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pileup and metagene: browse by default, output folders as input, a file picker, wider zoom-out (0.16.6) - #19
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…le picker, wider zoom-out (0.16.6) - `faba pileup` and `faba metagene` open full screen by default; `--batch-process` (alias `--batch-mode`) prints or writes instead, as they do without a terminal. `--interactive` is still accepted, hidden. - Either takes a faba output directory, or a run record in it, in place of its files: pileup takes the site matrices of `--modality` (m6A, else A-to-I), one track per batch, with the site table and recorded GFF; metagene profiles the site table against the recorded GFF. - With no input, a browser asks: mark files to read together (pileup sums the marked matrices into one track, metagene profiles the marked site tables as one set of sites), or choose a whole output folder. Metagene also takes several site tables on the command line. - `--track` now regroups a directory's matrices too, instead of being dropped when a directory is given. - In the pileup browser, `-` past the whole gene reloads a span twice as wide, flanks and their genes included. - A spinner shows while the browsers load, when a load takes more than a moment. - Marking lives in the shared folder browser, which now also lists unzipped `.zarr` stores; one spinner frame set, one list of site modalities and one site-table name test.
pileup reads each track's matrices on its own thread and metagene each site table, then takes them in order, so an output folder with many batches, or several marked tables, loads in about the time of the slowest one.
… folder - The loading pop-up shows a bar of files read, and pileup reads the files of one track in parallel too, merging them in file order. - `-` past the whole gene keeps the gene's title and the cursor. - In the file picker Tab gives each marked matrix its own track, named after its batch; `--separate` does the same on the command line. - `M` in the pileup browser switches an output folder between its m6A and A-to-I sites, at the same gene or span. - The picker opens where the last choice was made.
…folder - `M` is handled in the browse loop itself: each modality's inputs are resolved and their gene list read once, the gene-list filter kept, and a failed switch stays at the cursor; an unknown modality says so. - The picked inputs and the separate-tracks choice live on the arguments; the picker returns its choice as a struct and opens its folder once. - The picker's last choice is kept per working folder, under the XDG cache directory. - One bar helper for the progress bars, one helper for the other site modality, and a merge for the per-file reads that takes over the first file's maps; the modality filter no longer allocates per row. - Leave the methods document as it was.
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What changes
faba pileupandfaba metageneopen full screen unless--batch-process(alias--batch-mode) is given, or there is no terminal. The old--interactiveis still accepted, hidden.--modality(m6A, else A-to-I), one track per batch, with the folder's site table and recorded GFF.--trackwith a directory. It now regroups the directory's matrices instead of being dropped.-past the whole gene reloads a span twice as wide, with the flanks and their genes, keeping the cursor and title.--separatedoes the same on the command line.Min the pileup browser switches an output folder between its m6A and A-to-I sites, at the same gene or span.Shared pieces
.zarrstores.crate::tui::SPINNER), the site modalities, the site-table name test, and the folder-of-a-run-record lookup.Checks
cargo testpasses.cargo clippy --all-targetsis clean, with and without--features hdf5.cargo fmtis applied.