Reduce memory consumption of very high-resolution merges #408
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This PR addresses a high memory consumption issue when a large number of very high resolution coolers are merged. It should improve the performance not only of
cooler merge
but also ofcooler cload pairs
andcooler load
.In pre-calculating offsets to use for the merge execution plan, we were loading (and concatenating) all
bin1_offset
indexes into memory. This isn't an issue for typical coolers, but can become prohibitively large for many inputs at high resolutions, where a single index vector can be ~2GB in size at human 10bp resolution.bin1_offset
index incrementally during merge execution planning. This results in a drastic improvement for merges involving e.g. 100s of datasets.cooler cload pairs
andcooler load
, and the max-merge option tocooler load
, to give the user more flexibility in controlling maximum memory consumption during the actual merge epochs.