_codon, add_CDS. Useful for different genetic codes.

2009-11-03
- Filter write_schedule allows more than two advisors as arguments of unique.

2009-07-10
- Filter add_stop_codon now works even on 5' incomplete transcripts 
  (bug fix in existing code which assumed 5' complete transcript)

2009-06-19
- Filter remove_short_transcripts now has new option minimum_exon_length.

2008-05-19
- version 1.05

2008-05-17
- New filter change_score is added which can do further manipulation
  of row scores.

2007-08-27:
- Filter add_CDS in filter_gtf can now find longest ORF
  in a transcript.
- New filter add_gene_id added, which can group transcripts to genes.
- New filter set_score added which can manipulate score of rows.

2007-04-03:
- version 1.04

2007-03-31:
- tools that run external processes now work even if the system shell
  is not bash.

2007-03-08:
- bug fix for problems with repeatmasker handling of long
  fasta names. Repeatmasker now uses CHUNKSIZE and CHUNKSEP 
  options in eh.config, as do all other tools.
- Options CHUNKSIZE and CHUNKSEP in eh.config are now
  optional, with defaults 100,000 and 1,000, respectively. 

2007-02-26:
- prepare-evidence can now use rpsblast (for example to align
  CDD database of profiles from NCBI, which contains Pfam 
  and other databases)

2007-02-22:
- Introns are now added to gtf output of exonhunter and scored for support.
- Small problem with support scoring fixed: first and last 
  nucleotide of each exon and intron are ignored in scoring 
  since they may represent a signal position (start/stop site, 
  splice site)

2007-02-06:
- version 1.03
  (small bug fixes, which should not influence distributed parts 
   of the software)

2006-12-30:
- version 1.02

2006-12-07:
- filter add_intergenic can add intergenic regions at both ends
  of a feature (e.g. gene) simultaneously, regardless of a strand.

2006-12-06:
- eh.config files can now use program "none" which does nothing.
  This is useful for using external alignments, when only about file 
  is added according to eh.config.
- exonhunter now has option --exclude that allows to ignore some
  sources of evidence with about file present in the temporary
  directory

2006-12-05:
- add option --continue to scripts prepare-evidence and program-wrapper.
  This option allows to continue interrupted prepare-evidence
  job, even if evidence is set to ALL. Also, results of repeatmasking
  are checked for completness.

2006-11-30:
- add filter compute_coverage to filter-gtf (the script that processes
  gtf files with evidence to int format used by advisors).

2006-08-03:
- add option gtf_output_suffix to write_gtf filter
  in  filter-gtf (the script that processes
  gtf files with evidence to int format used by advisors).

2006-08-02:
- add filter count_duplicates to filter-gtf (the script that processes
  gtf files with evidence to int format used by advisors).

2006-07-28:
- version 1.01

2006-07-25:
- fix permission problems in installation (oneliner.pl)

2006-07-24:
- eh.config can specify several runs of repeatmasking;
  only the one called repeat is used to produce masked file

- RepeatMasker can be used with a library specified by option
  EVIDENCE_<name>_FILES
  If you specify library, leave option REPEATMASKER_SPECIES empty

- Bug fix: when one evidence name is prefix of another, such as repeat
  and repeat-other, --restart option in prepare-evidence would not work
  correctly. Now the problem occurs only when the longer name starts
  with a number after a dashm such as repeat and repeat-1.

2006-07-06:
- version 1.0
