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