Improve performance of reading vcf file. #29
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totakke
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Feb 17, 2017
src/cljam/vcf/reader.clj
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| (let [[fields gt-fields] (->> (cstr/split line #"\t") | ||
| [line header kws] | ||
| (let [[fields gt-fields] (->> (.split ^String line "\t") | ||
| clojure.lang.LazilyPersistentVector/createOwning |
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These two lines have potentially degradation risk. Please add comment describing that this implementation is for performance issue.
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Thank you for the advice.
I've added comments about performance and link to this PR.
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totakke
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Improve performance of reading vcf file.
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Perfect! 💯 |
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This PR improves performance of reading VCF file.
cljam.vcf.readeris slow when reading VCF files like 1000genome which contains enormous number of genotype fields (> 2500).This PR fixed 3 problems to make it more than 2x faster.
keywordcallsinternfor symbol and keyword which causes locking for static state of runtime.apply hash-mapinstead ofmerge zipmap. I don't know why butzipmapuses persistent map.hash-mapwill use transient hash map and this would be faster.clojure.string/splitwithjava.lang.String/split. Some implementations optimizejava.lang.String/splitwith single character as delimiter to avoid usingjava.util.regex.Pattern.