Compressed list data structure

[jkanche]

• compressed list data structure
• rds2py wrapper for compressed list
• migrating genomicrangeslist to use compressed lists

[hpages]

Interesting! For the record the CompressedList representation in Bioconductor started as a hack to work around the inefficiency of the more natural/straighforward SimpleList representation. With SimpleList you just create your individual S4 objects, store them in an ordinary list, and process that thing with lapply or for loops. However this approach is extremely inefficient when the list contains thousands or millions of S4 objects. Are you seeing this kind of bottlenecks in Python too? Just curious.

[jkanche]

I haven't done any benchmarks, but my guess is its going to be inefficient as well in python, example, its probably efficient to apply a function on a single numpy vector than a list of numpy vectors.

[jkanche]

also BiocPy/GenomicRanges#148

[jkanche]

working on https://github.com/biocpy/compressed-lists