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Performance wrapper

Andrea Telatin edited this page Oct 26, 2021 · 6 revisions

Using a wrapper and a 11Mb test BAM file. The wrapper written in Python uses the communicate method from subprocess, while the Perl wrapper uses IPC::Run3.

Command Mean [ms] Min [ms] Max [ms] Relative
cat example_data/panel_01.bam | covtobed 569.5 ± 13.9 549.4 587.1 1.00
covtobed example_data/panel_01.bam 572.0 ± 19.1 543.6 601.8 1.00 ± 0.04
./covtobed.pl example_data/panel_01.bam 599.8 ± 9.9 584.8 614.3 1.05 ± 0.03
./covtobed.py example_data/panel_01.bam 611.6 ± 29.5 584.5 660.4 1.07 ± 0.06
cat example_data/panel_01.bam | ./covtobed.py 645.9 ± 18.6 628.0 679.2 1.13 ± 0.04
cat example_data/panel_01.bam | ./covtobed.pl 648.5 ± 26.2 621.4 692.2 1.14 ± 0.05
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