Repository navigation
Re-implementing rowsum/colsum for HDF5Matrix #41
Description
I just noticed that bsseq has been broken in devel for a while due to the removal of the rowsum,HDF5Matrix-method (which I okayed back in 1a6a44f#comments).
I now remember why I had this method: if the data are so large that they need to be stored in HDF5 then the result of rowsum()/colsum() may itself be so large that it can't be stored in memory.
Therefore, the method I had allowed for this by allowing the result to be written to an HDF5RealizationSink (it also allowed me some extra control over the result, such as writing 2 separate rowsum()s to the same file as in PeteHaitch/DelayedMatrixStats@27712d7).
Would it be possible to have a rowsum()/colsum() that supports realizing the result to a RealizationSink as it goes?
I will try to find time to do this if you're okay with it.
Activity
hpages commentedon Mar 5, 2019
I see. I didn't realize you had a use case for writing the result of
rowsum()orcolsum()to a file, sorry. I will implement this.lshep commentedon Mar 28, 2019
Any chance of getting this change sooner than later so bsseq can pass on the devel builder before the release? Its been broken since 2/01/19
PeteHaitch commentedon Apr 17, 2019
Hi @hpages, will you have time to do this before the BioC 3.9 deadline or should I backport the functionality to bsseq as an internal helper function?
Add .colsum() and .rowsum()