├── .gitignore ├── LICENSE.txt ├── README.md ├── data ├── SG10000001_S1_L001_R1_001.bam └── SG10000001_S1_L001_R1_001.bam.bai ├── lib ├── apache-ant-1.8.2-bzip2.jar ├── argparse4j-0.1.0.jar ├── bcprov-jdk15on-152.jar ├── commons-compress-1.11 │ └── commons-compress-1.11.jar ├── commons-compress-1.4.1.jar ├── commons-jexl-2.1.1.jar ├── commons-logging-1.1.1.jar ├── htsjdk.jar ├── jackson-core-asl-1.9.13.jar ├── jackson-mapper-asl-1.9.13.jar ├── junit.jar ├── org.hamcrest.core_1.3.0.v201303031735.jar ├── snappy-java-1.0.3-rc3.jar ├── testng-5.5-jdk15.jar └── xz-1.5.jar ├── src └── com │ └── sg │ └── secram │ ├── Main.java │ ├── compression │ ├── BaseHalfByteMap.java │ ├── LossyQualityScore.java │ ├── SecramDataSeries.java │ ├── SecramEncodingKey.java │ ├── SecramFieldCodec.java │ ├── SecramRecordCodec.java │ └── SecramRecordCodecFactory.java │ ├── encryption │ ├── BouncyCastle_AES_CTR.java │ ├── DummyCipher.java │ ├── OPE.java │ ├── SECRAMEncryptionFactory.java │ └── SECRAMEncryptionMethod.java │ ├── example │ ├── Bam2SecramDir.java │ ├── Bam2SecramFile.java │ └── Secram2BamFile.java │ ├── impl │ ├── SECRAMContainerIterator.java │ ├── SECRAMFileConstants.java │ ├── SECRAMFileReader.java │ ├── SECRAMFileWriter.java │ ├── SECRAMIterator.java │ ├── SECRAMSecurityFilter.java │ ├── SecramIndex.java │ ├── converters │ │ ├── BAMRecordBuilder.java │ │ ├── Bam2Secram.java │ │ ├── Secram2Bam.java │ │ └── SecramRecordBuilder.java │ └── records │ │ ├── PosCigar.java │ │ ├── PosCigarFeature.java │ │ ├── PosCigarFeatureCode.java │ │ ├── ReadHeader.java │ │ └── SecramRecord.java │ ├── structure │ ├── SecramBlock.java │ ├── SecramBlockContentType.java │ ├── SecramCompressionHeader.java │ ├── SecramCompressionHeaderFactory.java │ ├── SecramContainer.java │ ├── SecramContainerFactory.java │ ├── SecramContainerIO.java │ ├── SecramContainerParser.java │ ├── SecramHeader.java │ └── SecramIO.java │ └── util │ ├── ReferenceUtils.java │ ├── SECRAMUtils.java │ └── 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