@jbrowse/cli 5.0.0-beta.8 → 5.0.0-beta.9

package/README.md

@@ -13,7 +13,7 @@ or by using a script file.
 
 A simple script that does not use @jbrowse/cli at all may just look like this
 
-```
+```js
 const config = JSON.parse(fs.readFileSync('config.json', 'utf8'))
 // do something with config.tracks, config.assemblies, etc.
 fs.writeFileSync('config.json', JSON.stringify(config, null, 2))
@@ -43,7 +43,7 @@ npx @jbrowse/cli create myfolder
 It is likely preferable in most cases to install the tools globally with
 `npm install @jbrowse/cli -g` however
 
-```
+```text
 
 JBrowse CLI
 
@@ -78,7 +78,7 @@ Use "jbrowse <command> --help" for more information about a command.
 
 ## jbrowse create
 
-```
+```text
 Downloads and installs the latest JBrowse 2 release
 
 Usage: jbrowse create [localPath] [options]
@@ -123,7 +123,7 @@ $ jbrowse create --listVersions
 
 ## jbrowse add-assembly
 
-```
+```text
 Add an assembly to a JBrowse 2 configuration
 
 Usage: jbrowse add-assembly <sequence> [options]
@@ -242,7 +242,7 @@ $ jbrowse add-assembly GRCh38.fa --load copy --config '{"sequence":{"formatAbout
 
 ## jbrowse add-track
 
-```
+```text
 Add a track to a JBrowse 2 configuration
 
 Usage: jbrowse add-track <track> [options]
@@ -354,8 +354,7 @@ VcfTabixAdapter and SplitVcfTabixAdapter.
 For pairwise synteny adapters (PAF/Delta/Chain) --assemblyNames is query,target
 — the reverse of the minimap2/nucmer input order. For the multi-genome PAF
 adapters (MultiGenomePAFAdapter, MultiGenomeIndexedPAFAdapter) it is instead the
-full list of assemblies the file covers, in any order, since one multi-genome
-file backs every pair.
+full list of assemblies the file covers, in any order.
 
 Examples:
 
@@ -393,7 +392,7 @@ $ jbrowse add-track https://mywebsite.com/genes.gff3.gz --density https://mywebs
 
 ## jbrowse validate
 
-```
+```text
 Check a JBrowse configuration for errors, including the ones JBrowse itself
 accepts silently
 
@@ -414,16 +413,25 @@ nothing. That is what this command is mainly for.
 
 Two levels are reported:
 
-  error    JBrowse accepts it and silently does the wrong thing — an unknown    
-       slot, a key a defaultSession view or display does not declare, a         
-  track naming an assembly the config never defines, a defaultSession           
-naming a trackId that does not exist, a duplicate trackId. Exits 1.
+  error    JBrowse silently does the wrong thing, or refuses to load it — an    
+       unknown slot, a key a defaultSession view or display does not           
+declare, a track naming an assembly the config never defines, a           
+defaultSession naming a trackId that does not exist, a duplicate           
+trackId. Exits 1.
 
   warning  JBrowse will complain by itself on load, or handles it — a type name 
           the core plugins do not register (expected if one of your plugins     
       registers it), or a legacy key a migration rewrites, such as a view       
     nesting its settings under "init". Never fails the run.
 
+A LinearMarkDisplay loads whenever its keys and value types are right and says
+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
+rule that made it.
+
 Types registered by plugins are not known to this command, so they come through
 as warnings rather than errors.
 
@@ -450,7 +458,7 @@ $ jbrowse validate config.json --json
 
 ## jbrowse text-index
 
-```
+```text
 Make a text-indexing file for any given track(s).
 
 Usage: jbrowse text-index [options]
@@ -560,7 +568,7 @@ $ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes
 
 ## jbrowse admin-server
 
-```
+```text
 Start up a small admin server for JBrowse configuration
 
 Usage: jbrowse admin-server [options]
@@ -607,7 +615,7 @@ $ jbrowse admin-server --host 0.0.0.0
 
 ## jbrowse upgrade
 
-```
+```text
 Upgrades JBrowse 2 to latest version
 
 Usage: jbrowse upgrade [localPath] [options]
@@ -655,7 +663,7 @@ $ jbrowse upgrade --nightly
 
 ## jbrowse make-pif
 
-```
+```text
 creates pairwise indexed PAF (PIF), with bgzip and tabix
 
 Usage: jbrowse make-pif <file> [options]
@@ -716,7 +724,7 @@ $ jbrowse make-pif input.paf --threads 8
 
 ## jbrowse make-density
 
-```
+```text
 Counts feature starts per bin into a bigWig, the density sidecar a track draws
 where the region is too large to fetch its features
 
@@ -772,7 +780,7 @@ $ jbrowse make-density genes.gff3.gz --assembly hg38.fa --bin 10000 --out genes.
 
