Bio::ViennaNGS v0.19.2

• added FeatureBase role; adjusted Feature classes & tests

Bio::ViennaNGS v0.19

• added Bio::ViennaNGS::FeatureIntervalN

Bio::ViennaNGS v0.18

• added dump()method to Bio::ViennaNGS::FeatureInterval, Bio::ViennaNGS::MinimalFeature and Bio::ViennaNGS::Feature
• make all attributes of Bio::ViennaNGS::FeatureInterval rw

Bio::ViennaNGS v0.17.5

• added scripts/fasta_regex.pl

Bio::ViennaNGS v0.17.4

• fixed handling of multi-Fasta files in bed2nt2aa.pl

Bio::ViennaNGS v0.17.1

• version is now declared at a unique location within ViennaNGS.pm
• updated README
• updated POD

Bio::ViennaNGS v0.17

• 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

Bio::ViennaNGS v0.16

• 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

Bio::ViennaNGS v0.15

• 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

Bio::ViennaNGS v0.14

• updated mkdircheck()
• updated rmdircheck()
• fixed directory creation in bam_split.pl
• updated POD in Tutorials