RustQC's Qualimap module currently reimplements only rnaseq mode (confirmed in the docs at /rna/qualimap/: "RustQC reimplements the rnaseq mode of Qualimap"). bamqc mode — Qualimap's other, more generic analysis mode — doesn't have an equivalent.
Why this matters: bamqc and rnaseq mode measure genuinely different things. bamqc is generic genomic BAM QC (coverage depth/breadth, GC content, insert size distribution, mapping quality, per-chromosome coverage) and needs no GTF/annotation at all. rnaseq mode is RNA-seq specific (exonic/intronic/intergenic read origin, 5'→3' transcript coverage bias, strand specificity, junction analysis) and requires one. A pipeline that wants both currently has to keep running the original Java Qualimap alongside RustQC just for bamqc — which, like the geneBody_coverage/read_GC gap in #127, undercuts RustQC's "one tool replaces N" value proposition for anyone who wants both QC angles.
Concrete motivation: We evaluated RustQC as a drop-in replacement for a production Snakemake RNA-seq pipeline's QC stage. Every other tool we use had a direct equivalent (see #127 for the only other gap we found); bamqc mode is the one piece of our current Qualimap usage RustQC can't cover, so we're stuck vendoring the original Qualimap Java tool solely for that.
Ask: Please consider adding bamqc mode (or an equivalent generic-BAM-QC subset of it) as an enhancement, alongside the existing rnaseq mode. Happy to help validate against real Qualimap output on our data, same as offered in #127.
RustQC's Qualimap module currently reimplements only
rnaseqmode (confirmed in the docs at/rna/qualimap/: "RustQC reimplements the rnaseq mode of Qualimap").bamqcmode — Qualimap's other, more generic analysis mode — doesn't have an equivalent.Why this matters:
bamqcandrnaseqmode measure genuinely different things.bamqcis generic genomic BAM QC (coverage depth/breadth, GC content, insert size distribution, mapping quality, per-chromosome coverage) and needs no GTF/annotation at all.rnaseqmode is RNA-seq specific (exonic/intronic/intergenic read origin, 5'→3' transcript coverage bias, strand specificity, junction analysis) and requires one. A pipeline that wants both currently has to keep running the original Java Qualimap alongside RustQC just forbamqc— which, like thegeneBody_coverage/read_GCgap in #127, undercuts RustQC's "one tool replaces N" value proposition for anyone who wants both QC angles.Concrete motivation: We evaluated RustQC as a drop-in replacement for a production Snakemake RNA-seq pipeline's QC stage. Every other tool we use had a direct equivalent (see #127 for the only other gap we found);
bamqcmode is the one piece of our current Qualimap usage RustQC can't cover, so we're stuck vendoring the original Qualimap Java tool solely for that.Ask: Please consider adding
bamqcmode (or an equivalent generic-BAM-QC subset of it) as an enhancement, alongside the existingrnaseqmode. Happy to help validate against real Qualimap output on our data, same as offered in #127.