Revision history for Perl extension Bio::ViennaNGS.

0.01  Fri Sep 13 12:02:47 2013
	- original version; created by h2xs 1.23 with options
		-XA -n ViennaNGS
	- added get_stranded_subsequence()

0.02  Mon Nov 4 2013
	- added split_bam()
        - added scripts/bam_split.pl

0.03  Tue Nov 5 2013
    	- added bam2bw()
	- updated README

0.04  Tue Nov 26 2013
	- added scripts/DEXSeq_gff2bed.pl
	- updated README

0.05  Thu Apr 03 2014
	- added bed2bw()
	- updated and extended bam_split()
	- updated scripts/bam_split.pl
	- adjusted perl shebang in /scripts

0.06  Fri Sep 19 2014
	- adjusted perl shebang in /scripts
	- added normalize_multicov.pl in /scripts. For that purpose:
	- added computeTPM()
	- added parse_multicov()
	- added write_multicov()
	- added featCount_data() accessor for @featCount AoHoH 
	- added normalization support for bigWigs generated from scripts/bam_split.pl
	- refactored split_bam()
	- intermediate bedGraph files are now removed in bed2bw()

0.07  Mon Sep 29 2014
	- minimum version of Bio::Perl is 1.006924
	- minimum version of Bio::DB::Sam is 1.39
	- added scripts/splice_site_summary.pl
	- added scripts/assembly_hub_constructer.pl prototype
	- added bed2bigBed()
	- use IPC::Cmd for running external tools in bed2bigBed()
	- use Carp for error handling
	- refactored bam2bw()
	- refactored bed2bw()
	- removed scripts/ensembl_fa2bed.pl

0.08  Tue Sep 30 2014
	- added tests for third-party utilities
	- use Carp for error handling throughout the module
	- updated documentation

0.09  Thu Oct 2 2014
	- changed namespace to Bio::ViennaNGS
	- adjusted utilities to use new namespace
	- everything is exported via @EXPORT_OK now
	- updated README

0.10  Thu Nov 27 2014
	- 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

0.11 Wed Dec 10 2014
	- 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
	
0.12 Wed Feb 11 2015
	- 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