ERNE (2.1.1)

  * bugfix: erne-filter does not properly trim 5' streatch of Ns
  * bugfix: erne-map and erne-bs5 aligning outside of sequences (when indel search is turned on)

ERNE (2.1)

  * improved: erne-meth now uses compressed counters. Space in RAM reduced by approximately 4 times.
  * improved: optimized code of cw-bwt algorithm in the BWTIL library. Faster reference construction.
  * bugfix: removed elements <> in README, which caused problems in the html version of the manual

Nicola Prezza <nicolapr@gmail.com>

ERNE (2.0)

  * changed: BWTIL library integrated (new BWT algorithm)
  * changed: default data structure is DBHASH
  * improved: best and fast indel search (by default)
  * improved: ERNE-BS5 use new data structure and indels search
  * bug: parallel version is not working properly, use version 1.4.5

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.4.5)

  * bugfix: read 1 insert size is not computed
  * bugfix: parallel version crashes with lot of nodes
  * bugfix: reads 2s are incorrectly marked as primary/secondary when all multiple-hit alignments are printed
  * bugfix: does not compile on OSX (see https://github.com/tsuna/boost.m4/issues/19)

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.4.4)

  * improvement: added new parameters and features to erne-meth
  * bugfix: samtools/picard use bam_reg2bin(-1,0) instead of 0 for bam.core.bin (http://sourceforge.net/p/samtools/mailman/message/29891604/)

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.4.3)

  * bugfix: Sanger format fastq with big quality values (outside format range) are detected as Illumina format fastq 
  * bugfix: Illumina HISEQ "." inside sequences are not interpreted as "N" 
  * bugfix: erne-filter does not use --contamination-reference

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.4.2)

  * bugfix: data_structures::Random::nextUInt() return wrong values
  * improvment: bwt-hash performance enhanched
  * improvement: minor issue resolved
  * changed: --quality-boost renamed to --ignore-quality

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.4.1)

  * bugfix: segfault on erne-filter

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.4)

  * improvement: changed structure for a better manutenibility
  * improvement: erne-pmap and erne-pcreate reimplemented for faster alignments
  * improvement: faster load and save using buffer
  * improvement: faster and more reliable version of erne-meth
  * improvement: added support for MPICH2
  * added: erne-pbs5, parallel version of erne-bs5
  * changed: erne-dmap and erne-dcreate are now called erne-pmap and erne-pcreate
  * changed: changed "-gdb" suffix to "-dbg"
  * bugfix: erne-filter does not honour --errors
  * bugfix: BIG ENDIAN is not detected
  * bugfix: other minor bugs solved

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.3)

  * bugfix: erne-meth delete input bam
  * improvement: optimized search algorithm in erne-map: search on all strands before to increase allowed errors in seed
  * improvement: optimized search algorithm in erne-map: stop search at the i-th block if a read is found with i-1 errors
  * improvement: added --errors-per-base options in erne-map
  * improvement: added --q, --quality-boost and --cl options in erne-map for search with the BWT-Hash data structure
  * improvement: added --output-prefix option in erne-meth
  * improvement: added --delta-m option in erne-meth
  * improvement: erne-bs5 divided in erne-bs5 (methylation alignment) and erne-meth (methylation analysis)
  * improvement: added BWT-Hash data structure. erne-create add the prefix .ebh if option --bwt-hash is specified.
  * improvement: better implementation of erne-dmap

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.2)

  * improvement: erne-bs5 --skip-alignment recognize automatically single-end vs. paired-end reads
  * improvement: erne-create add the correct suffix (.eht/.ehm); erne-filter, erne-map and erne-bs5 requires a reference file with the correct suffix
  * improvement: erne-filter can compress the output file(s) (added options --gzip and --bzip2)
  * improvement: erne-dmap can now handle gap and indels
  * improvement: erne-bs5 doesn't require temporary files for intermediates steps
  * improvement: add deletion search (--ref-deletion-max-gap)
  * improvement: erne-bs5: reduced the number of temporary files created while methylation reconstruction
  * new author: Fabio Tardivo <tardivo.fabio@gmail.com>
  * changed: erne-map --print-first now is --print-at-most
  * changed: erne-filter --reference option now is --contamination-reference (as in erne-map)
  * changed: --errors-rate now must be >= 5
  * changed: added --aligned-reads-thr option to erne-bs5
  * bugfix: --gap option works only on one strand
  * bugfix: programs enter in a endless loop if a directory is specified instead of a file
  * bugfix: --indels doesn't works properly in erne-bs5
  * bugfix: erne-filter output remove informations from ID fields
  * bugfix: erne-filter --no-auto-trim doesn't works
  * bugfix: erne-bs5 --skip-alignment doesn't works
  * bugfix: erne-map --print-all does not work properly (affect erne-bs5 also)
  * bugfix: minor bugs solved
  * bugfix: in paired-end alignment some first read are incorrectly flagged as quality discarded
  * bugfix: erne-create crashes if fasta sequences are empty

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.1)

  * improvement: erne-bs5: check if the two reads in a pair are overlapping
  * improvement: increased maximum read length up to 600bp
  * improvement: erne-bs5: unmapped reads are saved in a separated BAM file
  * improvement: better single gap insertion/deletion detection for erne-map and erne-bs5
  * bugfix: alignment input with fasta insteqad of fastq format doesn't work
  * bugfix: erne-create: segfault with low k values
  * bugfix: erne-map and erne-bs5: the read size must be equal or greater than seed size
  * bugfix: erne-bs5: run incorrectly when temporary bam/sam files are without alignments 
  * bugfix: erne-map: --print-all prints in an uncorrect order with single read alignments (affects erne-bs5 too)
  * removed: erne-map and erne-bs5: useless parameters
  * removed: erne-map and erne-bs5: obsolete option --auto-errors (if used, a warning message is printed)

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.0.2)

  * bugfix: erne-filter --query2 is no longer required
  * improvment: added --chunk-size option to erne-filter that permit to tune how many reads must be processed by each thread 

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.0.1)

  * minor bugfixes 

Cristian Del Fabbro <delfabbro@appliedgenomics.org>

ERNE (1.0)

  * First stable release, based on rNA v1.0.1 (ERNE-DMAP is based on rNA v0.9.8) http://iga-rna.sourceforge.net 

Cristian Del Fabbro <delfabbro@appliedgenomics.org>
