George Pimm
George Pimm
Testing some implementations we have internally I've found the following code to perform quite well: https://gist.github.com/jorj1988/a2f2f14719d46074900dd563dc31a1c7 It does a delta >> zigzag >> expand to 32 bit >> streambyte encode
I've experimented with a prefix sum for shuffle and didnt see much of a performance increase for my test set. I'd be interested in seeing a more competent implementation of...
Hmm, I sort of see what you're saying, but I'm having trouble putting together code to implement it - do you have a psuedo code example of what youre suggesting?
thanks - ill take a look
Thats a new one - thanks @billytcl, We will take a look and try to work out whats going on internally... - George
A short term workaround might be to work in smaller batches, if that helps? If you are able to rerun with `POD5_DEBUG=1` set during the execution it may provide us...
Ok - no worries. Could you try using `view` rather than `inspect` - this will cut down the size of the input csv to subset: ```pod5 view --include "read_id, channel"...
Hi James, `num_minknow_events` is a count of the number of internal minknow events in the file, this can be used to estimate bases in the file, bu multiplying by some...
The values are calculated deep in the minknow analysis engine, where we have context over the ongoing state of each channel. Hope that helps, - George
I agree - I'll update. - George