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broadinstitute / catch / 401
94%
master: 94%

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Build:
LAST BUILD BRANCH: v1.5.1
DEFAULT BRANCH: master
Ran 15 Sep 2022 05:40PM UTC
Jobs 2
Files 67
Run time 3min
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haydenm
Fix bug in set_cover_filter with no candidate probes

There can be some cases where set_cover_filter is run with no input
candidate probes. For instance, if sequences are clustered and a
cluster/grouping has just 1 sequence that is both short (roughly the
length of a probe) and contains a string of Ns, then no candidate probes
will be constructed for it. This may happen sporadically because there
is randomness in the clustering algorithm.

In that case of a grouping with no input probes, set_cover_filter had
crashed. The call to
`probe.construct_kmer_probe_map_to_find_probe_covers()` on line 398 of
set_cover_filter.py returns an empty kmer_probe_map. Then, the call to
`probe.SharedKmerProbeMap.construct()` leads to a ValueError (line 708
of probe.py).

This commit fixes that case by checking for 0 candidate probes and
ensuring that the filter runs successfully, yielding 0 probes.

1822 of 2072 branches covered (87.93%)

19 of 19 new or added lines in 3 files covered. (100.0%)

5723 of 6070 relevant lines covered (94.28%)

1.89 hits per line

Jobs
ID Job ID Ran Files Coverage
1 401.1 15 Sep 2022 05:40PM UTC 0
94.28
Travis Job 401.1
2 401.2 15 Sep 2022 05:43PM UTC 0
94.28
Travis Job 401.2
Source Files on build 401
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