* Metagene per isoform, GFF picker and gene search in qc (0.16.2)
* metagene: every coding isoform, per-transcript widths
Sites are placed on every coding transcript that contains them, 1/k on
each of k (--isoforms weighted, the default; `all` counts the site on
each). The longest-isoform election is gone: it left sites on other
isoforms' exons off-transcript and put sites near a proximal poly(A)
site mid-3'UTR. Bin counts are fractional; the TSV prints them to four
decimals and --dist-measures gains a `weight` column.
Region widths come from medians over the transcripts carrying a site,
each counted once, rather than over sites: with many sites per gene,
long-3'UTR genes set the medians alone and drew the CDS too narrow.
* metagene plots: boundaries and region colours
Dashed dividers mark the start and stop codons, with the region names
between them; the tick under each name used to read as a boundary.
Bars are coloured by region (Okabe-Ito), in the figure and on the
terminal.
* qc view: browse for an annotation, pick a gene, coverage by default
`g` opens a pop-up browser for a GTF/GFF, also offered when the recorded
one is not on this machine; the annotation the view ends on goes into
qc.run.json and the printed command. The browser is shared with the
input-directory prompt.
In the gene search, the arrow keys move through the matches; Enter
selects the gene and leaves the search, Esc goes back.
The gene and metagene bars add up read coverage at the kept sites by
default; `c` cycles to converted reads and to sites.
* Review fixes; Shift+Enter alone applies, q and p ask first
* review fixes
The annotation browser makes its directory absolute, so going up from a
relative input directory no longer ends in an empty listing. A picked
annotation that fails to read is not recorded; the one the view started
with is, and options.gff follows the view's choice. Region medians leave
out transcripts without that region (MetaPlotR drops the NA), so CDS
fragments cannot pull a UTR's median, and its bins, to zero. Sums of
1/k shares print as whole numbers. The metagene's off-transcript count
says it is sites. An annotation path is checked to exist, not to be a
regular file, so a FIFO or a FUSE mount still reads.
* keys
Shift+Enter is the only key that opens the confirmation and applies;
`A` and `y` no longer do. Esc closes pop-ups and never leaves the view.
With any threshold changed, `q` and `p` ask first, and only the same
key again leaves.