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cnobles / iGUIDE

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.
https://iguide.readthedocs.io/en/latest/
GNU General Public License v3.0
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High memory requirement for issue #38

Closed cnobles closed 5 years ago

cnobles commented 5 years ago

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

cnobles commented 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.