Revision history for Perl extension 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