broadinstitute / catch
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haydenm 
Parallelize creation of distance matrix for clustering

Filling in the condensed distance matrix, in the cluster module, is (by
far) the bottleneck of clustering input sequences. But this can be
easily parallelized. This commit uses a multiprocessing.Pool to break up
entries in the condensed matrix, and has separate processes fill in
those entries.

1516 of 1709 branches covered (88.71%)

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5193 of 5459 relevant lines covered (95.13%)

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Builds Branch Commit Type Ran Committer Via Coverage
294 cluster-genomes Parallelize creation of distance matrix for clustering Filling in the condensed distance matrix, in the cluster module, is (by far) the bottleneck of clustering input sequences. But this can be easily parallelized. This commit uses a multiprocess... push haydenm travis-ci-com pending completion  
295 cluster-genomes Parallelize creation of distance matrix for clustering Filling in the condensed distance matrix, in the cluster module, is (by far) the bottleneck of clustering input sequences. But this can be easily parallelized. This commit uses a multiprocess... Pull #25 web-flow travis-ci-com pending completion  
293 cluster-genomes Describe --cluster-and-design-separately argument in README Pull #25 web-flow travis-ci-com pending completion  
292 cluster-genomes Describe --cluster-and-design-separately argument in README push haydenm travis-ci-com pending completion  
291 cluster-genomes Add --cluster-from-fragments argument to design.py push haydenm travis-ci-com pending completion  
290 cluster-genomes Pass along target_genomes as a method argument This commit attempts to make sure that filter objects do not store state dependent on what they are filtering (probes and their target genomes). This is necessary to re-use the same filter object mul... push haydenm travis-ci-com pending completion  
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