 ## jbrowse sort-gff
 
-```
+```text
 Sort a GFF or GTF for tabix — the two share a refname/start column layout. It is
 `sort -k1,1 -k4,4n` with LC_ALL=C and a tab separator, plus every line starting
 with # kept at the top rather than sorted into the data. Takes a file, or the
@@ -800,7 +808,7 @@ $ tabix -p gff sorted.gtf.gz
 
 ## jbrowse sort-bed
 
-```
+```text
 Sort a BED file for tabix. It is `sort -k1,1 -k2,2n` with LC_ALL=C and a tab
 separator, plus every line starting with # kept at the top rather than sorted
 into the data. Takes a file, or the same data on stdin
@@ -822,7 +830,7 @@ $ tabix sorted.bed.gz
 
 ## jbrowse add-connection
 
-```
+```text
 Add a connection to a JBrowse 2 configuration
 
 Usage: jbrowse add-connection <connectionUrlOrPath> [options]
@@ -878,7 +886,7 @@ $ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId
 
 ## jbrowse add-track-json
 
-```
+```text
 Add a track configuration directly from a JSON hunk to the JBrowse 2
 configuration
 
@@ -921,7 +929,7 @@ $ jbrowse add-track-json track.json --out /path/to/jb2/
 
 ## jbrowse remove-track
 
-```
+```text
 Remove a track configuration from a JBrowse 2 configuration. Be aware that this
 can cause crashes in saved sessions that refer to this track!
 
@@ -950,7 +958,7 @@ $ jbrowse remove-track my_track_id --target /path/to/jb2/config.json
 
 ## jbrowse set-default-session
 
-```
+```text
 Set a default session with views and tracks
 
 Usage: jbrowse set-default-session [options]

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

@@ -29,10 +29,8 @@ export function buildTrackConfig({ trackType, trackId, name, assemblyNames, cate
 // nothing was supplied, so the track omits displayDefaults entirely.
 //
 // Takes `trackType` so it can refuse a key none of that track's displays
-// declares. `--color` on an alignments track is the reachable case — that
-// display declares `colorBy`, expandTrackConfigShorthand drops the unmatched
-// key with a console warning, and the command otherwise wrote the dead setting
-// and exited 0.
+// declares: expandTrackConfigShorthand drops an unmatched key with a console
+// warning, and the command otherwise wrote the dead setting and exited 0.
 export function mergeDisplayDefaults({ configObj, color, height, displayDefaults, trackType, }) {
     const fromJson = displayDefaults
         ? parseJsonFlag(displayDefaults, '--displayDefaults')

package/dist/commands/add-track.js

@@ -148,8 +148,7 @@ export async function run(args) {
         'For pairwise synteny adapters (PAF/Delta/Chain) --assemblyNames is ' +
         'query,target — the reverse of the minimap2/nucmer input order. For the ' +
         'multi-genome PAF adapters (MultiGenomePAFAdapter, MultiGenomeIndexedPAFAdapter) it is ' +
-        'instead the full list of assemblies the file covers, in any order, since ' +
-        'one multi-genome file backs every pair.';
+        'instead the full list of assemblies the file covers, in any order.';
     const examples = [
         '# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json',
         '$ jbrowse add-track /path/to/my.bam --load copy',

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

@@ -140,7 +140,7 @@ export async function run(args) {
             'the fine tier and doubles the file for nothing. Rebuild with --no-coarse, ' +
             'or align with a CIGAR (minimap2 -c) so low zooms have something cheaper to read.');
     }
-    // An all-vs-all PAF that does not state every pair indexes perfectly well and
+    // A multi-genome PAF that does not state every pair indexes perfectly well and
     // then draws an empty synteny band for each pair the aligner never emitted,
     // which reads as "no homology here" rather than as "never computed". This is
     // the moment someone is looking at the file, and the census it needs was
@@ -163,7 +163,7 @@ export async function run(args) {
             `(MAF) rather than a stack of pairwise bands.`);
     }
     const nextCommand = samples.size > 0
-        ? 'Next, add it as an all-vs-all synteny track (PanSN names detected):\n' +
+        ? 'Next, add it as a multi-genome synteny track (PanSN names detected):\n' +
             `  jbrowse add-track ${outputFile} --adapterType MultiGenomeIndexedPAFAdapter -a ${[...samples].sort().join(',')} --load copy`
         : 'Next, add it as a synteny track (set -a to your query,target assembly names):\n' +
             `  jbrowse add-track ${outputFile} -a query,target --load copy`;