Improve performance of BAM sequence encoding #35
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totakke
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Apr 3, 2017
src/cljam/util/sam_util.clj
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| (->> (for [i nibble-table j nibble-table] [i j]) | ||
| (apply concat) | ||
| cstr/join))) | ||
| (defonce ^:private ^:const base->nibble "=ACMGRSVTWYHKDBN") |
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base->nibble is not appropriate name. foo->bar should be used for a converter function.
Why using defonce? defonce has a merit when reloading a namespace. In this case, it seems to have no merit. Also two-bytes->byte-table and seq-byte-table.
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Thank you for the comment.
Fixed the names for static tables with comments to be more descriptive.
As sizes of these static tables are not so trivial (<17KB), I used defonce to mark that they shouldn't be reallocated / recalculated.
There're no advantages in runtime in the usual case, as you mentioned. I fixed them to def.
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Thank you! |
totakke
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Refactored bam encoding to use static table.
This PR improves performance of sequence encoding about 20x faster.
Old codes and tests are removed.