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 session

  • Use of external GnomAD exome/genome files (allows choosing GnomAD version)

  • Classes ExtractAnnotations,BinaryGnomadReader,BinaryGnomadWriter and GnomADIndexReader 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 static

  • Shuffler : 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 methods

  • Gamma : added toString(), changed add(boolean phenotype) returns true instead of void

  • RankedGammaList : added add(int, boolean), add(int, Gamma), printDebug(), changed add(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 data

  • WSS : changed externalisation of classes Gamma and RankedGammaList

  • 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