Changelog¶
1.0.4 (2021-09-21)¶
Core¶
GenotypesFileHandler : added
extractCanonicalAndHash
that allows getting hashed values from the original VCF file, in order to debug a sessionUse of external GnomAD exome/genome files (allows choosing GnomAD version)
Classes
ExtractAnnotations
,BinaryGnomadReader
,BinaryGnomadWriter
andGnomADIndexReader
to process a binary version of the GnomAD files
Client¶
ClientRun : added command line
--extractandhash
Filtering on external GnomAD files, with choice of subpopulation and choice of GnomAD version
Better management of Exception
RPP¶
RPPRun : added command line
--extractandhash
Filtering on external GnomAD files, with choice of subpopulation
TPS¶
1.0.3 (2021-07-21)¶
Core¶
Typo : in javadoc
Client¶
RPP¶
TPS¶
WSS : changed references to status or affected are changed to phenotypes, changed
x()
methods to staticShuffler : changed access to public for getNext()
Utils : added class providing static methods that are independent of the algorithms
TPSRun : changed output of
computeWSSRanksum
, add information and results of both optimized and unoptimized methodsGamma : added
toString()
, changedadd(boolean phenotype)
returnstrue
instead of voidRankedGammaList : added
add(int, boolean)
,add(int, Gamma)
,printDebug()
, changedadd(double, boolean)
simplified through use of boolean add instead of void
1.0.2 (2021-06-09)¶
Core¶
Client¶
RPP¶
RPP : added blacklist/whitelist of clients and connection log to prevent too frequent connections
TPS¶
WSS : fixed Count of shared variants within genes
WSS : optimized
x()
method, taking into account that there will be no missing dataWSS : changed externalisation of classes
Gamma
andRankedGammaList
ThirdPartyServer : fixed use of static final variable instead of hard-coded values
1.0.1 (2020-12-03)¶
Core¶
Quality Control : added QC on VCF data. The same QC is performed both on the Client’s and RPP’s data.
Client¶
TPSStatus : added TPSLogWindow
ResultsPane : changed JFrame instead of JOptionPane
RPP¶
TPS¶
1.0.0 (2020-10-02)¶
Core¶
Message : added class StartSession and SessionStarted to delay extraction
Client¶
End of Association Tests : added automatic results download
RPP¶
Session creation : changed to delay extraction
Data Extraction : added warning if extraction yields empty dataset
TPS¶
TPS Start : added number of genes/variants in initial Status