Bio-ToolBox-v2.01

• Update chromosome sorting to properly handle chromosomal arms, for
  example with Drosophila
• Change .groups.txt group file name to .col_groups.txt when writing
  column metadata file for scripts get_binned_data.pl and get_relative_data.pl
• Change back to _summary.txt file name when writing a summary file
• Change --blacklist option to --exclude in bam2wig.pl
• Improve error handling scenarios in data2wig.pl, including invalid indexes
• Fix bugs in manipulate_datasets.pl, including missing lines in the view function
  and restricting the addname function to only update a proper "Name" column
• Update any remaining POD text references about 0-base indexing to 1-base

BioToolBox-v2.00

• MAJOR UPDATE: Change all internal and user-oriented column indexing
  to 1-base instead of 0-base indexing, i.e. column numbers are now
  listed beginning with 1 instead of 0. WARNING!!! THIS WILL BREAK ALL
  PRE-EXISTING SCRIPTS AND CODE THAT USES HARD-CODED COLUMN INDEXES!!!
• MAJOR UPDATE: Use a single unified Bio::ToolBox::Parser module with
  subclasses for bed, gff, gtf, and ucsc table formats. NOTE: This changed
  name capitalization of Bio::ToolBox::Parser subclasses from parser
• Improve parsing of gtf files, especially with duplicate tags
• Replaced old table sorting algorithm to use numeric, mixed digit-string,
  and/or string sorting
• Improved accuracy of detecting standard columns such as name, ID, start, etc
• Add support for column median and trimmed-mean methods when generating a
  summary file
• Fix bug with filtering features by transcript_support_level and gencode
• Remove Bio::Seq::IO requirement for writing fasta files in data2fasta.pl
• Changed behavior to always use 1-base coordinate when generating coordinate
  strings, which is standard behavior e.g. with HTSlib (samtools and tabix) queries
• Improve support for coordinate lookup in merge_datasets.pl, including
  handling either 1-base or 0-base coordinate strings.
• Always report both transcript and gene name IDs and names in text output
  from get_gene_regions.pl
• Add bedpe format support
• Fix bugs with parsing file headers and assigning standard column metadata
• Fix bug with naming empirically derived introns
• Add option to skip chromosomes in get_gene_regions.pl
• Add option to adjust relative coordinates based on narrowPeak peak
  in get_features.pl
• Fix edge-case bugs with low-level bam parsing
• Speed up certain stats functions and improve detection of numbers
  in manipulate_datasets.pl
• Remove defunct supplementary tables in ucsc_table2gff3.pl
• Improve data format verification, and only run it when reading and writing
• Improve error reporting in scripts
• Use a proper prompting module for user-input
• Fix massive numbers of perlcritic and perltidy issues
• Hundreds of other bug fixes

BioToolBox-v1.691

• Fix critical error in script get_relative_data.pl
• Fix prerequisite version numbers leading to build failures
• Change a private function to a public function

BioToolBox-v1.69

• Revise genomic sorting by introducing a sane, logical chromosome
  ordering that smartly handles numerical, Roman, contigs, and
  alternate names. Sorting is done by both start and end coordinates.
  Sorting speed modestly improved.
• Improve handling of coordinates of Data Feature objects, including
  caching and setting.
• Add support for narrowPeak summit coordinate as reference point
  in multiple scripts.
• Improve handling of databases, including bigWigSet feature types.
  Make simplification of dataset names a little less aggressive.
• Include options for excluding chromosomes and/or intervals when
  generating a new list of genomic bins
• Improve tasting of file formats, keeping the file format of parsed files
  in the Data object.
• Allow non-stranded values when parsing UCSC files, including bed files.
• Optimize scoring subroutines
• Remove legacy subroutines from utility module
• Include new test file for utility functions
• Numerous other small changes and fixes

