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Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com> Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com> Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com> Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
New method 'simple' ignores CIGAR strings and covers the whole reference span between the first and last aligned position of each alignment (via htslib's bam_endpos), so soft-clip and inserted bases also count as covered. 'full' remains the default and is unchanged. Benchmark on a 102 GB Dorado 6mA BAM (GRCm39, ~100x): simple is ~1.2x faster on a 1 Mb region and roughly tied at 10-100 Mb, so the win is modest for long ONT reads. Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com> Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com> Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com> Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## devel #17 +/- ##
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Coverage 99.97% 99.97%
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Files 31 31
Lines 3832 3951 +119
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+ Hits 3831 3950 +119
Misses 1 1 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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