Feature Discussion

[Adamtaranto]

Creating this as a thread to discuss possible new features. Would they be useful? Are they within the scope? Let's find out.

Some things I'd like to see:

• Multithreaded file and string consumption
• Min / Max count thresholding
• Remove records by kmer or hash
• Subset table with list of hashes or kmers
• Serialise the KmerCountTable objects to disk + load saved objects
• Add / Subtract count tables against each other
• Basic distance metrics i.e. Jaccard, cosine similarity?
• Track total length of sequence consumed into a table (this will differ slightly from total number of kmers)
• Store hash:kmer pairs as HashMap for looking up original kmers (make optional for efficiency?)
• Text dump of kmers and counts to file
• Make tables iterable i.e. yield (hash,count) or (kmer,count)
• Protein, Dayhoff, and hp encodings for k-mers.

Add some examples for common Python use cases:

• Output kmer counts that can be used as input for Genomescope or Smudgeplot
• Convert counts to histogram bins