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v.1.9.3 (svn 516)
	- Fixed bug where wig definition lines may not be written when no
	alignments exist in the first 2 Mb of a chromosome when converting a bam
	file to a wig file in script bam2wig.pl. Definition lines are now always
	written. Thanks to Matt J. for reporting.
	- Fixed bug where the format_with_commas sub was not properly imported
	into the tim_db_helper library
	- Fixed bug where the bed output from script get_features.pl did not
	properly report strand information. 

v.1.9.2 (svn 510)
	- Fixed critical bug where codon changes were not reported correctly for
	minus strand genes in script locate_SNPs.pl. Thanks to Craig K. for
	reporting.

v.1.9.1 (svn 507)
	- Added critical code to interpret strand information from input files
	such as Bed and GFF into BioPerl standards. Essential for collecting
	stranded data. Also properly writes back strand information for valid
	Bed and GFF files
	- Updated and unified internal library methods for validating and
	requesting database feature types. By default, all database features are
	presented to the user as a list when selecting database features to
	collect data. The source_exclude parameter in the biotoolbox.cfg
	configuration file is now deprecated.
	- Upgraded script get_intersecting_features.pl to automatically
	recognize input file columns and search for more than 1 feature type
	- Fixed bug in script get_datasets.pl where the program will not
	continue when only a data database was provided
	- Fixed bug of requesting index when using a .kgg file as a gene list in
	script pull_features.pl
	- Fixed bug in generating file name for Treeview export function in
	script manipulate_datasets.pl
	- Fixed behavior when reading files to prevent adding the current
	program name to the metadata when the input file does not have this
	metadata
	- Minor updates to script novo_wrapper.pl
	
v.1.9.0 (svn 493)
	- Added new script get_features.pl which generates a list of features
	for one or more feature types from a database. Information about the
	features may be returned, including name, type, and coordinates. Sub
	features may be included. The data may be written as a BioToolBox
	formatted text file, GFF or BED.
	- Added new script correlate_position_data.pl that calculates a Pearson
	correlation between the score values at identical positions along a
	feature between two datasets. This helps in identifying changes in
	spatial distribution of values. An option for calculating shifts is also
	available.
	- Improved Big File generation such that Bio::DB::BigWig or
	Bio::DB::BigBed is no longer required just to generate the big file, as
	conversion uses external utilities anyway.
	- Fixed generation of bin values when calculating distribution
	frequencies in scripts data2frequency.pl and graph_histogram.pl

v.1.8.7 (svn 487)
	- Added new command line options to script merge_datasets.pl to control
	the program's behavior. The "--lookupname" option allows you to specify
	the name of the lookup column, while "--manual" turns off all automatic
	guessing of columns. Also improved handling of original_file metadata.
	- Added a new option to collect data from long features (such as genomic
	annotations) instead of point data (microarray or sequence data) in
	script get_relative_data.pl.
	- Added option to convert to and from Roman numerals in chromosome names
	and support for wig files in script change_chr_prefix.pl
	- Added option to change the IP port number when connecting to a remote
	MySQL database host in script get_ensembl_annotation.pl
	- Fixed bug to properly close opened files in script split_data_file.pl
	and avoid unnecessary error messages.
	- Modified statements and warnings regarding step and span values in
	script data2wig.pl

v.1.8.6 (svn 477)
	- Added numerous enhancements and bug fixes to script data2wig.pl,
	including automatically assigning the span parameter in the wig file,
	identifying coordinate columns, adding command line options for
	coordinate columns, and updating the POD documentation
	- Improved the treeview export function in script manipulate_datasets.pl
	to include different manipulations, including median center of genes or
	datasets, converting to Z-scores, and converting null values. Also
	changed the default output name to <basename>.cdt.
	- Added advanced option to script merge_datasets.pl to specify the
	column order on the command line instead of interactively. Also
	increased the number of columns that can be specified as letters.
	- Added the "value" command line option to specify the type of data to
	collect to the script find_enriched_regions.pl. Also added the sum
	method plus some improvements for identifying depleted regions.
	- Updated the script run_cluster.pl to accept any file name as input,
	and added basic file format validation checks prior to running the
	cluster algorithm, among a few other minor improvements
	- Improved handling of error messages when attempting to open databases
	that do not exist or can not otherwise be opened.
	- Added more support for reading bedgraph files, dealing with track
	lines and possibly empty lines
	- Collecting data from bigWig files that use spanned features (span > 1
	bp) are now collected at every base rather than just the start position
	- Fixed bug where more than two files were not properly merged using
	lookup in script merge_datasets.pl
	- Fixed bug to allow data to be collected for Bed files from indexed
	data files without specifying a database in script get_datasets.pl

v.1.8.5 (svn 461)
	- Fixed critical bug where all knownGene feature strands are reversed in
	script ucsc_table2gff3.pl
	- Fixed critical bug where the sign is flipped when generating Z-scores
	with script manipulate_datasets.pl
	- Added new functions "convert null values" and "absolute value" to
	script manipulate_datasets.pl
	- Added additional file format checks when writing formatted files
	including GFF, BED, and SGR. File extensions may automatically change to
	default txt if the format does not match.
	- Better handling of input Bed files and generating appropriate default
	file names in script data2gff.pl
	- Improved merging of datasets by lookup, and loosened restrictions on
	metadata checking, issuing warnings instead, in script merge_datasets.pl
	- Loosened restrictions on metadata differences and failures in script
	join_data_file.pl
	- Included fix for finding column indices when name is prefixed with #
	- Added another check to avoid returning undefined values from BigWig
	data collection