BarcodeMapper 1.2.4

Added

• Run ultrastrict (0% edits, 120 aligned bases), strict (2%, 100), standard (3%, 80) and permissive (5%, 60) from one Bowtie2 mapping pass by default. Use --stringency to select levels; preset flags add levels, and -m/-c add a custom level.
• The HTML report has an Overview comparing retained fragments, classified share, rank resolution, taxa per rank, kingdom composition and samples, followed by a detailed tab for each level.
• Level tabs now include a collapsible taxonomy cladogram and sample detection grid with bubble and heatmap views, plus CSV downloads for every report table and visible or all taxonomy rows.
• The grid supports arrow-key tree navigation, a resizable taxonomy column, sorting samples by the focused taxon, and selecting a sunburst sample from a column header. CSV exports guard text that begins with =, +, -, @, a quote, tab, carriage return or line feed.

Changed

• The report uses one phylum colour map across the composition bars, detection grid and sunburst, shows the sample selector only beside the Taxonomy section, embeds the BarcodeMapper logo and uses the full page width. Only sunburst taxa whose whole lineage is present are drawn.
• A default run now writes four level-named taxonomy TSVs instead of one; a run with one selected level still writes to -o. Each run keeps one HTML report and one manifest.
• -m/-c now define a custom level, which can be combined with presets. Preset flags are additive.
• Extraction, taxonomy and aggregation intermediates now live in per-level directories in the working directory.
• The manifest field samples.<sample>.assigned_read_ids is now a per-level object {level: count} instead of a single count.
• Merged TSV rows are now sorted by Taxonomy, with Unclassified first.