Engine read caching. #4902
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Engine read caching. #4902
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Codecov Report
@@ Coverage Diff @@
## master #4902 +/- ##
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+ Coverage 18.644% 86.845% +68.201%
- Complexity 4635 32366 +27731
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Files 1261 1994 +733
Lines 73745 149492 +75747
Branches 11768 16506 +4738
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+ Hits 13749 129826 +116077
+ Misses 57944 13642 -44302
- Partials 2052 6024 +3972
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magicDGS
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Jun 18, 2018
| @Advanced | ||
| @Argument(fullName = "reads-look-ahead-window-size", shortName="reads-look-ahead-window-size", | ||
| doc = "Window size for reads look-ahead query caching") | ||
| protected int readsLookaheadWindowSize = 100 * 1024; |
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I don't think that this should be exposed to the user, but being similar to the feature-cache: it should be choosen by the walker-class what is the best value.
| * | ||
| * @return true if read caching should be used, otherwise false | ||
| */ | ||
| public boolean useReadCaching() { |
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This could be a getReadsLookaheadWindowSize instead, returning a value with the meaning of disable (0? -1?) and let each walker-class to choose how the cache is handled. A tool can always implement an argument to modify this value.
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Rebased this to do some testing with current master. |
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cmnbroad
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Feb 14, 2022
| ***************************************************************************************************/ | ||
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| /******************************************************** | ||
| * LocatableCache tests using SideReadInputCacheStrategy |
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This test is really testing SideReadInputCacheStrategy behavior, so maybe it should be moved to a SideReadInputCacheStrategyUnitTest class.
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Allow tools to opt-in for read caching (enabled in this PR for CNNScoreVariants and FilterAlignmentArtifacts) when issuing forward-only queries such as those used to query a ReadsContext for all reads backing each variant.
The cache matches the (sometimes surprising - see #4901) results that are returned when caching is not used, specifically that an unmapped but placed read that is mated with a mapped read is only returned if the start position overlaps the interval query interval, whereas the mapped read is returned if any part of the read overlaps the query interval.