What's new in ERNE 2.1
Mar 17, 2015
- 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
New in ERNE 2.0 (Sep 30, 2014)
- bugfix: read 1 insert size is not computed
- 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)
- 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 1.4.4
New in ERNE 1.4.4 (May 27, 2014)
- 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/)
New in ERNE 1.4.3 (May 27, 2014)
- 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
New in ERNE 1.4.2 (May 27, 2014)
- bugfix: data_structures::Random::nextUInt() return wrong values
- improvment: bwt-hash performance enhanched
- improvement: minor issue resolved
- changed: --quality-boost renamed to --ignore-quality
New in ERNE 1.4.1 (May 27, 2014)
- bugfix: segfault on erne-filter
New in ERNE 1.4 (May 27, 2014)
- 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
New in ERNE 1.3 (May 27, 2014)
- 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
New in ERNE 1.2 (May 27, 2014)
- 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
- 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
New in ERNE 1.1 (May 27, 2014)
- 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)