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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