@jbrowse/plugin-gtf 2.4.1 → 2.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (8) hide show
  1. package/dist/GtfAdapter/configSchema.d.ts +12 -1
  2. package/dist/util.js +3 -3
  3. package/dist/util.js.map +1 -1
  4. package/esm/GtfAdapter/configSchema.d.ts +12 -1
  5. package/esm/util.js +3 -3
  6. package/esm/util.js.map +1 -1
  7. package/package.json +2 -2
  8. package/src/util.ts +4 -4
package/dist/GtfAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,13 @@
1
- declare const GtfAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const GtfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ gtfLocation: {
6
+ type: string;
7
+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ };
12
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
13
  export default GtfAdapter;
package/dist/util.js CHANGED
@@ -33,9 +33,9 @@ function featureData(data) {
33
33
  if (data.attributes[a] !== null) {
34
34
  let attr = data.attributes[a];
35
35
  if (Array.isArray(attr) && attr.length === 1) {
36
- // gtf uses double quotes for text values in the attributes column, remove them
37
- const formattedAttr = attr[0].replace(/^"|"$/g, '');
38
- attr = formattedAttr;
36
+ // gtf uses double quotes for text values in the attributes column,
37
+ // remove them
38
+ attr = `${attr[0]}`.replace(/^"|"$/g, '');
39
39
  }
40
40
  f[b] = attr;
41
41
  }
package/dist/util.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;AAaA,SAAgB,WAAW,CAAC,IAAgB;IAC1C,MAAM,CAAC,GAA4B,EAAE,GAAG,IAAI,EAAE,CAC7C;IAAC,CAAC,CAAC,KAAgB,IAAI,CAAC,CAAA,CAAC,uBAAuB;IACjD,CAAC,CAAC,MAAM,GAAG,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA,CAAC,iBAAiB;IACrF,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAC5B,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAA;IACzB,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;QACvB,OAAO,CAAC,CAAC,KAAK,CAAA;KACf;IACD,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;QACvB,OAAO,CAAC,CAAC,KAAK,CAAA;KACf;IACD,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC;QAC5B,OAAO;QACP,KAAK;QACL,UAAU;QACV,OAAO;QACP,aAAa;QACb,QAAQ;QACR,OAAO;QACP,QAAQ;KACT,CAAC,CAAA;IACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE;QAC5C,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAA;QACvB,IAAI,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YACxB,gDAAgD;YAChD,gCAAgC;YAChC,CAAC,IAAI,GAAG,CAAA;SACT;QACD,IAAI,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;YAC/B,IAAI,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YAC7B,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;gBAC5C,+EAA+E;gBAC/E,MAAM,aAAa,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;gBACnD,IAAI,GAAG,aAAa,CAAA;aACrB;YACD,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;SACZ;KACF;IACD,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,QAAQ,CAAA;IACtB,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,WAAW,CAAA;IAEtB,gFAAgF;IAChF,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,EAAE;QACzD,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,cAAc,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CACtD,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CACjD,CAAA;KACF;IAED,OAAO,CAAC,CAAC,cAAc,CAAA;IACvB,OAAO,CAAC,CAAC,IAAI,CAAA;IACb,OAAO,CAAC,CAAC,gBAAgB,CAAA;IACzB,gDAAgD;IAChD,OAAO,CAAC,CAAC,SAAS,CAAA;IAClB,OAAO,CAAC,CAAC,UAAU,CAAA;IACnB,OAAO,CAAC,CAAC,QAAQ,CAAA;IACjB,OAAO,CAAC,CAAC,WAAW,CAAA;IACpB,OAAO,CAAC,CAAC,KAAK,CAAA;IAEd,IAAI,CAAC,CAAC,aAAa,EAAE;QACnB,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,aAAa,CAAA;KACzB;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AA/DD,kCA+DC"}
1
