Partition sweep #216
Partition sweep #216
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Pull request merged into ged-lab/bleeding-edge
…g-edge Updates since graceful-fail2 pull
Bleeding edge
…es explicit things i hear)
…ith python glue, appear to be outputting correct colors
Partition sweep
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Test FAILed. |
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test this please |
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Test PASSed. |
| # consume the partitioned fasta with which to label the graph | ||
| ht = khmer.LabelHash(K, HT_SIZE, N_HT) | ||
| print >>sys.stderr, 'consuming fastp...' | ||
| ht.consume_partitioned_fasta_and_tag_with_labels(input_fastp) |
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Is input_fastp optional? If it is then you need to deal with the fact that it may be empty. If it isn't (as I suspect) then tell the parser above
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Test PASSed. |
| * Find all labels associated with the sequence | ||
| * For now, check /every/ k-mer with find_all_tags | ||
| */ | ||
| unsigned int LabelHash::sweep_sequence_for_labels(const std::string& seq, |
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This method has no code testing coverage
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Please fix the two long lines left and add unit tests for labelhash_consume_sequence_and_tag_with_labels & LabelHash::sweep_sequence_for_labels. Assuming that nothing else pops up from your fixes I will then merge |
…sequence_and_tag_with_labels
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Test FAILed. |
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Test FAILed. |
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please test this Jed |
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The function sweep_sequence_for_labels was deprecated in favor of sweep_label_neighborhood; it has been removed. |
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Test PASSed. |
Bugs found by coverity from partition_sweep #216
Bugs found by coverity from partition_sweep #216
Merged branch from cswelcher/khmer to ged-lab/khmer; new pull request reflecting that.
See here for original comments.