├── .circleci └── config.yml ├── .dockerignore ├── .gitignore ├── Dockerfile ├── LICENSE.txt ├── NOTICE.txt ├── README.md ├── bin ├── seqspark └── seqspark-db ├── conf ├── log4j.properties └── reference.conf ├── docs ├── index.html ├── manual.md ├── reference.md └── spark.md ├── install ├── project └── assembly.sbt └── src ├── main ├── resources │ └── reference.conf └── scala │ └── org │ └── dizhang │ └── seqspark │ ├── MetaAnalysis.scala │ ├── SeqSpark.scala │ ├── SingleStudy.scala │ ├── annot │ ├── Chain.scala │ ├── IntervalTree.scala │ ├── Location.scala │ ├── NucleicAcid.scala │ ├── RefGene.scala │ ├── Regions.scala │ ├── VariantAnnotOp.scala │ ├── VariantDB.scala │ └── dbNSFP.scala │ ├── assoc │ ├── AssocMaster.scala │ ├── AssocMethod.scala │ ├── Burden.scala │ ├── Encode.scala │ ├── SKAT.scala │ ├── SKATO.scala │ ├── SKATO2.scala │ ├── SNV.scala │ ├── SumStat.scala │ └── VT.scala │ ├── ds │ ├── Bed.scala │ ├── Counter.scala │ ├── Genotype.scala │ ├── Pedigree.scala │ ├── Phenotype.scala │ ├── Region.scala │ ├── SafeMatrix.scala │ ├── SemiGroup.scala │ ├── SummaryStatistic.scala │ ├── VCF.scala │ └── Variant.scala │ ├── meta │ ├── MetaMaster.scala │ └── MetaMethod.scala │ ├── numerics │ ├── Integrate.scala │ ├── Qags.scala │ ├── Qelg.scala │ ├── Qk21.scala │ ├── Qpsrt.scala │ └── package.scala │ ├── stat │ ├── Emmax.scala │ ├── HypoTest.scala │ ├── Kinship.scala │ ├── LCCSDavies.scala │ ├── LCCSLiu.scala │ ├── LCCSResampling.scala │ ├── LinearCombinationChiSquare.scala │ ├── NonCentralChiSquare.scala │ ├── PCA.scala │ ├── Regression.scala │ ├── Resampling.scala │ ├── ScoreTest.scala │ ├── TestResult.scala │ └── WaldTest.scala │ ├── util │ ├── Command.scala │ ├── ConfigValue.scala │ ├── Constant.scala │ ├── General.scala │ ├── GroupParser.scala │ ├── InputOutput.scala │ ├── LogicalParser.scala │ ├── Opt.scala │ ├── QueryParser.scala │ ├── SeqContext.scala │ └── UserConfig.scala │ └── worker │ ├── Annotation.scala │ ├── Association.scala │ ├── Export.scala │ ├── Genotypes.scala │ ├── Import.scala │ ├── Pipeline.scala │ ├── QualityControl.scala │ ├── Samples.scala │ ├── Variants.scala │ └── package.scala └── test ├── resources ├── anno.conf ├── assoc.conf ├── demo.conf ├── geno.dat ├── geno2.dat ├── log4j.properties ├── pheno.tsv ├── qc.conf └── reference.conf └── scala └── org └── dizhang └── seqspark ├── BaseSpecs.scala ├── SingleStudySpec.scala ├── assoc ├── SKATO2Spec.scala ├── SKATOSpec.scala └── SKATSpec.scala ├── ds └── GenotypeSpec.scala ├── numerics ├── IntegrateSpec.scala ├── Qk21Spec.scala └── QpsrtSpec.scala └── util ├── LogicalParserSpec.scala ├── QueryParserSpec.scala └── UserConfigSpec.scala /.circleci/config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/statgenetics/seqspark/HEAD/.circleci/config.yml -------------------------------------------------------------------------------- /.dockerignore: 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