Add mean and median sequence length to Basic Statistics (#203)#204
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ewels wants to merge 1 commit into
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Add mean and median sequence length to Basic Statistics (#203)#204ewels wants to merge 1 commit into
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Implements s-andrews#203. The Basic Statistics module currently reports only the range of read lengths; this adds "Mean sequence length" and "Median sequence length" rows so users (and downstream tools such as MultiQC) get accurate values straight from the source rather than estimating them. The mean is total bases / total sequences (2 d.p.); the median is derived from a per-length histogram over non-filtered sequences (for an even count, the two central values averaged and rounded up). Both are added to the ResultsTable model, so they appear in the interactive results panel, the HTML report, and fastqc_data.txt together. Integration test approved files updated accordingly. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Hah, you beat me to it in 54b336e 😆 Comparing implementations now.. |
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Closing to build on what you pushed already instead. See #205 |
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Closes #203.
The Basic Statistics module currently reports only the range of read lengths (
min-max). This adds two rows so users get accurate mean and median read lengths straight from the source, rather than having downstream tools like MultiQC estimate them from the binned length distribution:Implementation
Locale.ROOT, so the decimal separator is locale-independent).ResultsTablemodel, so they appear consistently in the interactive results panel, the HTML report, andfastqc_data.txt.The histogram grows on demand using the same idiom as
SequenceLengthDistribution.Testing
antand ran the compiled FastQC on theminimalandcomplextest files; confirmed the new rows appear correctly in bothfastqc_data.txtand the HTML report.FileContentsTestapproved files (data + HTML, forminimalandcomplex). The HTML snapshots add only the two new table rows; the embedded chart images are unchanged.🤖 Generated with Claude Code