Comments (5)
The Javascript regex dialect looks close the Python one and is made available via in C++11, if we wanted to foist a C++11 requirement on users. (Probably still premature at this point.)
from khmer.
Actually, it looks like the POSIX regex support is in the GNU C library. Some reading on the Web seems to indicate that it is supported in other C libraries as well. We'll go with that.
from khmer.
I'm more concerned with the sledgehammer approach - adding a new requirement and a new library into khmer doesn't strike me as the simplest response to this issue :). But let's see how it goes...
from khmer.
Hey, I'm the one who's supposed to complain about additional dependencies. :-) (For example, our dependency on 'screed', which is not even up on PyPI.)
Like I mentioned above, it appears that the POSIX regex stuff is nearly ubiquitous in the Unix world (and you confirmed that it available on MacOS X). Given that it is implemented as part of the C library on most systems and that we are already using the C library (obviously), I don't see this as an additional dependency.
But, I agree, let's see how this goes. Would rather write one line of regex than 3 or 4 lines of C++ string methods, but maybe that's just me.
from khmer.
On Fri, Feb 15, 2013 at 10:46:43AM -0800, Eric McDonald wrote:
Hey, I'm the one who's supposed to complain about additional dependencies. :-) (For example, our dependency on 'screed', which is not even up on PyPI.)
Like I mentioned above, it appears that the POSIX regex stuff is nearly ubiquitous in the Unix world (and you confirmed that it available on MacOS X). Given that it is implemented as part of the C library on most systems and that we are already using the C library (obviously), I don't see this as an additional dependency.
Ahh, OK. In that case I agree.
But, I agree, let's see how this goes. Would rather write one line of regex than 3 or 4 lines of C++ string methods, but maybe that's just me.
Fair enough.
from khmer.
Related Issues (20)
- Filtering out reads with low-abundance k-mers (contaminant reads) HOT 4
- Normalize-by-median.py script as a module HOT 1
- Screed DeprecationWarning (Python 3.9) HOT 3
- Khmer (specifically `reverse_complement`) only intended for upper-case sequences? HOT 2
- Is the normalize-by-median.py script deterministic? HOT 2
- Malformed citation file
- script for digital normalization of shotgun mategenomic data HOT 8
- Error in khmer installation
- load-graph.py runtime HOT 1
- Error when Interleaving data HOT 1
- LICENSE bug report HOT 2
- normalize-by-median.py the total of the reads indicated in the report does not match the input
- Result differences from input bias HOT 3
- cppcheck is not reporting the many of the warnings which falls under style option/category HOT 1
- New count-min estimator
- https//canadatechmanufacturing
- Plaid Id
- Plaid Id
- Installation fails with Python 3.12 HOT 3
- khmer is unmaintained. what now? HOT 3
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from khmer.