@jbrowse/plugin-bed 5.0.0-beta.1 → 5.0.0-beta.3

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

@@ -16,6 +16,11 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BedTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    readonly densityAdapter: {
+        readonly type: 'frozen';
+        readonly defaultValue: null;
+        readonly description: 'optional quantitative sub-adapter (e.g. a BigWigAdapter over a features-per-bin bigWig) drawn as a density band where the region is too large to fetch features; null disables it';
+    };
     /**
      * #slot
      * location of the bgzip-compressed BED, sorted by position. Must be bgzip
@@ -41,7 +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/BedTabixAdapter/configSchema.js

@@ -1,4 +1,5 @@
 import { ConfigurationSchema, expandTabixShorthand, tabixIndexFields, } from '@jbrowse/core/configuration';
+import { densityAdapterConfigSchemaFields } from '@jbrowse/core/data_adapters/BaseAdapter';
 export function normalizeSnapshot(snap) {
     return expandTabixShorthand(snap, 'bedGzLocation');
 }
@@ -63,6 +64,7 @@ const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
         description: 'Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)',
         defaultValue: false,
     },
+    ...densityAdapterConfigSchemaFields,
 }, {
     explicitlyTyped: true,
     /**

package/esm/BigBedAdapter/configSchema.d.ts

@@ -14,6 +14,11 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    readonly densityAdapter: {
+        readonly type: 'frozen';
+        readonly defaultValue: null;
+        readonly description: 'optional quantitative sub-adapter (e.g. a BigWigAdapter over a features-per-bin bigWig) drawn as a density band where the region is too large to fetch features; null disables it';
+    };
     /**
      * #slot
      * location of the BigBed file. It carries its own index and summary zoom

package/esm/BigBedAdapter/configSchema.js

@@ -1,4 +1,5 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { densityAdapterConfigSchemaFields } from '@jbrowse/core/data_adapters/BaseAdapter';
 export function normalizeSnapshot(snap) {
     return snap.uri
         ? {
@@ -60,6 +61,7 @@ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
         description: 'Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)',
         defaultValue: false,
     },
+    ...densityAdapterConfigSchemaFields,
 }, {
     explicitlyTyped: true,
     /**

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.1",
+  "version": "5.0.0-beta.3",
   "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.1"
+    "@jbrowse/core": "^5.0.0-beta.3"
   },
   "publishConfig": {
     "access": "public"