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CHANGELOG
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CHANGELOG
3.0.0
- added disease category for groups
- added sub-categories for groups
- added data source like disgenet, gaad, and kegg disease
- updated functions according to new changes
2.4.3 (2022-10-01)
- fixed an issue in downloading datasets from multiple sites
- updated from Python2 to Python3
2.2.5 (2019-03-15)
- updated contact information
- updated dbSNP, MINT and PharmGKB loaders
- removed support for generating LD Profiles
2.2.4 (2017-04-14)
- updated HTTP downloader to identify as User-Agent: RitchieLab/LOKI
- updated remote file paths for dbSNP, GO and PharmGKB loaders
2.2.3 (2016-05-09)
- updated gwas loader to use the new EBI host and file format
- added support for downloading from sources which do not support HTTP HEAD
2.2.2 (2015-12-14)
- added support for headers in HTTP download requests
- added special namespace '*', equivalent to '', to lookup by any namespace
2.2.1 (2014-06-27)
- fixed a bug in liftOver when the input start position was inside a gap
- fixed a bug in the coordinate normalization of the chainfiles loader
- normalized the region coordinate convention across LOKI
- added the "extra" data field in all liftOver inputs and outputs
- made loki-build verbose by default, with --quiet to suppress notices
2.2.0 (2014-05-27)
- added support for HTTP (but not SOCKS) proxy servers for downloading source
data via HTTP
- added support for parsing updated genome build identities from
http://genome.ucsc.edu/FAQ/FAQreleases.html
- added warnings for unrecognized builds which could lead to mismatched data
- added a tally of SNP role records with unrecognized Entrez GeneIDs
- added support for (mandatory) "extra" data fields on all lookup inputs,
which is returned with all corresponding output records
2.1.0 (2013-07-19)
- updated dbsnp loader to handle incomplete SNP roles in dbSNP's data download
- added "gwas" catalog source loader and supporting tables and methods
2.0.1 (2013-05-02)
- updated pfam loader to 2.1 to handle the new release's file format
- fixed loki-build option --temp-directory to apply to SQLite temp files
- fixed loki-build option --archive to skip re-archive if --cache-only is used
- fixed a bug in the stack trace output in the event of an error during update
- fixed a bug in the updater which would mask the original error if the error-
handler itself caused an additional error
- added a source file metadata check to skip updates when the source loader
code and all data files are unchanged since the last update
- new loki-build option --force-update to skip the metadata check
- separated the optimization and finalization of knowledge database files; the
updater always optimizes at the end, but finalizes only by request
- new loki-build option --no-optimize to skip the automatic optimization step
- fixed a bug in the UCSC ECR loader that increased the minimum region size
2.0.0 (2013-02-14)
- first public release