@jbrowse/plugin-config 3.0.5 → 3.2.0

package/dist/FromConfigSequenceAdapter/configSchema.js

@@ -7,5 +7,8 @@ const sequenceConfigSchema = (0, configuration_1.ConfigurationSchema)('FromConfi
         type: 'frozen',
         defaultValue: [],
     },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
+}, {
+    explicitlyTyped: true,
+    implicitIdentifier: 'adapterId',
+});
 exports.default = sequenceConfigSchema;

package/dist/NcbiSequenceReportAliasAdapter/configSchema.js

@@ -15,5 +15,18 @@ const NcbiSequenceReportAliasAdapterConfigSchema = (0, configuration_1.Configura
         defaultValue: true,
         description: 'forces usage of the UCSC names over the NCBI style names from a FASTA',
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                location: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 exports.default = NcbiSequenceReportAliasAdapterConfigSchema;

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -10,13 +10,20 @@ class RefNameAliasAdapter extends BaseAdapter_1.BaseAdapter {
         }
         const results = await (0, io_1.openLocation)(loc, this.pluginManager).readFile('utf8');
         const refColumn = this.getConf('refNameColumn');
-        return results
+        const refColumnHeaderName = this.getConf('refNameColumnHeaderName');
+        const lines = results
             .trim()
             .split(/\n|\r\n|\r/)
-            .filter(f => !!f && !f.startsWith('#'))
+            .filter(f => !!f);
+        const header = lines.filter(f => f.startsWith('#'));
+        const headerCol = refColumnHeaderName && header.length
+            ? header.at(-1).split('\t').indexOf(refColumnHeaderName)
+            : refColumn;
+        return lines
+            .filter(f => !f.startsWith('#'))
             .map(row => {
             const aliases = row.split('\t');
-            const [refName] = aliases.splice(refColumn, 1);
+            const refName = aliases[headerCol];
             return {
                 refName: refName,
                 aliases: aliases.filter(f => !!f.trim()),

package/dist/RefNameAliasAdapter/configSchema.d.ts

@@ -10,5 +10,10 @@ declare const RefNameAliasAdapter: import("@jbrowse/core/configuration/configura
         type: string;
         defaultValue: number;
     };
+    refNameColumnHeaderName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default RefNameAliasAdapter;

package/dist/RefNameAliasAdapter/configSchema.js

@@ -14,5 +14,23 @@ const RefNameAliasAdapter = (0, configuration_1.ConfigurationSchema)('RefNameAli
         type: 'number',
         defaultValue: 0,
     },
-}, { explicitlyTyped: true });
+    refNameColumnHeaderName: {
+        type: 'string',
+        description: 'alternative to refNameColumn, instead looks at header (starts with # and finds column name)',
+        defaultValue: '',
+    },
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                location: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 exports.default = RefNameAliasAdapter;

package/esm/FromConfigSequenceAdapter/configSchema.js

@@ -5,5 +5,8 @@ const sequenceConfigSchema = ConfigurationSchema('FromConfigSequenceAdapter', {
         type: 'frozen',
         defaultValue: [],
     },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
+}, {
+    explicitlyTyped: true,
+    implicitIdentifier: 'adapterId',
+});
 export default sequenceConfigSchema;

package/esm/NcbiSequenceReportAliasAdapter/configSchema.js

@@ -13,5 +13,18 @@ const NcbiSequenceReportAliasAdapterConfigSchema = ConfigurationSchema('NcbiSequ
         defaultValue: true,
         description: 'forces usage of the UCSC names over the NCBI style names from a FASTA',
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                location: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 export default NcbiSequenceReportAliasAdapterConfigSchema;

package/esm/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -8,13 +8,20 @@ export default class RefNameAliasAdapter extends BaseAdapter {
         }
         const results = await openLocation(loc, this.pluginManager).readFile('utf8');
         const refColumn = this.getConf('refNameColumn');
-        return results
+        const refColumnHeaderName = this.getConf('refNameColumnHeaderName');
+        const lines = results
             .trim()
             .split(/\n|\r\n|\r/)
-            .filter(f => !!f && !f.startsWith('#'))
+            .filter(f => !!f);
+        const header = lines.filter(f => f.startsWith('#'));
+        const headerCol = refColumnHeaderName && header.length
+            ? header.at(-1).split('\t').indexOf(refColumnHeaderName)
+            : refColumn;
+        return lines
+            .filter(f => !f.startsWith('#'))
             .map(row => {
             const aliases = row.split('\t');
-            const [refName] = aliases.splice(refColumn, 1);
+            const refName = aliases[headerCol];
             return {
                 refName: refName,
                 aliases: aliases.filter(f => !!f.trim()),

package/esm/RefNameAliasAdapter/configSchema.d.ts

@@ -10,5 +10,10 @@ declare const RefNameAliasAdapter: import("@jbrowse/core/configuration/configura
         type: string;
         defaultValue: number;
     };
+    refNameColumnHeaderName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default RefNameAliasAdapter;

package/esm/RefNameAliasAdapter/configSchema.js

@@ -12,5 +12,23 @@ const RefNameAliasAdapter = ConfigurationSchema('RefNameAliasAdapter', {
         type: 'number',
         defaultValue: 0,
     },
-}, { explicitlyTyped: true });
+    refNameColumnHeaderName: {
+        type: 'string',
+        description: 'alternative to refNameColumn, instead looks at header (starts with # and finds column name)',
+        defaultValue: '',
+    },
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                location: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 export default RefNameAliasAdapter;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "3.0.5",
+  "version": "3.2.0",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",
@@ -36,7 +36,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@jbrowse/core": "^3.0.5",
+    "@jbrowse/core": "^3.2.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "mobx": "^6.0.0",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "a03749efe19e51609922272b845a331897346789"
+  "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
 }