@jbrowse/cli 5.0.0-beta.10 → 5.0.0-beta.13

package/README.md

@@ -340,14 +340,14 @@ any other appearance setting (labels, mouseover, filter).
 --multiwig bundles several BigWigs into one MultiQuantitativeTrack, in place of
 the positional track argument: pass a comma-separated list of BigWig files/URLs,
 or a .json file with an array of BigWig locations or subadapter objects (each
-carrying its own name/color/group). With --load, local list entries are copied
-like any other track file.
+with its own name/color/group). With --load, local list entries are copied like
+any other track file.
 
 --density attaches a features-per-bin bigWig (jbrowse make-density) as the
 adapter's densityAdapter, the band a display draws where the region is too large
 to fetch features. A local <file>.density.bw beside the track file is attached
 without the flag; a URL cannot be probed, so a remote sidecar needs it. The
-adapters carrying the slot are BamAdapter, CramAdapter, HtsgetBamAdapter,
+adapters with the slot are BamAdapter, CramAdapter, HtsgetBamAdapter,
 Gff3TabixAdapter, GtfTabixAdapter, BedTabixAdapter, BigBedAdapter,
 VcfTabixAdapter and SplitVcfTabixAdapter.
 
@@ -382,7 +382,7 @@ $ jbrowse add-track genes.gff3.gz --load copy --color 'jexl:feature.strand==1?"b
 # bundle several BigWigs into one MultiQuantitativeTrack (no positional track arg)
 $ jbrowse add-track --multiwig a.bw,b.bw,c.bw --load copy --name "Coverage"
 
-# ...or from a sources.json carrying per-row name/color for each BigWig
+# ...or from a sources.json with per-row name/color for each BigWig
 $ jbrowse add-track --multiwig sources.json --name "CATlas ATAC"
 
 # attach a remote density sidecar (a local genes.gff3.density.bw needs no flag)
@@ -429,7 +429,7 @@ what it cannot draw in a corner notice rather than refusing the track. This
 command runs the display's own rule list over every "marks" list in the file: an
 error where a mark draws nothing, never draws or a step cannot run, and a
 warning where a slot waits unread or the marks draw in an arrangement the author
-may not have meant. With --json each finding carries the stable "rule" id of the
+may not have meant. With --json each finding has the stable "rule" id of the
 rule that made it.
 
 Types registered by plugins are not known to this command, so they come through
@@ -756,7 +756,7 @@ SplitVcfTabixAdapter declare. add-track attaches it on its own when the default
 <file>.density.bw sits beside the track file, so building it before adding the
 track is all it takes; --density attaches one by path or URL.
 
-GFF3 counts only top-level features — a line whose attributes carry no Parent= —
+GFF3 counts only top-level features — a line whose attributes have no Parent= —
 so a gene is one count rather than one per exon. GTF, BED and VCF have no parent
 link to follow, so every record counts.
 

package/dist/commands/add-track-utils/adapter-utils.js

@@ -1,5 +1,5 @@
 import fs from 'node:fs';
-import { adapterTypesToTrackTypeMap, formats, matchFormat, resolveIndexType, sidecarCandidateNames, trackTypeForAdapter, } from '@jbrowse/add-track-core';
+import { adapterTypesToTrackTypeMap, fileNameOf, formats, matchFormat, resolveIndexType, sidecarCandidateNames, trackTypeForAdapter, } from '@jbrowse/add-track-core';
 import { isURL } from '../../types/common.js';
 import { densitySidecarPath } from '../shared/density.js';
 import { configManifest } from '../validate/configManifest.generated.js';
@@ -134,14 +134,6 @@ export function makeLocationProtocol(protocol) {
         throw new Error(`invalid protocol ${protocol}`);
     };
 }
-/**
- * The bare filename the format table matches against — the same thing
- * `@jbrowse/core`'s `getFileName` hands the guesser chain, so a path and a URL
- * with a presigned query string both reduce to what the regexes expect.
- */
-export function fileNameOf(location) {
-    return (location.replaceAll('\\', '/').split('/').at(-1)?.split(/[?#]/)[0] ?? '');
-}
 // resolves the file-layout spec that both the adapter config and the copied
 // file set derive from, honoring an explicit --adapterType. `typeOverride` is
 // the label to stamp on the adapter when the extension's layout is reused under

package/dist/commands/add-track.js

@@ -136,13 +136,13 @@ export async function run(args) {
         '--multiwig bundles several BigWigs into one MultiQuantitativeTrack, in ' +
         'place of the positional track argument: pass a comma-separated list of ' +
         'BigWig files/URLs, or a .json file with an array of BigWig locations or ' +
-        'subadapter objects (each carrying its own name/color/group). With --load, ' +
+        'subadapter objects (each with its own name/color/group). With --load, ' +
         'local list entries are copied like any other track file.\n\n' +
         '--density attaches a features-per-bin bigWig (jbrowse make-density) as the ' +
         "adapter's densityAdapter, the band a display draws where the region is too " +
         'large to fetch features. A local <file>.density.bw beside the track file is ' +
         'attached without the flag; a URL cannot be probed, so a remote sidecar needs ' +
-        'it. The adapters carrying the slot are BamAdapter, CramAdapter, ' +
+        'it. The adapters with the slot are BamAdapter, CramAdapter, ' +
         'HtsgetBamAdapter, Gff3TabixAdapter, GtfTabixAdapter, BedTabixAdapter, ' +
         'BigBedAdapter, VcfTabixAdapter and SplitVcfTabixAdapter.\n\n' +
         'For pairwise synteny adapters (PAF/Delta/Chain) --assemblyNames is ' +
@@ -174,7 +174,7 @@ export async function run(args) {
         '# bundle several BigWigs into one MultiQuantitativeTrack (no positional track arg)',
         '$ jbrowse add-track --multiwig a.bw,b.bw,c.bw --load copy --name "Coverage"',
         '',
-        '# ...or from a sources.json carrying per-row name/color for each BigWig',
+        '# ...or from a sources.json with per-row name/color for each BigWig',
         '$ jbrowse add-track --multiwig sources.json --name "CATlas ATAC"',
         '',
         '# attach a remote density sidecar (a local genes.gff3.density.bw needs no flag)',

package/dist/commands/make-density/index.js

@@ -46,7 +46,7 @@ export async function run(args) {
         'SplitVcfTabixAdapter declare. add-track attaches it on its own when the ' +
         'default <file>.density.bw sits beside the track file, so building it before ' +
         'adding the track is all it takes; --density attaches one by path or URL.\n\n' +
-        'GFF3 counts only top-level features — a line whose attributes carry no ' +
+        'GFF3 counts only top-level features — a line whose attributes have no ' +
         'Parent= — so a gene is one count rather than one per exon. GTF, BED and VCF ' +
         'have no parent link to follow, so every record counts.\n\n' +
         'BAM and CRAM are out of scope: read depth is not feature density, and the ' +