Accelerate preprocess #71
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marghoob
reviewed
Apr 19, 2021
| // std::time_t end_time_3p0 = std::chrono::system_clock::to_time_t(end_3p0); | ||
| // std::cout << "elapsed_3p0 time: " << elapsed_seconds_3p0.count() << "s\n"; | ||
| // auto start_3p1 = std::chrono::system_clock::now(); | ||
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| if (calculate_qual) { |
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ii is used both in the outermost and the innermost loops. Better to have different names here.
marghoob
reviewed
Apr 19, 2021
| @@ -352,18 +414,24 @@ struct Options { | |||
| std::string ref_; | |||
| bool calculate_qual_stat_ = false; | |||
| bool fully_contained_ = false; | |||
| float min_allele_freq_ = 0.01; | |||
| float snp_min_allele_freq_ = 0.01; | |||
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Such constants should be declared somewhere else. Things like these would be good candidates for refactoring the code.
marghoob
reviewed
Apr 19, 2021
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| auto start_main = std::chrono::system_clock::now(); |
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Using scoped timers would simplify this performance measurement.
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Improving preprocessing speed