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META-INF
- MANIFEST.MF
net
- sf
  - samtools
    - AbstractBAMFileIndex.java
    - AbstractSAMHeaderRecord.java
    - AlignmentBlock.java
    - apps
      - TimeChannel.java
      - TimeRandomAccessFile.java
    - BAMFileConstants.java
    - BAMFileReader.java
    - BAMFileSpan.java
    - BAMFileWriter.java
    - BAMIndex.java
    - BAMIndexContent.java
    - BAMIndexer.java
    - BAMIndexMetaData.java
    - BamIndexValidator.java
    - BAMIndexWriter.java
    - BAMRecord.java
    - BAMRecordCodec.java
    - Bin.java
    - BinaryBAMIndexWriter.java
    - BinaryCigarCodec.java
    - BinaryTagCodec.java
    - BinList.java
    - BrowseableBAMIndex.java
    - CachingBAMFileIndex.java
    - Chunk.java
    - Cigar.java
    - CigarElement.java
    - CigarOperator.java
    - DiskBasedBAMFileIndex.java
    - example
      - ExampleSamUsage.java
    - FileTruncatedException.java
    - FixBAMFile.java
    - LinearIndex.java
    - NotPrimarySkippingIterator.java
    - SAMBinaryTagAndValue.java
    - SAMException.java
    - SAMFileHeader.java
    - SAMFileReader.java
    - SAMFileSource.java
    - SAMFileSpan.java
    - SAMFileWriter.java
    - SAMFileWriterFactory.java
    - SAMFileWriterImpl.java
    - SAMFormatException.java
    - SAMProgramRecord.java
    - SAMReadGroupRecord.java
    - SAMRecord.java
    - SAMRecordComparator.java
    - SAMRecordCoordinateComparator.java
    - SAMRecordIterator.java
    - SAMRecordQueryNameComparator.java
    - SAMRecordSetBuilder.java
    - SAMRecordUtil.java
    - SAMSequenceDictionary.java
    - SAMSequenceRecord.java
    - SAMSortOrderChecker.java
    - SAMTag.java
    - SAMTagUtil.java
    - SAMTestUtil.java
    - SAMTextHeaderCodec.java
    - SAMTextReader.java
    - SAMTextWriter.java
    - SAMTools.java
    - SAMUtils.java
    - SAMValidationError.java
    - SQTagUtil.java
    - TextCigarCodec.java
    - TextTagCodec.java
    - TextualBAMIndexWriter.java
    - util
      - AsciiLineReader.java
      - AsciiLineReaderImpl.java
      - AsciiWriter.java
      - BinaryCodec.java
      - BlockCompressedFilePointerUtil.java
      - BlockCompressedInputStream.java
      - BlockCompressedOutputStream.java
      - BlockCompressedStreamConstants.java
      - BlockGunzipper.java
      - BufferedLineReader.java
      - CloseableIterator.java
      - CloserUtil.java
      - CoordMath.java
      - DateParser.java
      - HttpUtils.java
      - IOUtil.java
      - Iso8601Date.java
      - LineReader.java
      - Md5CalculatingInputStream.java
      - Md5CalculatingOutputStream.java
      - PeekIterator.java
      - RuntimeEOFException.java
      - RuntimeIOException.java
      - SeekableBufferedStream.java
      - SeekableFileStream.java
      - SeekableHTTPStream.java
      - SeekableStream.java
      - SequenceUtil.java
      - SortingCollection.java
      - SortingLongCollection.java
      - StopWatch.java
      - StringLineReader.java
      - StringUtil.java