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CHANGELOG
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CHANGELOG
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14-01-28_Version_0.2.2 (Revision 441)
Wed Jan 29 12:06:32 MST 2014
-Adding bin/footprint from Seq_Analysis
-Adding gal_indexer
-Adding bin/gene_CDS_footprint
-New CPAN style html docs for GAL
-Library cleanup, documentation updates and various other changes
-Updates to gtf2gff3
-Adding warnings when mrna.pm can not return CDS or protein sequence
-Added progress counter to Storage::SQLite::load_files
-Adding --template option to gff_tool
-Adding templates/gff_tool_gvf_example2.tt
-Adding gal_remove_transcripts and gal_gff_tool
-adding fix_gvf function to bin/gff_tool
-Added --clean to gal_protein_genes
-Adding GAL::Base::open_file
--------------------------------------------------------------------------------
13-10-25_Version_0.2.1 (Revision: 399)
Fri Oct 25 14:30:53 MDT 2013
-Addition of HTML documentation pages GAL/docs/html/GAL.html
-Many updates to docs filewide
-Many additions, updates and bug fixes library wide.
--------------------------------------------------------------------------------
12-12-11_Version_0.2.0 (Revision: 364)
Tue Dec 11 14:11:56 MST 2012
-First major public release.
-Significant updates and additions library wide.
-Updates to SQLite schema and indexing to improve performance.
-Extensive updates and additions to testing throught bin and lib.
-Extensive updates and additions to Schema::Result::Feature
subclasses.
-Addition of Schema::ResultSet::Feature.pm.
-Extensive updates and additions to parser subclasses.
-Addition of Interval.pm.
-Adding HTML docs
-Reworking the schema to link attributes via feature_idx rather than
feature_id
-Adding GAL::List and GAL::Interval functionality to
lib/GAL/Schema/ResultSet/Feature.pm
-Updates to error handling in lib/GAL/Parser.pm validate_feature
-Adding bin/examples/gal_benchmark_recursion
-Adding lib/GAL/Interval/Span and associated changes
-Adding stuff for Module::Build deployment/building
-Optimizations to indexes and adding analyze to SQLite for significant
speedup
-Removing subject_id from the schema
-Adding a ton of tests mostly in the
500_schema_result_feature_gene/transcript/mrna classes
-Adding/fixing translation_start/end methods, UTR methods several more
bin/t tests and their scripts
-Adding a whole lotta tests to bin/t along with test data
-Lots of updates in lib/GAL/t/200_parser_* and additions in bin/t/*.t
as well as associated file shuffling
-Adding bin/examples for gal_*scripts
-A whole sh*t-load of testing updates!
-Many updates to bin/fastq_tool including adding sub seq_only and
adjustments to Illumin 1.5+ handling
-Adding t/gal_test_all.t
-Minor (but fatal) bug fix on
lib/GAL/Schema/Result/Feature/transcript.pm
-sort order to gene::mRNAs
-Adding dclone to Feature.pm attributes_hash
-Switching to Statistics::Descriptive::Discrete for significant
speed/memory improvements for sam_inspector
-Adding error messages to gff3_validator for the case when Parent tag
refers to the ID of a missing feature
-Adding strand based sorting for feature retrival methods
(i.e. $transcript->exons)