[Bioc-devel] ShortReadQ Serialisation Slow and Creates Large File

[Dario Strbenac]

Good day,

Accidentally using save instead of writeFastq lead me to noticing how large a ShortReadQ object on disk is. A small set of reads 

> RNAreads
class: ShortReadQ
length: 42680 reads; width: 50..100 cycles

was saved two ways. As a text file, they take 11 MB uncompressed. But, when saved in binary format, the size on disk is 2.0 GB. Is a lot of unnecessary detail saved when the object is serialised?

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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia