search

dib-lab / kProcessor

kProcessor: kmers processing framework.
https://kprocessor.readthedocs.io
BSD 3-Clause "New" or "Revised" License
11 stars 1 forks source link

kProcessor interface #86

Open shokrof opened 3 years ago

shokrof commented 3 years ago

kDataFrame.hpp: create an interface for all the public functions classes: 1) kDataframeIterator(not _kDataframeIterator) 2) kDataframe 3) dbgIterator 4) kDataframeMQF-MAP-PHMAP

Algorithms.hpp: 1) parseSequences(allversions) 2) countKmersFromFile and string 3)load KMC 4) transform and transform in place 5) filter 2 versions 6) aggregate 2 versions 7) merge 8) union and intersect and Diff 9) you decide about the kmerdecocer fns 10) index and index mega and index priorityqueue 11) inner join

defaultColumn.hpp: 1) Column 2) vectorColumn: it is a template make a version for int,bool,double,uint32_t 3) mixVectors 4)QueryColorColumn 5) prefixtrie 6) dedupicated column it a template make a version for: a) deduplicatedColumn<vector, mixVectors> b) deduplicatedColumn<vector, prefixTrie> c) deduplicatedColumn<vector, insertColorColumn>

mr-eyes commented 3 years ago

Please note that functions with anonymous functions as input can't be wrapped like:

There's a file called extend_algorithms that we can add custom versions of the functions in it with unique names. The currently implemented functions in that file are extracted from the kDifferentialExpression usecase.

shokrof commented 3 years ago

I want to make sure that I understand correctly! you finished the wrapper for those functions but it cant take python lambda functions and has to use functions from extend algorithms.

mr-eyes commented 3 years ago

Yes, passing lambda function in Python wrapper isn't supported.

On Sun, Aug 29, 2021, 1:35 PM Mostafa Shokrof @.***> wrote:

I want to make sure that I understand correctly! you finished the wrapper for those functions but it cant take python lambda functions and has to use functions from extend algorithms.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dib-lab/kProcessor/issues/86#issuecomment-907776730, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABWVPKDMGPMI6D3GJIYAK63T7ILQXANCNFSM5CEO2JEA .