Bio::ViennaNGS v0.13

This is a bugfix release:

• fixed an issue in Bio::ViennaNGS::FeatureChain
• updated POD

Bio::ViennaNGS v0.12

• 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 PODs and README

Bio::ViennaNGS v0.11

• integrated Bio::ViennaNGS::AnnoC
• integrated Bio::ViennaNGS::Fasta
• removed obsolete bam2bw()
• added scripts/bam_to_bigwig.pl
• added scripts/bed2bedGraph.pl
• added scripts/extend_bed.pl
• added scripts/kmer_analysis.pl
• added scripts/MEME_XML_motif_extractor.pl
• added scripts/trim_fastq.pl
• refactored scripts/bam_to_bigwig.pl
• refactored scripts/splice_site_summary.pl
• refactored scripts/bam_split.pl
• refactored scripts/gff2bed.pl
• added Moose-based classes for feature handling
• renamed bed2bw() to bam_or_bed2bw() and refactored it accordingly to properly handle BAM files
• added '-split' option to 'genomeCoverageBed' call in bam_or_bed2bw()
• updated MakeMaker scripts (MANIFEST and Makefile.PL)
• minimum version of Bio::Root::Version is now 1.00690001
• added some tests
• ship demo files in share/ folder
• updated POD and README

Bio::ViennaNGS v0.10

• requires Perl >= 5.12.0
• added sortbed()
• added uniquify_bam()
• added scripts/bam_uniq.pl
• added scripts/sj_visualizer.pl
• refactored scripts/motiffinda.pl
• removed development version of scripts/assembly_hub_constructer.pl
• made scripts/gff2bed.pl work with OO Bio::ViennaNGS::AnnoC
• removed get_stranded_subsequence (now lives in Bio::ViennaNGS::Fasta)
• updated POD

Bio::ViennaNGS v0.09

• changed namespace to Bio::ViennaNGS
• adjusted utilities to use new namespace
• everything is exported via @EXPORT_OK now
• updated README

ViennaNGS v0.08

• added tests for third-party utilities
• use Carp for error handling throughout the module
• updated documentation