Investigate performance of buffering for GemMappabilityReader

magicDGS / ReadTools

A Universal Toolkit for Handling Sequence Data from Different Sequencing Platforms

https://magicdgs.github.io/ReadTools/

MIT License

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Open magicDGS opened 5 years ago

magicDGS commented 5 years ago

The implementation in #480 is working, but it is reading byte by byte the sequence. A possibility to improve performance is to:

Use an internal buffer to maintain cache bytes (using FastLineReader.readToEndOfOutputBufferOrEoln)
Change the reader implementation in use (FastLineReader vs. other): I've already tried a BufferedLineReader, but I found problems with eol/eof.