0.2.0a1 (2015-08-13) #################### *changes since 0.1.7 (2014-05-10)* Bug Fixes $$$$$$$$$ * Removed previous Ensembl data; <0.3% of previous sequences were inconsistent with newer ensembl releases Changes $$$$$$$ * Added liftover mechanism to bootstrap new schemas from existing data * Standardize on "NCBI" as origin name * When RefSeq transcript exon structures differ between chromosome and patch versions, use chromosome version [`0926cf34e173 `_] * Use explicit sequence sources when loading sequences * Bumped schema version to 1.1 for addition of associated_accessions and tx_similarity_v New Features $$$$$$$$$$$$ * New data: ensembl-79, refseq 2015-07-31 * Added RefSeq NR (non-coding) transcripts * Added geneacs (associated accessions) * Added transcript similarity view [`40a4e734d606 `_] with multiple similarity metrics (*experimental*) * Added Change Log to documentation * Developed and documented release flow w/tools * Implement gene-based data subsets for testing loading * Explicitly set cds_{start,end}_i to None when not defined in txinfo (for non-coding transcripts) [`e82011d1b02c `_] Other Changes $$$$$$$$$$$$$ * Added uta subcommand and make rule to update materialized views [`b1f2ef185320 `_] * Add load-origin from tsv file; update ensembl Makefile rules [`dc421df5ef19 `_] * Added "mega-test" and "the-whole-kielbasa" test targets * Added indexes to tx_def_summary_mv [`c1cda1cfd4c9 `_] * Enforce FK relationship from exon_set.tx_ac to transcript.ac [`ad5309895b5c `_] * Facilitate restartability in ensembl-fetch by creating canonical gene order and batching fetches * Standardize on schema name as uta_1_1 for dev, then rename on release * Updated code to use new eutils [`#171 `_, `d831e02f51fa `_] * Update to use bioutils instead of bdi [`769eea9241e4 `_] * Updated to use the aligner from uta-tools-align (f.k.a. locus-lib-bio) [`a1f492a32f5e `_]