Addition of threading in GroupReadsByUmi and some other performance optimizations. #950
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Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #950 +/- ##
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Coverage 95.61% 95.62%
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Files 126 126
Lines 7321 7354 +33
Branches 504 502 -2
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+ Hits 7000 7032 +32
- Misses 321 322 +1
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nh13
approved these changes
Dec 2, 2023
| .getOrElse(-1) | ||
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| if (searchFromIdx >= 0) { | ||
| val hits = taskSupport match { |
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Since taskSupport is defined outside this loop, would you consider making a partial function to use here (or use currying), so you don't have to match each time?
| @@ -513,13 +577,14 @@ class GroupReadsByUmi | |||
| @arg(flag='x', doc= """ | |||
| |DEPRECATED: this option will be removed in future versions and inter-contig reads will be | |||
| |automatically processed.""") | |||
| @deprecated val allowInterContig: Boolean = true | |||
| @deprecated val allowInterContig: Boolean = true, | |||
| @arg(flag='@', doc="Number of threads to use when comparing UMIs. Only recommended for amplicon or similar data.") val threads: Int = 1, | |||
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Suggested change
| @arg(flag='@', doc="Number of threads to use when comparing UMIs. Only recommended for amplicon or similar data.") val threads: Int = 1, | |
| @arg(flag='@', doc="Number of threads to use when comparing UMIs. Only recommended for amplicon or similar data.") val threads: Int = 1, |
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