├── .github └── ISSUE_TEMPLATE │ └── error-report-template.md ├── .gitignore ├── LICENSE ├── README.md ├── manifest.mf ├── nbproject ├── build-impl.xml ├── genfiles.properties ├── licenseheader.txt ├── project.properties └── project.xml ├── recipe ├── build.sh └── meta.yaml ├── rnabloom ├── rnabloom_logo.png ├── src └── rnabloom │ ├── RNABloom.java │ ├── bloom │ ├── BloomFilter.java │ ├── BloomFilterInterface.java │ ├── CascadingBloomFilter.java │ ├── CountingBloomFilter.java │ ├── CountingBloomFilterInterface.java │ ├── PairedKeysBloomFilter.java │ ├── PairedKeysPartitionedBloomFilter.java │ ├── SimpleBloomFilter.java │ ├── buffer │ │ ├── AbstractLargeBitBuffer.java │ │ ├── AbstractLargeByteBuffer.java │ │ ├── BufferComparator.java │ │ ├── LargeBitBuffer.java │ │ ├── LargeByteBuffer.java │ │ ├── UnsafeBitBuffer.java │ │ └── UnsafeByteBuffer.java │ └── hash │ │ ├── CanonicalHashFunction.java │ │ ├── CanonicalLeftVariantsNTHashIterator.java │ │ ├── CanonicalNTHashIterator.java │ │ ├── CanonicalPairedNTHashIterator.java │ │ ├── CanonicalPredecessorsNTHashIterator.java │ │ ├── CanonicalRightVariantsNTHashIterator.java │ │ ├── CanonicalStrobe3HashIterator.java │ │ ├── CanonicalStrobeHashIterator.java │ │ ├── CanonicalSuccessorsNTHashIterator.java │ │ ├── HashFunction.java │ │ ├── HashedInterval.java │ │ ├── HashedPositions.java │ │ ├── LeftVariantsNTHashIterator.java │ │ ├── MinimizerHashIterator.java │ │ ├── NTHash.java │ │ ├── NTHashIterator.java │ │ ├── PairedNTHashIterator.java │ │ ├── PredecessorsNTHashIterator.java │ │ ├── ReverseComplementNTHashIterator.java │ │ ├── ReverseComplementPairedNTHashIterator.java │ │ ├── RightVariantsNTHashIterator.java │ │ ├── Strobe3HashIterator.java │ │ ├── StrobeHashIterator.java │ │ ├── StrobeHashIteratorInterface.java │ │ └── SuccessorsNTHashIterator.java │ ├── graph │ ├── BloomFilterDeBruijnGraph.java │ ├── CanonicalKmer.java │ └── Kmer.java │ ├── io │ ├── CompressedFastaRecord.java │ ├── Constants.java │ ├── ExtendedPafRecord.java │ ├── FastGZIPOutputStream.java │ ├── FastaFilteredSequenceIterator.java │ ├── FastaPairReader.java │ ├── FastaReader.java │ ├── FastaRecord.java │ ├── FastaWriter.java │ ├── FastaWriterWorker.java │ ├── FastqFilteredReader.java │ ├── FastqFilteredSequenceIterator.java │ ├── FastqPairReader.java │ ├── FastqReader.java │ ├── FastqRecord.java │ ├── FastxFilePair.java │ ├── FastxPairReader.java │ ├── FastxPairSequenceIterator.java │ ├── FastxReaderInterface.java │ ├── FastxSequenceIterator.java │ ├── FileFormatException.java │ ├── NucleotideBitsReader.java │ ├── NucleotideBitsWriter.java │ ├── PafReader.java │ ├── PafRecord.java │ ├── PairedReadSegments.java │ └── SequenceFileIteratorInterface.java │ ├── olc │ ├── ComparableInterval.java │ ├── HashedInterval.java │ ├── Interval.java │ ├── Layout.java │ ├── NamedInterval.java │ ├── OverlapCoords.java │ └── OverlapLayoutConsensus.java │ └── util │ ├── BitSequence.java │ ├── CommandLine.java │ ├── Common.java │ ├── FileUtils.java │ ├── FlaggedBitSequence.java │ ├── FloatRollingWindow.java │ ├── GraphUtils.java │ ├── IntervalUtils.java │ ├── LongRollingWindow.java │ ├── MiniFloat.java │ ├── NTCardHistogram.java │ ├── PafUtils.java │ ├── PolyAAdaptorTrimmer.java │ ├── PolyATailFinder.java │ ├── SeqBitsUtils.java │ ├── SeqSubsampler.java │ ├── SeqUtils.java │ ├── Timer.java │ └── WeightedBitSequence.java └── test └── Tests.java /.github/ISSUE_TEMPLATE/error-report-template.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bcgsc/RNA-Bloom/HEAD/.github/ISSUE_TEMPLATE/error-report-template.md -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | /nbproject/private/ 2 | /dist/ 3 | -------------------------------------------------------------------------------- /LICENSE: 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