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Speed up Bio::DB::Fasta using compiled regular expressions or Inline::C #96

Merged
merged 5 commits into from
Dec 24, 2014
Merged

Speed up Bio::DB::Fasta using compiled regular expressions or Inline::C #96

merged 5 commits into from
Dec 24, 2014

Commits on Dec 18, 2014

  1. Using compiled regexps in s/// speeds up seq/subseq() by about 7% fro… 

    …m 7.76s to 7.22s over 32358 calls on Variant Effect Prediction data.
    Rocky Bernstein committed Dec 18, 2014
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Commits on Dec 19, 2014

  1. Another regular expression which benefits from compiling

    Rocky Bernstein committed Dec 19, 2014
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  2. If we have Inline::C around, use that to speed up remove carriage ret… 

    …urns and

line feeds (\n) and (\r).
    Rocky Bernstein committed Dec 19, 2014
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Commits on Dec 20, 2014

  1. Fasta.pm: Add my variable in strip_crnl and rename from strip_nlcr. D… 

    …ocument better

Build.PL: add Inline::C recommended dependency.
.gitignore: ignore _Inline directories that Inline::C creates.
    Rocky Bernstein committed Dec 20, 2014
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  2. Faster, more idiomatic C code. Use stiop_crln() in the other place it… 

    … is used.
    Rocky Bernstein committed Dec 20, 2014
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