@jbrowse/plugin-bed 5.0.0-beta.2 → 5.0.0-beta.4

package/esm/BedGraphTabixAdapter/configSchema.d.ts

@@ -42,7 +42,7 @@ declare const BedGraphTabixAdapter: import("@jbrowse/core/configuration/configur
                 readonly uri: '/path/to/my.gz.tbi';
                 readonly locationType: 'UriLocation';
             };
-            readonly description: 'location of the tabix index. Only needed when it is not named `<file>.tbi` (or `.csi`), which is what the `uri` shorthand assumes.';
+            readonly description: 'location of the tabix index. Only needed when it is not named `<file>.tbi`, which is what the `uri` shorthand assumes — a `.csi` beside the file is reached with `csi: true` rather than by spelling this out.';
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     /**

package/esm/BedTabixAdapter/configSchema.d.ts

@@ -46,7 +46,7 @@ declare const BedTabixAdapter: import("@jbrowse/core/configuration/configuration
                 readonly uri: '/path/to/my.gz.tbi';
                 readonly locationType: 'UriLocation';
             };
-            readonly description: 'location of the tabix index. Only needed when it is not named `<file>.tbi` (or `.csi`), which is what the `uri` shorthand assumes.';
+            readonly description: 'location of the tabix index. Only needed when it is not named `<file>.tbi`, which is what the `uri` shorthand assumes — a `.csi` beside the file is reached with `csi: true` rather than by spelling this out.';
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     /**

package/esm/generateUcscTranscript.js

@@ -1,9 +1,23 @@
-// type guard: narrows input fields to required + non-zero when true
+// type guard: narrows input fields to required when true
 // strand===0 means unstranded — likely not a gene
+//
+// Blocks are what make a transcript, and UCSC's own format definition calls
+// them exons. Thickness says whether the transcript CODES, which is a separate
+// axis: an lncRNA, a spliced EST and any other 12-column feature with
+// thickStart===thickEnd is a transcript by every structural measure, so it is
+// not tested here. `generateUcscTranscript` reads the same equality to emit
+// exons and no CDS.
+//
+// This does conflate a spliced alignment with a transcript, deliberately: a
+// bigPsl track (`est`, `intronEst`, `mrna`, `xenoMrna`, IsoSeq) has an empty
+// thick range too, so it promotes where the same alignment as GFF3
+// `cDNA_match` does not. BED12 carries no column that separates one from an
+// lncRNA, and the promotion stays honest without one — no CDS children, so the
+// sequence panel withholds CDS and protein and HGVS stays `n.`, and the type
+// is `transcript` rather than `mRNA`.
 export function isUcscTranscript(input) {
     return (input.thickStart !== undefined &&
         input.thickEnd !== undefined &&
-        input.thickStart !== input.thickEnd &&
         input.blockCount !== undefined &&
         input.blockCount > 0 &&
         input.strand !== undefined &&
@@ -43,8 +57,13 @@ export function generateUcscTranscript(data) {
         .sort((a, b) => a.start - b.start);
     const fiveUTR = strand > 0 ? 'five_prime_UTR' : 'three_prime_UTR';
     const threeUTR = strand > 0 ? 'three_prime_UTR' : 'five_prime_UTR';
+    // thickStart===thickEnd is UCSC for no coding region, and the block walk
+    // below cannot express that: a thick point inside a block would emit a
+    // zero-length CDS carrying a phase, and one outside every block would make
+    // the whole transcript UTR.
     const { cdsEndStat, cdsStartStat } = rest;
-    if (cdsStartStat === 'none' && cdsEndStat === 'none') {
+    if (thickStart === thickEnd ||
+        (cdsStartStat === 'none' && cdsEndStat === 'none')) {
         return {
             ...rest,
             uniqueId,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "5.0.0-beta.2",
+  "version": "5.0.0-beta.4",
   "type": "module",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
@@ -27,7 +27,7 @@
     "@jbrowse/mobx-state-tree": "^6.5.1",
     "mobx": "^7.0.3",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.2"
+    "@jbrowse/core": "^5.0.0-beta.4"
   },
   "publishConfig": {
     "access": "public"