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