Streaming unique-kmers.py using consume_fasta #1204
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This was referenced Jul 29, 2015
luizirber
force-pushed
the
feature/omp_streaming
branch
from
797124f to
e13f5f9
Compare
|
cc #1053 |
luizirber
force-pushed
the
feature/omp_streaming
branch
from
e13f5f9 to
1d003d2
Compare
|
Update: I moved |
|
|
|
||
| if (!PyArg_ParseTuple(args, "s", &filename)) { | ||
| if (!PyArg_ParseTuple(args, "s|O", &filename, &output_records_o)) { |
There was a problem hiding this comment.
Should output_records be a keyword on this method? I think it makes more sense, because calling it is a bit weird (check https://github.com/dib-lab/khmer/pull/1204/files#diff-7f09af630bd7b293c0827bba1d411617R120 for an example).
This also raises the question: do we want to do this in other places? We do have a lot of default arguments in the extension glue code that are not exposed nicely to Python land...
There was a problem hiding this comment.
keyword is fine by me; how about a post-2.0 issue for the 2nd question?
luizirber
force-pushed
the
feature/omp_streaming
branch
from
1d003d2 to
f7b94d0
Compare
luizirber
force-pushed
the
feature/omp_streaming
branch
from
a4716b4 to
01abd68
Compare
luizirber
force-pushed
the
feature/omp_streaming
branch
from
84106a2 to
28abbda
Compare
|
LGTM. Merge once the tests pass. |
luizirber
added a commit
that referenced
this pull request
Aug 10, 2015
Streaming unique-kmers.py using consume_fasta
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Revert
unique-kmers.pychanges and use consume_fasta again. I wrote awrite_recordequivalent in C++ for this, currently living inlib/HLLCounter.cc, but I think this should probably go inlib/read_parsers.cc.(reopening #1177 now that #1176 was merged)