Closed cnobles closed 5 years ago
This issue has been resolved (for now) with a revision to the BLAT coupling algorithm. The major change here was a switchover from using GRanges exclusively to using GRanges and indices in the form of compressed atomic vectors (from the IRanges package). Most changes were implemented in commit 961c96a98f01819e597200ea0fd7216f6557a939, while a working version is available in release v0.9.9.
When running large datasets, this line is the start of the high memory issue that can prevent scalable increase in processing. Look into alternatives.
https://github.com/cnobles/iGUIDE/blob/00981f0099905251d4b804e510203b67bbbb11ce/tools/rscripts/couple.R#L628