fix case-sensitivity of python-facing k-mer functions

[camillescott]

Currently, several functions exposed in python-land are case sensitive in regards to hashing. For example,

1. get
2. forward_hash
3. consume -- not sure

The result is that python code which deals directly with k-mers can fail silently on mixed-case sequence.

Assigning myself. Potential solution: wrap these functions in init.py and call upper(). Seems like a lot of overhead, though I would presume any code working with large numbers of individual k-mers would be moved to c++ land anyway.

[ctb]

On Wed, Apr 02, 2014 at 10:16:41AM -0700, Camille Scott wrote:

Currently, several functions exposed in python-land are case sensitive in regards to hashing. For example,

1. get
2. forward_hash
3. consume -- not sure

The result is that python code which deals directly with k-mers can fail silently on mixed-case sequence.

Assigning myself. Potential solution: wrap these functions in init.py and call upper(). Seems like a lot of overhead, though I would presume any code working with large numbers of individual k-mers would be moved to c++ land anyway.

I think the Python functions in _khmermodule should call uppercase, if
they don't do it in the lib/ land.

[mr-c]

@camillescott Any progress?

[mr-c]

@camillescott @ctb Does this need to go into the known-issues list? My understanding is that it doesn't impact script users, only Python/C++ API users.

[ctb]

no need

[ctb]

The command line issue is dealt with in #1435. This issue can remain around for when we start making guarantees about the Python API.