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Added mechanisms for retrieving tags by position within a sequence#749

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luizirber merged 5 commits into
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feature/tag_with_position
Feb 8, 2015
Merged

Added mechanisms for retrieving tags by position within a sequence#749
luizirber merged 5 commits into
masterfrom
feature/tag_with_position

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@ctb

@ctb ctb commented Feb 1, 2015

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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.

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ctb commented Feb 1, 2015

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(a review would be welcome, but not yet ready for merge.)

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ctb commented Feb 7, 2015

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  • Is it mergable?
  • Did it pass the tests?
  • If it introduces new functionality in scripts/ is it tested?
    Check for code coverage.
  • Is it well formatted? Look at make pep8, make diff_pylint_report,
    make cppcheck, and make doc output. Use make format and manual
    fixing as needed.
  • Did it change the command-line interface? Only additions are allowed
    without a major version increment. Changing file formats also requires a
    major version number increment.
  • Is it documented in the ChangeLog?
  • Was a spellchecker run on the source code and documentation after
    changes were made?

@ctb

ctb commented Feb 7, 2015

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Ready for review @luizirber @camillescott @mr-c

Comment thread khmer/_khmermodule.cc Outdated

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What is this comment?

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Removed.

Comment thread khmer/_khmermodule.cc Outdated

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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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ctb commented Feb 8, 2015

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Thanks @luizirber - ready for re-review.

@luizirber

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LGTM

luizirber added a commit that referenced this pull request Feb 8, 2015
Added mechanisms for retrieving tags by position within a sequence
@luizirber luizirber merged commit b63bd94 into master Feb 8, 2015
Comment thread khmer/_khmermodule.cc

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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

@mr-c mr-c mentioned this pull request Feb 11, 2015
mr-c added a commit that referenced this pull request Feb 11, 2015
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3 participants