@jbrowse/plugin-sequence 2.2.0 → 2.2.1

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 (42) hide show
  1. package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts +0 -4
  2. package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js +2 -2
  3. package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js.map +1 -1
  4. package/dist/TwoBitAdapter/TwoBitAdapter.js +7 -7
  5. package/dist/TwoBitAdapter/TwoBitAdapter.js.map +1 -1
  6. package/dist/index.js +0 -2
  7. package/dist/index.js.map +1 -1
  8. package/esm/IndexedFastaAdapter/IndexedFastaAdapter.d.ts +0 -4
  9. package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js +2 -2
  10. package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js.map +1 -1
  11. package/esm/TwoBitAdapter/TwoBitAdapter.js +7 -7
  12. package/esm/TwoBitAdapter/TwoBitAdapter.js.map +1 -1
  13. package/esm/index.js +0 -2
  14. package/esm/index.js.map +1 -1
  15. package/package.json +2 -2
  16. package/src/BgzipFastaAdapter/__snapshots__/BgzipFastaAdapter.test.ts.snap +3 -3
  17. package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts +0 -11
  18. package/src/IndexedFastaAdapter/__snapshots__/IndexedFastaAdapter.test.ts.snap +3 -3
  19. package/src/TwoBitAdapter/__snapshots__/TwoBitAdapter.test.ts.snap +6 -6
  20. package/src/__snapshots__/index.test.js.snap +2 -2
  21. package/src/index.ts +0 -2
  22. package/dist/GCContentAdapter/GCContentAdapter.d.ts +0 -17
  23. package/dist/GCContentAdapter/GCContentAdapter.js +0 -89
  24. package/dist/GCContentAdapter/GCContentAdapter.js.map +0 -1
  25. package/dist/GCContentAdapter/configSchema.d.ts +0 -3
  26. package/dist/GCContentAdapter/configSchema.js +0 -17
  27. package/dist/GCContentAdapter/configSchema.js.map +0 -1
  28. package/dist/GCContentAdapter/index.d.ts +0 -3
  29. package/dist/GCContentAdapter/index.js +0 -44
  30. package/dist/GCContentAdapter/index.js.map +0 -1
  31. package/esm/GCContentAdapter/GCContentAdapter.d.ts +0 -17
  32. package/esm/GCContentAdapter/GCContentAdapter.js +0 -86
  33. package/esm/GCContentAdapter/GCContentAdapter.js.map +0 -1
  34. package/esm/GCContentAdapter/configSchema.d.ts +0 -3
  35. package/esm/GCContentAdapter/configSchema.js +0 -15
  36. package/esm/GCContentAdapter/configSchema.js.map +0 -1
  37. package/esm/GCContentAdapter/index.d.ts +0 -3
  38. package/esm/GCContentAdapter/index.js +0 -16
  39. package/esm/GCContentAdapter/index.js.map +0 -1
  40. package/src/GCContentAdapter/GCContentAdapter.ts +0 -99
  41. package/src/GCContentAdapter/configSchema.ts +0 -22
  42. package/src/GCContentAdapter/index.ts +0 -22
package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts CHANGED
@@ -2,15 +2,11 @@ import { IndexedFasta } from '@gmod/indexedfasta';
2
2
  import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
3
3
  import { NoAssemblyRegion } from '@jbrowse/core/util/types';
4
4
  import { Feature } from '@jbrowse/core/util';
5
- import { AnyConfigurationModel } from '@jbrowse/core/configuration';
6
- import PluginManager from '@jbrowse/core/PluginManager';
7
- import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
8
5
  export default class extends BaseSequenceAdapter {
9
6
  protected setupP?: Promise<{
10
7
  fasta: IndexedFasta;
11
8
  }>;
12
9
  private seqCache;
13
- constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
14
10
  getRefNames(opts?: BaseOptions): Promise<string[]>;
15
11
  getRegions(opts?: BaseOptions): Promise<{
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12
  refName: string;
package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js CHANGED
@@ -11,8 +11,8 @@ const util_1 = require("@jbrowse/core/util");
11
11
  const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
12
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  const QuickLRU_1 = __importDefault(require("@jbrowse/core/util/QuickLRU"));
13
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  class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
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- constructor(config, getSubAdapter, pluginManager) {
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- super(config, getSubAdapter, pluginManager);
14
+ constructor() {
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+ super(...arguments);
16
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  this.seqCache = new abortable_promise_cache_1.default({
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  cache: new QuickLRU_1.default({ maxSize: 200 }),
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  fill: async (args, signal) => {
