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CHANGELOG
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CHANGELOG
2.4.3 (2023-09-15)
- updated from Python2 to Python3
- updated LOKI loaders
- fixed a bug in removing redundant results
2.4.2 (2019-03-15)
- fixed a bug in PARIS which may have inflated the reported permutation significance in some cases
- modified PARIS output report formats to reduce redundancy and simplify batch processing
- updated LOKI loaders for dbSNP, MINT and PharmGKB
- removed support for generating LD Profiles during LOKI installation
2.4.1 (2017-04-17)
- fixed a bug in PARIS which included non-gene regions
- updated LOKI loaders for dbSNP, GO and PharmGKB
2.4.0 (2016-05-09)
- implemented the PARIS algorithm with the corresponding --paris output option and other related configuration options
- added limited support for user-defined knowledge (custom gene groups) in --filter and --paris modes
- added --allow-ambiguous-snps option to accept input SNPs with multiple known positions
- fixed a bug in --region-match-bases with a negative value so that it correctly functions like --region-position-margin except for region-region matching
- updated LOKI loaders for gwas and dbsnp
2.3.0 (2015-12-14)
- changed default --report-genome-build option to 'yes'
- added --grch-build-version and --ucsc-build-version options to specify the
reference gnome build of user input; if it does not match the build used
in the provided LOKI database, liftOver will be automatically applied
- added --coordinate-base and --regions-half-open options to specify the
coordinate system conventions of user input and program output
- changed the any-namespace special tag from empty '' to '*'
- fixed a bug in installation on Windows platforms
2.2.0 (2014-06-04)
- fixed a bug when matching gene regions to input regions of size 1
- added support for "extra" input data to be stored with SNPs, positions,
regions, genes and groups, and corresponding output columns snp_extra, etc.
- (LOKI) added support for parsing updated genome build identities from
http://genome.ucsc.edu/FAQ/FAQreleases.html
- (LOKI) added warnings for unrecognized genome builds which could lead to
mismatched data
- (LOKI) added a tally of SNP role records with unrecognized Entrez GeneIDs
2.1.2 (2014-03-31)
- fixed a bug in the 'biopolymer_chr' output column (which is part of
the 'generegion' output shortcut) which caused a crash with certain
combinations of input data and requested output
- (LOKI) added support for HTTP (but not SOCKS) proxy servers for downloading
source data via HTTP
2.1.1 (2013-08-21)
- fixed a bug in model expansion that caused some models to be duplicated in
reverse order, and some types to be paired with themselves as a model
2.1.0 (2013-07-19)
- REGION_POSITION_MARGIN is now applied when matching positions to
upstream/downstream gene annotations
- added "gwas_rs" output option
- updated dbsnp loader to handle incomplete SNP roles in dbSNP's data download
- added support for "upstream" and "downstream" gene annotation; the shorthand
outputs provide the gene label and distance, but "_id", "_start" and "_stop"
suffixes are also available (i.e. "upstream_start")
- added support for "gwas" catalog ananotation by way of RS# or chr/position,
with a corresponding LOKI source loader; the shorthand output provides the
trait, SNPs, OR/beta, allele 95% CI, risk allele frequency and PubMed ID
- removed the file timestamp check in --verify-source-file; file size and hash
should suffice, and not all sources provide stable timestamps anyway
- fixed a bug in the LOKI updater which would mask the original error if the
error-handler itself caused an additional error
2.0.0 (2013-02-14)
- first public release