Replace memoizing cache for parsed CIGARs with core.memoize's LU cache #189
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
cljam has a memoizing cache for parsed CIGAR strings, and it tends to limitlessly increase in size after a long-term process such as pileup. The following chart shows how large the whole memory usage got during a certain run of variant call using cljam's pileup. Note that the bottom line of the used heap size is steadily getting higher as time goes along:
This PR replaces the memoizing cache with core.memoize's LU cache, limiting the cache size to an appropriate upper bound. Also, it defines a new system property named
cljam.sam.cigar.cache-size
to specify the upper bound of cache size when launching the JVM.After applying the change, memory usage would grow as follows. In this case, the bottom line keeps as low as the beginning throughout the whole run.
See here for the detailed data for the above charts.