Bio-ViennaNGS
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- requires Perl >= 5.10.0
- minimum version of Bio::DB::Sam is 1.37
- integrated Bio::ViennaNGS::Bam
- integrated Bio::ViennaNGS::BamStat
- integrated Bio::ViennaNGS::BamStatSummary
- integrated Bio::ViennaNGS::Bed
- integrated Bio::ViennaNGS::ExtFeature
- integrated Bio::ViennaNGS::SpliceJunc
- integrated Bio::ViennaNGS::Tutorial
- integrated Bio::ViennaNGS::UCSC
- integrated Bio::ViennaNGS::FeatureLine
- added scripts/assembly_hub_generator.pl
- added scripts/bam_quality_stat.pl
- added scripts/Tutorial_pipeline00.pl
- added scripts/Tutorial_pipeline01.pl
- added scripts/Tutorial_pipeline02.pl
- added scripts/Tutorial_pipeline03.pl
- added scripts/track_hub_constructor.pl
- renamed Bio::ViennaNGS.pm to Bio::ViennaNGS::Util.pm
- migrated BAM specific code from Bio::ViennaNGS::Util
to Bio::ViennaNGS::Bam
- migrated expression/normalization code from Bio::ViennaNGS::Util
to Bio::ViennaNGS::Expression
- refactored scripts/normalize_multicov.pl
- removed scripts/motiffinda.pl from distribution
- added static templates for the Assembly and Track Hub generator
- updated POD and README
0.13 Thu Feb 14 2015
- fixed an issue in Bio::ViennaNGS::FeatureChain
- updated POD
0.14 Tue Feb 24 2015
- updated mkdircheck()
- updated rmdircheck()
- fixed directory creation in bam_split.pl
- updated POD in Tutorials
0.15 Mon Jul 6 2015
- fixed path creation in bed_or_bam2bw()
- fixed scalar initialization bug
- fixed bug in Bio::ViennaNGS::BamStat
- scripts/bam_to_bigwig.pl can now produce normalized bigWigs
- added functionality to compute RPKM in Bio::ViennaNGS::Expression
- added tests for UCSC.pm
- added tests for SpliceJunc.pm
0.16 Tue Oct 27 2015
- added Bio::ViennaNGS::FeatureInterval
- added Bio::ViennaNGS::BedGraphLine
- added Bio::ViennaNGS::Peak
- make Bio::ViennaNGS::MinimalFeature subclass of
Bio::ViennaNGS::FeatureInterval
- added scripts/rnaseq_peakfinder.pl
- added scripts/bed2nt2aa.pl
- updated POD and README
0.17 Fri Jun 09 2017
- added Bio::ViennaNGS::FeatureIO
- added Bio::ViennaNGS::Subtypes
- refactored Bio::ViennaNGS::Fasta to transparently coerce input
data into a Bio::DB::Fasta object
- refactored executables in scripts/ folder to new
Bio::ViennaNGS::Fasta interface
- changed output format in scripts/bed2nt2aa.pl to csv
- removed parse_bed6() and extend_chain() from Bio::ViennaNGS::Util
(bed I/O is now available in Bio::ViennaNGS::FeatureIO and chain
extension is available in bedtools)
- added uniquify_bam2() in Bio::ViennaNGS::Bam
- implemented correct handling of unmapped reads in
Bio::ViennaNGS::Bam
- replace '~' with $HOME in mkdircheck() within
Bio::ViennaNGS::Util
- fixed output path creation in rnaseq_peakfinder.pl,
splice_site_summary.pl
- refactored scripts/bam_uniq.pl
- refactored scripts/bed2nt2aa.pl
- added scripts/fasta_subgrep.pl
- added scripts/fasta_multigrep.pl
- migrated scripts/MEME_xml_motif_extractor.pl to
Bio-ViennaNGS-scripts-extra package on github
- updated POD
- removed Tutorial_pipeline{0,1,2}
- added unit tests
0.17.1 Sat Jun 10 2017
- version is now declared at a unique location within ViennaNGS.pm
- updated README
- updated POD
0.17.2 Mon Jun 26 2017
- fix check for valid RefSeq accession in UCSC.pm
0.17.3 Sun Jul 2 2017
- fixed missing parentheses in fasta_subgrep.pl
0.17.4 Wed Jul 19 2017
- fixed handling of multi-Fasta files in bed2nt2aa.pl
0.17.5 Mon Aug 07 2017
- added scripts/fasta_regex.pl
0.18 Thu Feb 15 2018
- added dump()method to Bio::ViennaNGS::FeatureInterval,
Bio::ViennaNGS::MinimalFeature and Bio::ViennaNGS::Feature
- make all attributes of Bio::ViennaNGS::FeatureInterval rw
0.18.1 Thu 24 May 2018
- ignore case in regex match in fasta_regex.pl
- allow keeping temporary bedGraph files in BAM to bigWig and
BED to bigWig conversion
- refactored temporary file handling in Bio::ViennaNGS::Peak
- ignore case in regex match in scripts/fasta_regex.pl
- refactored scripts/bed2bedGraph.pl
- argument error checks in Fasta.pm
0.19 Tue 3 Jul 2018
- added Bio::ViennaNGS::FeatureIntervalN
0.19.1 Tue 7 Aug 2018
- added Fasta test to distribution
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