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broadinstitute / catch / 370
94%
master: 94%

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Build:
LAST BUILD BRANCH: v1.5.1
DEFAULT BRANCH: master
Ran 11 Jul 2022 06:15PM UTC
Jobs 2
Files 67
Run time 2min
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haydenm
Make default clustering method be simple search for connected components

This commit adds `utils.cluster.find_connected_components()` to identify
connected components in a graph in which sequences are adjacent iff
their estimated distance is within a threshold. As with previous
clustering, distances with this method continue to be estimated using a
MinHash family, e.g., as in the Mash paper (Ondov et al. 2016).

The commit makes this method the default for clustering because it
should be less memory-intensive than the existing hierarchical approach
for large numbers of input sequences; it does not need to store a
pairwise distance matrix. It adds an argument to design.py to specify
the clustering method, so the hierarchical clustering method---which
appears to be faster---can still be used.

1756 of 1998 branches covered (87.89%)

90 of 90 new or added lines in 3 files covered. (100.0%)

5536 of 5862 relevant lines covered (94.44%)

1.89 hits per line

Jobs
ID Job ID Ran Files Coverage
1 370.1 11 Jul 2022 06:17PM UTC 0
94.56
Travis Job 370.1
2 370.2 11 Jul 2022 06:15PM UTC 0
94.44
Travis Job 370.2
Source Files on build 370
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