├── .gitignore ├── AlignerBoost ├── .classpath ├── .gitignore ├── .gitignore~ ├── .project ├── .settings │ └── org.eclipse.jdt.core.prefs ├── COPYRIGHT ├── LICENSE.txt ├── README.md ├── examples │ ├── AB_demo_experiment_design.conf │ └── README.example ├── lib │ ├── ant-1.8.1-apache-bcel.jar │ ├── bcel-5.2.jar │ ├── commons-math3-3.6.1-javadoc.jar │ ├── commons-math3-3.6.1.jar │ ├── htsjdk-2.1.1.jar │ └── libIntelDeflater.so └── src │ └── edu │ └── upenn │ └── egricelab │ ├── AlignerBoost │ ├── AlignerBoost.java │ ├── EnvConstants.java │ ├── Fastq2NR.java │ ├── FastqReadQC.java │ ├── FilterSAMAlignPE.java │ ├── FilterSAMAlignSE.java │ ├── NGSExpDesign.java │ ├── PrepareFastqQCCmd.java │ ├── PrepareFilterAlnCmd.java │ ├── PrepareMapCmd.java │ ├── PrepareNRCmd.java │ ├── PrepareTrimCmd.java │ ├── SAMAlignFixer.java │ ├── SNP.java │ ├── UpdateMappedStats.java │ ├── UpdateNRStats.java │ ├── UpdateTotalStats.java │ ├── UpdateTrimmedStats.java │ ├── package-info.java │ └── utils │ │ ├── BedToAbsCover.java │ │ ├── BedToWig.java │ │ ├── ClassSummSAM.java │ │ ├── ClassifyBED.java │ │ ├── ClassifySAM.java │ │ ├── ClassifyVCF.java │ │ ├── FilterSamById.java │ │ ├── FilterWigFix.java │ │ ├── FilterWigVar.java │ │ ├── GTypeIndex.java │ │ ├── GenomeInterval.java │ │ ├── IUPACNucl.java │ │ ├── PercentProcessStatusTask.java │ │ ├── ProcessStatusTask.java │ │ ├── SamToAbsCover.java │ │ ├── SamToBinCover.java │ │ ├── SamToCoverSumm.java │ │ ├── SamToRegionCount.java │ │ ├── SamToRelCover.java │ │ ├── SamToWig.java │ │ ├── Stats.java │ │ ├── StringUtils.java │ │ ├── WigFixToRegionRelCover.java │ │ ├── WigVarToRegionRelCover.java │ │ └── package-info.java │ └── ucsc │ ├── BED.java │ ├── BED12.java │ ├── BED4.java │ ├── BED6.java │ ├── ColorRGB.java │ ├── GFF.java │ ├── GFF3.java │ ├── GTF.java │ └── package-info.java ├── README.md └── test └── AB_demo_experiment_design.conf /.gitignore: -------------------------------------------------------------------------------- 1 | test/ 2 | 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