+ {"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;AAaA,SAAgB,WAAW,CAAC,IAAgB;IAC1C,MAAM,CAAC,GAA4B,EAAE,GAAG,IAAI,EAAE,CAC7C;IAAC,CAAC,CAAC,KAAgB,IAAI,CAAC,CAAA,CAAC,uBAAuB;IACjD,CAAC,CAAC,MAAM,GAAG,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA,CAAC,iBAAiB;IACrF,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAC5B,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAA;IACzB,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;QACvB,OAAO,CAAC,CAAC,KAAK,CAAA;KACf;IACD,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;QACvB,OAAO,CAAC,CAAC,KAAK,CAAA;KACf;IACD,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC;QAC5B,OAAO;QACP,KAAK;QACL,UAAU;QACV,OAAO;QACP,aAAa;QACb,QAAQ;QACR,OAAO;QACP,QAAQ;KACT,CAAC,CAAA;IACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE;QAC5C,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAA;QACvB,IAAI,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YACxB,gDAAgD;YAChD,gCAAgC;YAChC,CAAC,IAAI,GAAG,CAAA;SACT;QACD,IAAI,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;YAC/B,IAAI,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAsB,CAAA;YAClD,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;gBAC5C,mEAAmE;gBACnE,cAAc;gBACd,IAAI,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;aAC1C;YACD,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;SACZ;KACF;IACD,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,QAAQ,CAAA;IACtB,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,WAAW,CAAA;IAEtB,gFAAgF;IAChF,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,EAAE;QACzD,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,cAAc,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CACtD,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CACjD,CAAA;KACF;IAED,OAAO,CAAC,CAAC,cAAc,CAAA;IACvB,OAAO,CAAC,CAAC,IAAI,CAAA;IACb,OAAO,CAAC,CAAC,gBAAgB,CAAA;IACzB,gDAAgD;IAChD,OAAO,CAAC,CAAC,SAAS,CAAA;IAClB,OAAO,CAAC,CAAC,UAAU,CAAA;IACnB,OAAO,CAAC,CAAC,QAAQ,CAAA;IACjB,OAAO,CAAC,CAAC,WAAW,CAAA;IACpB,OAAO,CAAC,CAAC,KAAK,CAAA;IAEd,IAAI,CAAC,CAAC,aAAa,EAAE;QACnB,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,aAAa,CAAA;KACzB;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AA/DD,kCA+DC"}
package/esm/GtfAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,13 @@
1
- declare const GtfAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
1
+ declare const GtfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
+ /**
3
+ * #slot
4
+ */
5
+ gtfLocation: {
6
+ type: string;
7
+ defaultValue: {
8
+ uri: string;
9
+ locationType: string;
10
+ };
11
+ };
12
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
13
  export default GtfAdapter;
package/esm/util.js CHANGED
@@ -30,9 +30,9 @@ export function featureData(data) {
30
30
  if (data.attributes[a] !== null) {
31
31
  let attr = data.attributes[a];
32
32
  if (Array.isArray(attr) && attr.length === 1) {
33
- // gtf uses double quotes for text values in the attributes column, remove them
34
- const formattedAttr = attr[0].replace(/^"|"$/g, '');
35
- attr = formattedAttr;
33
+ // gtf uses double quotes for text values in the attributes column,
34
+ // remove them
35
+ attr = `${attr[0]}`.replace(/^"|"$/g, '');
36
36
  }
37
37
  f[b] = attr;
38
38
  }
package/esm/util.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAaA,MAAM,UAAU,WAAW,CAAC,IAAgB;IAC1C,MAAM,CAAC,GAA4B,EAAE,GAAG,IAAI,EAAE,CAC7C;IAAC,CAAC,CAAC,KAAgB,IAAI,CAAC,CAAA,CAAC,uBAAuB;IACjD,CAAC,CAAC,MAAM,GAAG,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA,CAAC,iBAAiB;IACrF,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAC5B,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAA;IACzB,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;QACvB,OAAO,CAAC,CAAC,KAAK,CAAA;KACf;IACD,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;QACvB,OAAO,CAAC,CAAC,KAAK,CAAA;KACf;IACD,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC;QAC5B,OAAO;QACP,KAAK;QACL,UAAU;QACV,OAAO;QACP,aAAa;QACb,QAAQ;QACR,OAAO;QACP,QAAQ;KACT,CAAC,CAAA;IACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE;QAC5C,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAA;QACvB,IAAI,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YACxB,gDAAgD;YAChD,gCAAgC;YAChC,CAAC,IAAI,GAAG,CAAA;SACT;QACD,IAAI,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;YAC/B,IAAI,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YAC7B,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;gBAC5C,+EAA+E;gBAC/E,MAAM,aAAa,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;gBACnD,IAAI,GAAG,aAAa,CAAA;aACrB;YACD,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;SACZ;KACF;IACD,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,QAAQ,CAAA;IACtB,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,WAAW,CAAA;IAEtB,gFAAgF;IAChF,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,EAAE;QACzD,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,cAAc,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CACtD,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CACjD,CAAA;KACF;IAED,OAAO,CAAC,CAAC,cAAc,CAAA;IACvB,OAAO,CAAC,CAAC,IAAI,CAAA;IACb,OAAO,CAAC,CAAC,gBAAgB,CAAA;IACzB,gDAAgD;IAChD,OAAO,CAAC,CAAC,SAAS,CAAA;IAClB,OAAO,CAAC,CAAC,UAAU,CAAA;IACnB,OAAO,CAAC,CAAC,QAAQ,CAAA;IACjB,OAAO,CAAC,CAAC,WAAW,CAAA;IACpB,OAAO,CAAC,CAAC,KAAK,CAAA;IAEd,IAAI,CAAC,CAAC,aAAa,EAAE;QACnB,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,aAAa,CAAA;KACzB;IACD,OAAO,CAAC,CAAA;AACV,CAAC"}
1
+ {"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAaA,MAAM,UAAU,WAAW,CAAC,IAAgB;IAC1C,MAAM,CAAC,GAA4B,EAAE,GAAG,IAAI,EAAE,CAC7C;IAAC,CAAC,CAAC,KAAgB,IAAI,CAAC,CAAA,CAAC,uBAAuB;IACjD,CAAC,CAAC,MAAM,GAAG,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA,CAAC,iBAAiB;IACrF,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAC5B,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAA;IACzB,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;QACvB,OAAO,CAAC,CAAC,KAAK,CAAA;KACf;IACD,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;QACvB,OAAO,CAAC,CAAC,KAAK,CAAA;KACf;IACD,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC;QAC5B,OAAO;QACP,KAAK;QACL,UAAU;QACV,OAAO;QACP,aAAa;QACb,QAAQ;QACR,OAAO;QACP,QAAQ;KACT,CAAC,CAAA;IACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE;QAC5C,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAA;QACvB,IAAI,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YACxB,gDAAgD;YAChD,gCAAgC;YAChC,CAAC,IAAI,GAAG,CAAA;SACT;QACD,IAAI,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;YAC/B,IAAI,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAsB,CAAA;YAClD,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;gBAC5C,mEAAmE;gBACnE,cAAc;gBACd,IAAI,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;aAC1C;YACD,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;SACZ;KACF;IACD,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,QAAQ,CAAA;IACtB,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,WAAW,CAAA;IAEtB,gFAAgF;IAChF,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,EAAE;QACzD,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,cAAc,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CACtD,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CACjD,CAAA;KACF;IAED,OAAO,CAAC,CAAC,cAAc,CAAA;IACvB,OAAO,CAAC,CAAC,IAAI,CAAA;IACb,OAAO,CAAC,CAAC,gBAAgB,CAAA;IACzB,gDAAgD;IAChD,OAAO,CAAC,CAAC,SAAS,CAAA;IAClB,OAAO,CAAC,CAAC,UAAU,CAAA;IACnB,OAAO,CAAC,CAAC,QAAQ,CAAA;IACjB,OAAO,CAAC,CAAC,WAAW,CAAA;IACpB,OAAO,CAAC,CAAC,KAAK,CAAA;IAEd,IAAI,CAAC,CAAC,aAAa,EAAE;QACnB,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,aAAa,CAAA;KACzB;IACD,OAAO,CAAC,CAAA;AACV,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-gtf",
3
- "version": "2.4.1",
3
+ "version": "2.5.0",
4
4
  "description": "JBrowse 2 gtf feature adapter",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -57,5 +57,5 @@
57
57
  "distModule": "esm/index.js",
58
58
  "srcModule": "src/index.ts",
59
59
  "module": "esm/index.js",
60
- "gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
60
+ "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
61
61
  }
package/src/util.ts CHANGED
@@ -41,11 +41,11 @@ export function featureData(data: FeatureLoc) {
41
41
  b += '2'
42
42
  }
43
43
  if (data.attributes[a] !== null) {
44
- let attr = data.attributes[a]
44
+ let attr = data.attributes[a] as string[] | string
45
45
  if (Array.isArray(attr) && attr.length === 1) {
46
- // gtf uses double quotes for text values in the attributes column, remove them
47
- const formattedAttr = attr[0].replace(/^"|"$/g, '')
48
- attr = formattedAttr
46
+ // gtf uses double quotes for text values in the attributes column,
47
+ // remove them
48
+ attr = `${attr[0]}`.replace(/^"|"$/g, '')
49
49
  }
50
50
  f[b] = attr
51
51
  }