Clarify RSeQC bam_stat proper pairs column title#3526
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ewels merged 4 commits intoApr 9, 2026
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RSeQC bam_stat.py only counts proper pairs among reads with MAPQ >= mapq_cut (default 30), but the General Statistics column was titled simply "Proper Pairs", matching the samtools stats column which counts all proper pairs regardless of MAPQ. This causes confusion when both columns appear side by side with very different percentages for the same sample. Add "(MAPQ>=30)" to the title and expand the description to explain the filtering. Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
ewels
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Thanks! I think we can get away with it being a little simpler / shorter? What do you think?
Could add some clarification in the MultiQC module docs as a compromise if you wanted.
Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
ewels
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May 7, 2026
Co-authored-by: Claude Opus 4.6 (1M context) <[email protected]>
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Summary
Context
RSeQC
bam_stat.pyapplies a default MAPQ >= 30 filter before counting. Its proper pairs percentage uses a filtered numerator (only MAPQ >= 30 reads) against total records as denominator, but the column title doesn't indicate any filtering is happening. This has caused confusion for users who expect the value to reflect all reads.Adding "(MAPQ>=30)" to the title makes the filtering immediately visible.
Changes
multiqc/modules/rseqc/bam_stat.py: Updatedtitleanddescriptionfor theproper_pairs_percentGeneral Statistics column header🤖 Generated with Claude Code