@jbrowse/plugin-gtf 2.4.0 → 2.4.2

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 (6) hide show
  1. package/dist/util.js +7 -9
  2. package/dist/util.js.map +1 -1
  3. package/esm/util.js +7 -9
  4. package/esm/util.js.map +1 -1
  5. package/package.json +2 -2
  6. package/src/util.ts +9 -9
package/dist/util.js CHANGED
@@ -13,7 +13,7 @@ function featureData(data) {
13
13
  if (data.frame === null) {
14
14
  delete f.score;
15
15
  }
16
- const defaultFields = [
16
+ const defaultFields = new Set([
17
17
  'start',
18
18
  'end',
19
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  'seq_name',
@@ -22,10 +22,10 @@ function featureData(data) {
22
22
  'source',
23
23
  'frame',
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  'strand',
25
- ];
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- Object.keys(data.attributes).forEach(a => {
25
+ ]);
26
+ for (const a of Object.keys(data.attributes)) {
27
27
  let b = a.toLowerCase();
28
- if (defaultFields.includes(b)) {
28
+ if (defaultFields.has(b)) {
29
29
  // add "suffix" to tag name if it already exists
30
30
  // reproduces behavior of NCList
31
31
  b += '2';
@@ -39,14 +39,12 @@ function featureData(data) {
39
39
  }
40
40
  f[b] = attr;
41
41
  }
42
- });
42
+ }
43
43
  f.refName = f.seq_name;
44
44
  f.type = f.featureType;
45
45
  // the SimpleFeature constructor takes care of recursively inflating subfeatures
46
- if (data.child_features && data.child_features.length) {
47
- f.subfeatures = data.child_features
48
- .map(childLocs => childLocs.map(childLoc => featureData(childLoc)))
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- .flat();
46
+ if (data.child_features && data.child_features.length > 0) {
47
+ f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc)));
50
48
  }
51
49
  delete f.child_features;
52
50
  delete f.data;
package/dist/util.js.map CHANGED
@@ -1 +1 @@
1
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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"}
package/esm/util.js CHANGED
@@ -10,7 +10,7 @@ export function featureData(data) {
10
10
  if (data.frame === null) {
11
11
  delete f.score;
12
12
  }
13
- const defaultFields = [
13
+ const defaultFields = new Set([
14
14
  'start',
15
15
  'end',
16
16
  'seq_name',
@@ -19,10 +19,10 @@ export function featureData(data) {
19
19
  'source',
20
20
  'frame',
21
21
  'strand',
22
- ];
23
- Object.keys(data.attributes).forEach(a => {
22
+ ]);
23
+ for (const a of Object.keys(data.attributes)) {
24
24
  let b = a.toLowerCase();
25
- if (defaultFields.includes(b)) {
25
+ if (defaultFields.has(b)) {
26
26
  // add "suffix" to tag name if it already exists
27
27
  // reproduces behavior of NCList
28
28
  b += '2';
@@ -36,14 +36,12 @@ export function featureData(data) {
36
36
  }
37
37
  f[b] = attr;
38
38
  }
39
- });
39
+ }
40
40
  f.refName = f.seq_name;
41
41
  f.type = f.featureType;
42
42
  // the SimpleFeature constructor takes care of recursively inflating subfeatures
43
- if (data.child_features && data.child_features.length) {
44
- f.subfeatures = data.child_features
45
- .map(childLocs => childLocs.map(childLoc => featureData(childLoc)))
46
- .flat();
43
+ if (data.child_features && data.child_features.length > 0) {
44
+ f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc)));
47
45
  }
48
46
  delete f.child_features;
49
47
  delete f.data;
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;QACpB,OAAO;QACP,KAAK;QACL,UAAU;QACV,OAAO;QACP,aAAa;QACb,QAAQ;QACR,OAAO;QACP,QAAQ;KACT,CAAA;IACD,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACvC,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAA;QACvB,IAAI,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE;YAC7B,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;IACH,CAAC,CAAC,CAAA;IACF,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,EAAE;QACrD,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,cAAc;aAChC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC;aAClE,IAAI,EAAE,CAAA;KACV;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,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"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-gtf",
3
- "version": "2.4.0",
3
+ "version": "2.4.2",
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": "78707a2bc3ba8489f26a590ef83f62ede945d048"
60
+ "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
61
61
  }
package/src/util.ts CHANGED
@@ -23,7 +23,7 @@ export function featureData(data: FeatureLoc) {
23
23
  if (data.frame === null) {
24
24
  delete f.score
25
25
  }
26
- const defaultFields = [
26
+ const defaultFields = new Set([
27
27
  'start',
28
28
  'end',
29
29
  'seq_name',
@@ -32,10 +32,10 @@ export function featureData(data: FeatureLoc) {
32
32
  'source',
33
33
  'frame',
34
34
  'strand',
35
- ]
36
- Object.keys(data.attributes).forEach(a => {
35
+ ])
36
+ for (const a of Object.keys(data.attributes)) {
37
37
  let b = a.toLowerCase()
38
- if (defaultFields.includes(b)) {
38
+ if (defaultFields.has(b)) {
39
39
  // add "suffix" to tag name if it already exists
40
40
  // reproduces behavior of NCList
41
41
  b += '2'
@@ -49,15 +49,15 @@ export function featureData(data: FeatureLoc) {
49
49
  }
50
50
  f[b] = attr
51
51
  }
52
- })
52
+ }
53
53
  f.refName = f.seq_name
54
54
  f.type = f.featureType
55
55
 
56
56
  // the SimpleFeature constructor takes care of recursively inflating subfeatures
57
- if (data.child_features && data.child_features.length) {
58
- f.subfeatures = data.child_features
59
- .map(childLocs => childLocs.map(childLoc => featureData(childLoc)))
60
- .flat()
57
+ if (data.child_features && data.child_features.length > 0) {
58
+ f.subfeatures = data.child_features.flatMap(childLocs =>
59
+ childLocs.map(childLoc => featureData(childLoc)),
60
+ )
61
61
  }
62
62
 
63
63
  delete f.child_features