├── .gitignore ├── .travis.yml ├── AUTHORS.md ├── CHANGES ├── LICENSE ├── README.md ├── appveyor.yml ├── gradle.properties ├── gradle └── wrapper │ ├── gradle-wrapper.jar │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat └── src ├── main └── kotlin │ └── org │ └── jetbrains │ └── bio │ ├── BBRomBuffer.kt │ ├── BetterSeekableBufferedStream.kt │ ├── CompressionType.kt │ ├── EndianAwareDataSeekableStream.kt │ ├── EndianBufferFactory.kt │ ├── EndianSeekableDataInput.kt │ ├── FastByteArrayOutputStream.kt │ ├── HeavyweightRomBuffer.kt │ ├── LightweightRomBuffer.kt │ ├── MMBRomBuffer.kt │ ├── MMBRomBufferFactory.kt │ ├── OrderedDataOutput.kt │ ├── RomBuffer.kt │ ├── RomBufferFactory.kt │ ├── ScoredInterval.kt │ ├── SeekableDataInput.kt │ ├── Support.kt │ ├── SynchronizedStreamAccessRomBuffer.kt │ ├── big │ ├── BPlusTree.kt │ ├── Bed.kt │ ├── BedGraph.kt │ ├── BigBed.kt │ ├── BigFile.kt │ ├── BigSummary.kt │ ├── BigWig.kt │ ├── Interval.kt │ ├── RTreeIndex.kt │ └── Wig.kt │ └── tdf │ ├── TdfDebug.kt │ ├── TdfFile.kt │ └── TdfTile.kt └── test ├── kotlin └── org │ └── jetbrains │ └── bio │ ├── BetterSeekableBufferedStreamTest.kt │ ├── EndianAwareDataSeekableStreamTest.kt │ ├── FastByteArrayOutputStreamTest.kt │ ├── RomBufferTest.kt │ ├── SeekableDataIOTest.kt │ ├── SupportTest.kt │ ├── TestSupport.kt │ ├── big │ ├── BPlusTreeTest.kt │ ├── BedEntryTest.kt │ ├── BedGraphTests.kt │ ├── BigBedFileTest.kt │ ├── BigFileTest.kt │ ├── BigWigFileTest.kt │ ├── IntervalTests.kt │ ├── RTreeIndexTest.kt │ ├── WigTests.kt │ └── ZoomLevelTest.kt │ └── tdf │ ├── TdfDebugTest.kt │ └── TdfFileTest.kt └── resources ├── bed12.nocolor.bed ├── bed6p4.bed ├── bed9.bb ├── concurrent.bb ├── concurrent.bw ├── concurrent.tdf ├── empty.bb ├── empty.bw ├── empty.tdf ├── example.bed12.bed ├── example.bed3.bed ├── example.bed6.bed ├── example.bed9.bed ├── example.igv ├── example.tdf ├── example.wig ├── example1-compressed.bb ├── example1.bb ├── example1.bed ├── example2.bb ├── example2.bw ├── example3.bb ├── example4.bb ├── f1.chrom.sizes ├── f2.chrom.sizes ├── fixed_step.bw ├── fixed_step_with_span.bw ├── hg19.chrom.sizes.gz ├── reduction_overflow.bed ├── variable_step.bw └── variable_step_with_span.bw /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JetBrains-Research/big/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JetBrains-Research/big/HEAD/.travis.yml -------------------------------------------------------------------------------- /AUTHORS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JetBrains-Research/big/HEAD/AUTHORS.md -------------------------------------------------------------------------------- /CHANGES: 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