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Performance wrapper
Andrea Telatin edited this page Oct 26, 2021
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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 |
Covtobed - Wiki - a simple tool to extract BED coverage tracks from BAM files