Open camillescott opened 10 years ago
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,
- get
- forward_hash
- 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.
@camillescott Any progress?
@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.
no need
The command line issue is dealt with in #1435. This issue can remain around for when we start making guarantees about the Python API.
Currently, several functions exposed in python-land are case sensitive in regards to hashing. For example,
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.