BioToolBox-v1.68

• Script bam2wig.pl script can now record both ends of paired-end
  fragments, rather than faking it as single-end. Paired-end start
  now respectes orientation. Added new option to only record either
  first or second read in a pair. Added new option to ignore
  zero intervals when writing bedGraph format. Changed multi-hit
  scoring to preferentially use NH instead of IH.
• Scripts get_binned_data.pl and get_relative_data.pl now
  can write out column names and associated datasets in separate
  groups file for use in plotting. Also specify score decimal format.
• Script get_features.pl has new option to only keep features with
  explicit tag value.
• High level ToolBox convenience function parse_file now includes
  basic default subfeatures exon, cds, and utr.
• Efficiency improvements in loading large text files by going
  back to chomp. Should still fail appropriately with wrong
  line endings.
• Feature objects now allow certain attribute methods to be both
  get and set, including seq_id, start, end, strand, name, and
  type, so long as the table does not contain parsed or database
  SeqFeature objects.
• Add Data object function to return any single row Feature without
  having to use an iterator.
• Add high level function for iterating over Bam alignments.
• Add support for intron subfeatures in Feature objects and data
  collection scripts.
• Allow bigWigToBedGraph to be explicitly used
• Better handling of verified dataset names
• Bug fixes and improvements in identifying database file
  formats and loading adapters.
• Bug fix in writing bgzip files.

BioToolBox-v1.67

• Add new option of smart coverage to script bam2wig that smartly handles pair-end alignments with gaps (introns)
• Add capability to collect from multiple datasets at once for scripts get_binned_data and get_relative_data. Summary files can now handle multiple datasets.
• Allow specific number of up and down windows in script get_relative_data.
• Add option to provide list of specific feature IDs to script get_features.
• Write shift correlation region data from bam2wig.
• Improve GTF export.
• Add utility function to simplify dataset names, used in data collection scripts. Strips path and everything after first period from dataset file names.
• Improve sort function in manipulate_datasets by taking a range of columns and sort by mean. Also addname function will overwrite a feature name if present.
• Adjust logic for setting a file extension when none is provided.
• Lots of additional minor fixes and changes

BioToolBox-v1.66

• Optimize data2wig fast mode, about 3 times faster
• Summary files now use a cleaned-up column name. Fix
  bugs with summary file generation.
• Bam2wig now properly reports alignment counts for each
  strand when provided with multiple input bam files
  (previously reported the same number).
• Fix bug where the Big adapter would crash when search
  coordinate was out of bound, unlike UCSC, HTS, and Sam.
• Improve GTF export with correct formatting and no longer
  export transcript lines.
• Improve GTF parsing where both transcripts and genes are
  inferred but coordinates where not updated correctly.

BioToolBox-v1.65

• Add function to read directly from bigWig files, and add
  support for bigWig files to script manipulate_wig
• Added options for filtering transcript Gencode or biotype
  in script get_gene_regions.
• Added option to discard low count features from script
  get_datasets.
• Add option to explicitly set number of columns of output
  bed file in script data2bed
• Update script get_feature_info to work with annotation files
• Optimize data2wig to handle fast option in more scenarios
• Coordinate string generation in manipulate_datasets takes
  start values as is
• Bug fixes in Bio::ToolBox, get_relative_data,
  manipulate_datasets, more

BioToolBox-v1.64

• Added support for Encode gappedPeak files. Also support for
  gleaning file formats from bed track lines. This should make
  future file formats easier to support in the future.
• Fix critical bug with skipping duplicate features from GTF
  files, particularly from Ensembl where exons share the same exon ID.
• Fix double-counting of stranded alignments in bam2wig script.
  Also correctly set minimum paired-end size.
• Fix bug to correctly count FPKM and TPM over length-adjusted
  features in script get_datasets.
• Fix bug with filtering transcripts in script get_features.
• Reset and clarify behavior regarding stop codons when parsing
  and exporting transcript features for various annotation formats.
• Add single-letter option support to script get_gene_regions.

BioToolBox-v1.63

• Added minimal Cram file support through the HTS adapter.
  Currently only supports the reference fasta listed in the Cram
  file header.
• Added fast paired-end option and paired-end start point options
  to script bam2wig. Temporary files now written to a temporary
  subdirectory, which can be specified. Extreme depth can now be
  handled properly by using 32 bit integers instead of 16. Splice
  segments can now be fractionally counted.
• Brought back and updated old script correlate_position_data to
  identify positional shifts in nucleosome or ChIP signal peaks.
• Added new SeqFeature methods to duplicate objects and delete
  subfeatures.
• Added option to format result numbers in script get_datasets.
• Fix numerous small bugs in scripts data2gff, data2fasta,
  get_intersecting_features, get_relative_data, and more