├── .gitignore ├── BED ├── AGV6UTR_covered_merged.bed └── allGeneRegionsCanonical.HG19.GRCh37.bed ├── LICENSE ├── Phase ├── .gitignore ├── .project ├── .settings │ └── org.eclipse.jdt.core.prefs ├── META-INF │ └── MANIFEST.MF ├── libraries │ ├── commons-cli-1.4.jar │ └── picard.jar └── src │ ├── .gitignore │ ├── .project │ ├── pom.xml │ └── src │ └── smartPhase │ ├── ConfidencePair.java │ ├── FilteredVariantReader.java │ ├── HaplotypeBlock.java │ ├── MutableCloseableIterator.java │ ├── PhaseCountTriple.java │ ├── SimpleVariant.java │ ├── SmartPhase.java │ ├── VariantIterator.java │ ├── VariantStrandPair.java │ └── VariantTuple.java ├── README.md ├── UseCase ├── CEU.ped ├── CEU_UseCase.bam ├── CEU_UseCase.bam.bai ├── CEU_UseCase.vcf.gz ├── CEU_UseCase.vcf.gz.tbi └── README.md ├── Validation ├── README.md ├── SimulationPipeline.sh ├── ValidationPipeline.sh ├── extract_SmartPhase_stats.pl ├── extract_WhatsHap_results.pl ├── get_phasing_errors.py └── ped │ ├── CEU.ped │ └── YRI.ped ├── 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