├── .classpath ├── .github └── workflows │ ├── create-release.yml │ └── maven.yml ├── .gitignore ├── .project ├── .settings ├── org.eclipse.core.resources.prefs └── org.eclipse.jdt.core.prefs ├── LICENSE ├── README.md ├── files ├── chains │ ├── hg19ToHg38.over.chain.gz │ └── hg38ToHg19.over.chain.gz └── pgs-calc ├── pom.xml ├── src ├── main │ ├── assembly │ │ └── assembly.xml │ ├── java │ │ └── genepi │ │ │ └── riskscore │ │ │ ├── App.java │ │ │ ├── commands │ │ │ ├── ApplyScoreCommand.java │ │ │ ├── ClearCacheCommand.java │ │ │ ├── CreateChunksCommand.java │ │ │ ├── CreateCollectionCommand.java │ │ │ ├── CreateHtmlReportCommand.java │ │ │ ├── DownloadMetaCommand.java │ │ │ ├── DownloadScoreCommand.java │ │ │ ├── FilterMetaCommand.java │ │ │ ├── LiftOverScoreCommand.java │ │ │ ├── MergeEffectsCommand.java │ │ │ ├── MergeInfoCommand.java │ │ │ ├── MergeScoreCommand.java │ │ │ ├── MergeVariantsCommand.java │ │ │ ├── ProcessHaploRegCommand.java │ │ │ ├── ResolveScoreCommand.java │ │ │ ├── ValidateScoreCommand.java │ │ │ └── VariantReadingException.java │ │ │ ├── io │ │ │ ├── Chunk.java │ │ │ ├── MetaFile.java │ │ │ ├── OutputFile.java │ │ │ ├── OutputFileReader.java │ │ │ ├── OutputFileWriter.java │ │ │ ├── PGSCatalog.java │ │ │ ├── PGSCatalogIDFile.java │ │ │ ├── ReportFile.java │ │ │ ├── RiskScoreFile.java │ │ │ ├── SamplesFile.java │ │ │ ├── ScoresFile.java │ │ │ ├── VariantFile.java │ │ │ ├── csv │ │ │ │ ├── CsvWithHeaderTableReader.java │ │ │ │ ├── CsvWithHeaderTableWriter.java │ │ │ │ └── TabixTableReader.java │ │ │ ├── dbsnp │ │ │ │ └── DbSnpReader.java │ │ │ ├── formats │ │ │ │ ├── PGSCatalogFormat.java │ │ │ │ ├── PGSCatalogHarmonizedFormat.java │ │ │ │ ├── PGSCatalogVariantsFormat.java │ │ │ │ ├── PRSwebFormat.java │ │ │ │ ├── RiskScoreFormatFactory.java │ │ │ │ └── RiskScoreFormatImpl.java │ │ │ ├── meta │ │ │ │ ├── JsonMetaFileReader.java │ │ │ │ ├── PGSCatalogCategoryFile.java │ │ │ │ ├── PGSCatalogMetaFile.java │ │ │ │ └── TabMetaFileReader.java │ │ │ ├── proxy │ │ │ │ └── ProxyReader.java │ │ │ ├── scores │ │ │ │ ├── IRiskScoreCollection.java │ │ │ │ ├── MergedRiskScoreCollection.java │ │ │ │ └── RiskScoreCollection.java │ │ │ └── vcf │ │ │ │ ├── FastRegionVCFFileReader.java │ │ │ │ ├── FastVCFFileReader.java │ │ │ │ ├── IVCFFileReader.java │ │ │ │ ├── MinimalVariantContext.java │ │ │ │ └── VCFLineParser.java │ │ │ ├── model │ │ │ ├── Population.java │ │ │ ├── PopulationMap.java │ │ │ ├── ReferenceVariant.java │ │ │ ├── RiskScore.java │ │ │ ├── RiskScoreSummary.java │ │ │ ├── Sample.java │ │ │ └── ScorePopulationMap.java │ │ │ └── tasks │ │ │ ├── ApplyScoreTask.java │ │ │ ├── CreateHtmlReportTask.java │ │ │ ├── LiftOverScoreTask.java │ │ │ ├── MergeEffectsTask.java │ │ │ ├── MergeReportTask.java │ │ │ ├── MergeScoreTask.java │ │ │ ├── MergeVariantsTask.java │ │ │ └── ResolveScoreTask.java │ └── resources │ │ └── templates │ │ ├── default │ │ ├── components │ │ │ ├── distribution.html │ │ │ ├── samples.html │ │ │ ├── score_details.html │ │ │ └── score_list.html │ │ ├── images │ │ │ └── logo.svg │ │ ├── index.html │ │ ├── report.css │ │ ├── report.js │ │ └── report.json │ │ ├── multi-page │ │ ├── components │ │ │ ├── score_list.html │ │ │ └── score_list.js │ │ ├── index.html │ │ ├── report.json │ │ ├── samples.html │ │ └── score.html │ │ └── txt │ │ └── index.html └── test │ └── java │ └── genepi │ └── riskscore │ ├── commands │ ├── ApplyScoreCommandTest.java │ ├── CreateHtmlReportCommandTest.java │ ├── MergeEffectsCommandTest.java │ ├── MergeVariantsCommandTest.java │ └── ResolveScoreCommandTest.java │ ├── io │ ├── RiskScoreFileTest.java │ ├── dbsnp │ │ └── DbSnpReaderTest.java │ └── proxy │ │ └── ProxyReaderTest.java │ └── tasks │ ├── ApplyScoreTaskTest.java │ ├── CreateHtmlReportTaskTest.java │ ├── MergeEffectsTaskTest.java │ ├── MergeScoreTaskTest.java │ └── MergeVariantsTaskTest.java └── test-data ├── .gitignore ├── PGS000001.txt.gz ├── PGS000018.txt.gz ├── PGS000781.txt.gz ├── PGS000899.txt.gz ├── PGS000957.txt.gz ├── PGS000958.txt.gz ├── PRSWEB_PHECODE153_CRC-Huyghe_PT_UKB_20200608.txt ├── cancer-prsweb.tab ├── chains ├── hg19ToHg38.over.chain.gz └── hg38ToHg19.over.chain.gz ├── chr20.dose.vcf.gz ├── chr20.scores.2.csv ├── chr20.scores.2.csv.format ├── chr20.scores.2.flips.csv ├── chr20.scores.csv ├── chr20.scores.csv.format ├── chr20.scores.csv.gz ├── chr20.scores.csv.gz.format ├── dbsnp-index.small.txt.gz ├── dbsnp-index.small.txt.gz.tbi ├── effects.chunk1.txt ├── effects.chunk2.txt ├── effects.expected.txt ├── lpa.snps.sorted.txt.gz ├── lpa.snps.sorted.txt.gz.tbi ├── merged.expected.txt ├── output.csv ├── pgs-catalog-small.json ├── pgs-ids.txt ├── report.json ├── samples-population.txt ├── samples.txt ├── scores.chunk1.txt ├── scores.chunk2.txt ├── single.hg38.vcf ├── single.vcf ├── single.wrong_chr.vcf ├── small.vcf ├── test.chr1.vcf ├── test.chr2.vcf ├── test.chr2.wrong.vcf ├── test.scores.csv ├── test.scores.csv.format ├── test.scores2.csv ├── test.scores2.csv.format ├── 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