Improve performance of reading BAM files. #22
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totakke
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Jan 25, 2017
| (let [nibble-table "=ACMGRSVTWYHKDBN"] | ||
| (->> (for [i nibble-table j nibble-table] [i j]) | ||
| (apply concat) | ||
| clojure.string/join))) |
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clojure.string/join -> cstr/join
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Thank you for the comment. I've fixed it and rebased. |
totakke
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Improve performance of reading BAM files.
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Thanks. This improvement has just been merged 👍 |
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This PR improves performance of reading alignments from a BAM file.
Decoding 4-bit encoded sequences takes approximately 70% of time during reading BAM.
I modified to use static byte-to-chars table to make decoding about 30x faster, therefore entire
cljam viewcommand got about 3x faster.I also modified project.clj to update dependencies.
After this modification, the largest bottleneck will be decoding optional fields which is about 4x slower than decoding a sequence.