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Improve performance of FASTA indexing #30

Merged
merged 1 commit into from
Mar 3, 2017
Merged

Improve performance of FASTA indexing #30

merged 1 commit into from
Mar 3, 2017

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totakke
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@totakke totakke commented Mar 3, 2017

Current FASTA indexer is critically slow because it uses java.io.RandomAccessFile to read a source FASTA. This commit improves the performance by using java.io.BufferedReader.

The following showd results of indexing 101MB FASTA.

;; before:
(time (fai/create-index "/tmp/refMrna.fa" "/tmp/refMrna.fa.fai"))
"Elapsed time: 73621.207302 msecs"

;; after:
(time (fai/create-index "/tmp/refMrna.fa" "/tmp/refMrna.fa.fai"))
"Elapsed time: 2986.332916 msecs"

@totakke totakke requested a review from alumi March 3, 2017 09:25
alumi
alumi approved these changes Mar 3, 2017
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Simple yet effective solution!

@alumi alumi merged commit be6037e into master Mar 3, 2017
@alumi alumi deleted the feature/improve-fasta-indexer branch March 3, 2017 15:18
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@alumi alumi alumi approved these changes

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@totakke @alumi