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dib-lab / khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
http://khmer.readthedocs.io/
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Rename counting_hash and hashbits at Python layer #872

Closed ctb closed 9 years ago

ctb commented 9 years ago

I suggest counting_table and/or bytegraph instead of counting_hash, and bitgraph instead of hashbits. (@mr-c has already renamed stopped using 'hash' in our scripts and docs).

counting_table could default to bigcounts=yes, bytegraph could default to bigcounts=no, but otherwise be the same structure.

Reason: I found it silly to be using counting_hash in my VanBUG talk when I was talking about graphs.

mr-c commented 9 years ago

How about countgraph & graph?

ctb commented 9 years ago

On Sat, Mar 14, 2015 at 07:38:02PM -0700, Michael R. Crusoe wrote:

How about countgraph & graph?

Imprecise - wouldn't "graph" be a superset of "countgraph"? What about "nodegraph"?

We haven't really been using the 1-bit graph implementation lately, but we may well in the future, as well as expanding to additional kinds of graphs - exact graphs of various flavors, and different sized bins. So maybe we can think about that, too.

mr-c commented 9 years ago

+1 for nodegraph + countgraph

ctb commented 9 years ago

On Sat, Mar 14, 2015 at 07:43:39PM -0700, Michael R. Crusoe wrote:

+1 for nodegraph + countgraph

Excellent.

camillescott commented 9 years ago

+1 node/countgraph as well

anotherthomas commented 9 years ago

I am working on this issue. It's been postponed until after the python3 port to avoid merge conflicts.