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no non-missing arguments to max; returning -Inf error when calling tag clusters #115

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da-bar opened this issue May 14, 2024 · 1 comment

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@da-bar
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da-bar commented May 14, 2024

In some datasets I get the following error when doing the ctss clustering with distclu>

Filtering out CTSSs below threshold...
Clustering...
	-> LateBlastula_rep1
Error: BiocParallel errors
  1 remote errors, element index: 32
  301 unevaluated and other errors
  first remote error:
Error in h(simpleError(msg, call)): error in evaluating the argument 'values' in selecting a method for function 'Rle': invalid 'times' argument
In addition: Warning message:
In max(start(ctss.ipos.chr)) :
  no non-missing arguments to max; returning -Inf

The reason, some scaffold are missing tags on one of the strand.
The function should be aware of this issue, but it ignores the test. One reason, in ClusterFunctions.R, line 66, the statement identical(ctss.ipos.chr, IPos()) doesn't give TRUE when ctss.ipos.chr is empty.
Suggestions: use isEmpty(ctss.ipos.ch) or length(ctss.ipos.ch) == 0 for testing if empty.
What do you think about this solution, @charles-plessy ?

@charles-plessy
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Hi @da-bar , I have refactored the clustering functions in the devel branch, and the call to identical isn't there anymore. Can I ask you to test if this also solves the problem ? (and if results are unchanged)

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