Added mechanisms for retrieving tags by position within a sequence #749
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(a review would be welcome, but not yet ready for merge.) |
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Ready for review @luizirber @camillescott @mr-c |
| return NULL; | ||
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| if (strlen(kmer_s) < counting->ksize()) { // @@ |
| Py_BEGIN_ALLOW_THREADS | ||
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| HashIntoType kmer, kmer_f, kmer_r; | ||
| kmer = _hash(kmer_s, counting->ksize(), kmer_f, kmer_r); |
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GCC complained about kmer being defined but not used in this function, do you see it being used in the future? If not maybe just ignore the return value and remove it from the previous line?
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Thanks @luizirber - ready for re-review. |
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LGTM |
Added mechanisms for retrieving tags by position within a sequence
| } catch (_khmer_signal &e) { | ||
| PyErr_SetString(PyExc_ValueError, e.get_message().c_str()); | ||
| return NULL; | ||
| } |
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1356-1357 lack testing coverage and won't be called ever anyhow
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fixed!
On Tue, Feb 10, 2015 at 11:16:55AM -0800, Michael R. Crusoe wrote:
- try {
unsigned int pos = 1;KMerIterator kmers(seq, counting->ksize());
while (!kmers.done()) {HashIntoType kmer = kmers.next();if (set_contains(counting->all_tags, kmer)) {posns.push_back(pos);tags.push_back(kmer);}pos++;}- } catch (_khmer_signal &e) {
PyErr_SetString(PyExc_ValueError, e.get_message().c_str());return NULL;- }
1356-1357 lack testing coverage and won't be called ever anyhow
Reply to this email directly or view it on GitHub:
https://github.com/ged-lab/khmer/pull/749/files#r24441205
C. Titus Brown, ctbrown@ucdavis.edu
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Thanks; making new pull request
This is primitive functionality enabling certain sorts of queries into the graph from within Python. /cc @camillescott; at some point we should chat more about how this intersects with labeling.