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CHANGES  view on Meta::CPAN

	identical postions in scripts data2wig.pl, bar2wig.pl, and
	useq2bigfile.pl.
	- Retired the outdated script just_blast_oligos.pl.

v1.5.1 (svn r193)
	- Fixed critical bug in script bar2wig.pl where values from multiple
	postions were not combined properly. Also fixed bug with processing a
	single bar file.
	- Removed required dependencies of bioperl for scripts bar2wig.pl and
	useq2bigfile.pl
	- Fixed small bug in tim_db_helper::bigbed library to ensure positions
	were withing the region of interest
	- Added mapping quality filter and other improvements to script
	bam2wig.pl
	- Changed score reporting to record mapping quality in script
	bam2gff_bed.pl

v1.5 (svn r184)
	- Added script useq2bigfile.pl for converting USeq archives
	- Added script check_dependencies.pl for assisting in checking for Perl
	module dependencies. It will help install the latest versions through
	CPAN
	- Changed the biotoolbox configuration file from lib/tim_db_helper.cfg
	to biotoolbox.cfg in the root directory.
	- Moved the biotoolbox configuration loader into a separate module as
	lib/tim_db_helper/config.pm. This avoids requiring installing BioPerl
	and loading all of tim_db_helper.pm when it may not be necessary.
	- Updated numerous scripts to reflect changes with the biotoolbox
	configuration loader.
	- added axes labeling options to scripts graph_data.pl and
	graph_histogram.pl
	- fixed bug in handling bed files in library tim_file_helper
	- minor fixes in script data2wig.pl
	- improved working with bigfile conversions
	- fixed minor bug in script big_file2gff3.pl when leaving files in the
	current directory

v1.4.4 (svn r162)
	- Added reads per million option to script bam2wig.pl
	- Added parent, exon, and transcript_length attributes to script
	get_feature_info.pl
	- Updated scripts find_enriched_regions.pl and map_transcripts.pl to
	work with with standalone data files (BigWig, BigBed, Bam)
	- Added configuration, description, and capabilities to working with
	SQLite database files in tim_db_helper
	- Added midpoint as acceptable coordinate in script data2wig.pl
	- Bug fixes to script locate_SNPs.pl and bam2wig.pl; library
	tim_db_helper::bam

v1.4.3 (svn r144)
	- Changed script bar2wig.pl to require method for combining values and
	removed interbase option
	- Updated peak indentification in script map_nucleosomes.pl to use the
	tag dataset and not the scan dataset
	- Updated script big_file2gff3.pl to produce more useful conf files with
	BigWigSets
	- Added overlap data column to ouput of script
	get_intersecting_features.pl and added --set_strand option to enforce
	directionality
	- Added three new functions to script manipulate_datasets.pl, including
	new column, strandsign, and mergestrand
	- Fixed script wig2data.pl so it works now
	- Updated script get_feature_info.pl to parse an attribute list from the
	command line
	- Improved handling of metadata when opening tim data files

v1.4.2 (svn r129)
	- Added fast low level coverage function to the script bam2wig.pl
	- Fixed script pull_features.pl to keep the order of features in the
	list file.
	- Fixed script bar2wig.pl to correctly identify the chromosome name.
	- Various bug fixes to the database library helper tim_db_helper.pm.

v1.4.1 (svn r119)
	- Fixed bug with get_ensembl_annotation.pl where a protein_coding gene
	encoding a transcript lacking a CDS will write inappropriate
	coordinates. These transcripts will not write start_codon, stop_codon,
	or CDS subfeatures.
	- Fixed bug with script get_intersecting_features.pl where selecting
	regions with a start, stop modifier was not being selected properly.
	- Fixed bug with tim_db_helper modules that prevented working with
	source data files specified in a database feature
	- Added log transformation of count in script bam2wig.pl

v1.4 (svn r111)
	- Added script bam2wig.pl for enumerating alignments and writing a wig
	file of the counts. 
	- Added script change_chr_prefix.pl for adding or stripping chromosome
	prefixes from data and annotation files.
	- Bug fixes to ucsc_table2gff3.pl.

v1.3 (svn r104)
	- Added ability to restrict data collection to exon subfeatures to
	script get_datasets.pl. Useful for RNA-seq analysis.
	- Added exon count as attribute to script get_feature_info.pl.
	- Bug fixes to get_datasets.pl.

v1.2 (svn r98)
	- Added support for bam files as a data source.
	- Updated data collection scripts to allow direct referencing of data
	source files, including bigWig, bigBed, and Bam files, on the command
	line, without having to reference the files from within the database.

v1.1 (svn r92)
	- Updated script ucsc_table2gff3.pl to use Bio::SeqFeature::Lite. Now
	outputs exon and codon features.
	- Updated script get_ensembl_annotation.pl to collect RNA features from
	Ensembl as well as generate exon and codon features.
	- Added script gff3_to_ucsc_table.pl to generate UCSC style refSeq
	tables from GFF3 formatted data.

v1.0.2 (svn r91)
	- Bug fixes to libs tim_file_helper and tim_db_helper
	- Bug fixes to scripts print_feature_types.pl,
	get_intersecting_features.pl, big_file2gff3.pl, graph_data.pl,
	graph_histogram.pl, graph_profile.pl

v1.0 (svn r68)
	- Initial public release of an archive. Previous versions were only
	available through SVN.