package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"IndexedFastaAdapter.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/IndexedFastaAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qDAAiD;AACjD,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,6CAA2D;AAC3D,sFAA2D;AAC3D,2EAAkD;AAIlD,eAAqB,SAAQ,iCAAmB;IAAhD;;QAGU,aAAQ,GAAG,IAAI,iCAAqB,CAAwB;YAClE,KAAK,EAAE,IAAI,kBAAQ,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC;YACrC,IAAI,EAAE,KAAK,EAAE,IAAO,EAAE,MAAoB,EAAE,EAAE;gBAC5C,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,IAAI,CAAA;gBAC3C,OAAO,KAAK,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;YACpE,CAAC;SACF,CAAC,CAAA;IAyFJ,CAAC;IAvFQ,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,OAAO,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAEM,KAAK,CAAC,UAAU,CAAC,IAAkB;QACxC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;QACnD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAEM,KAAK,CAAC,QAAQ;QACnB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QACnE,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAiB,CAAA;QAE/D,OAAO;YACL,KAAK,EAAE,IAAI,2BAAY,CAAC;gBACtB,KAAK,EAAE,IAAA,iBAAY,EAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;gBACtD,GAAG,EAAE,IAAA,iBAAY,EAAC,WAAW,EAAE,IAAI,CAAC,aAAa,CAAC;aACnD,CAAC;SACH,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,kBAAkB,CAAC,CAAA;QAC5C,OAAO,GAAG,CAAC,GAAG,KAAK,EAAE,IAAI,GAAG,CAAC,GAAG,KAAK,2BAA2B;YAC9D,CAAC,CAAC,IAAI;YACN,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACtC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,WAAW,CAAC,MAAwB,EAAE,IAAkB;QAC7D,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACpC,MAAM,IAAI,GAAG,MAAM,KAAK,CAAC,eAAe,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,MAAM,GAAG,EAAE,CAAA;YACjB,MAAM,SAAS,GAAG,MAAM,CAAA;YAExB,MAAM,CAAC,GAAG,KAAK,GAAG,CAAC,KAAK,GAAG,SAAS,CAAC,CAAA;YACrC,MAAM,CAAC,GAAG,GAAG,GAAG,CAAC,SAAS,GAAG,CAAC,GAAG,GAAG,SAAS,CAAC,CAAC,CAAA;YAC/C,KAAK,IAAI,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,IAAI,SAAS,EAAE;gBAChE,MAAM,CAAC,GAAG;oBACR,OAAO;oBACP,KAAK,EAAE,UAAU;oBACjB,GAAG,EAAE,UAAU,GAAG,SAAS;iBAC5B,CAAA;gBACD,MAAM,CAAC,IAAI,CACT,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,EAAE,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,MAAM,CAAC,CACpE,CAAA;aACF;YACD,MAAM,GAAG,GAAG,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;iBACpC,IAAI,CAAC,EAAE,CAAC;iBACR,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC;iBAChB,KAAK,CAAC,CAAC,EAAE,GAAG,GAAG,KAAK,CAAC,CAAA;YACxB,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AAlGD,4BAkGC"}
package/dist/TwoBitAdapter/TwoBitAdapter.js CHANGED
@@ -10,13 +10,6 @@ const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeatur
10
10
  const twobit_1 = require("@gmod/twobit");
11
11
  const configuration_1 = require("@jbrowse/core/configuration");
12
12
  class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
13
- constructor(config, getSubAdapter, pluginManager) {
14
- super(config, getSubAdapter, pluginManager);
15
- this.chromSizesData = this.initChromSizes();
16
- this.twobit = new twobit_1.TwoBitFile({
17
- filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(config, 'twoBitLocation'), this.pluginManager),
18
- });
19
- }
20
13
  async initChromSizes() {
21
14
  const conf = (0, configuration_1.readConfObject)(this.config, 'chromSizesLocation');
22
15
  // check against default and empty in case someone makes the field blank in
@@ -32,6 +25,13 @@ class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
32
25
  }
33
26
  return undefined;
34
27
  }
28
+ constructor(config, getSubAdapter, pluginManager) {
29
+ super(config, getSubAdapter, pluginManager);
30
+ this.chromSizesData = this.initChromSizes();
31
+ this.twobit = new twobit_1.TwoBitFile({
32
+ filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(config, 'twoBitLocation'), this.pluginManager),
33
+ });
34
+ }
35
35
  async getRefNames() {
36
36
  const chromSizesData = await this.chromSizesData;
37
37
  if (chromSizesData) {
package/dist/TwoBitAdapter/TwoBitAdapter.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"TwoBitAdapter.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/TwoBitAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAA6E;AAE7E,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,yCAAyC;AACzC,+DAA4D;AAK5D,MAAqB,aAAc,SAAQ,iCAAmB;IA4B5D,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAC3C,IAAI,CAAC,MAAM,GAAG,IAAI,mBAAU,CAAC;YAC3B,UAAU,EAAE,IAAA,iBAAY,EACtB,IAAA,8BAAc,EAAC,MAAM,EAAE,gBAAgB,CAAC,EACxC,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;IACJ,CAAC;IAlCO,KAAK,CAAC,cAAc;QAC1B,MAAM,IAAI,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC9D,2EAA2E;QAC3E,yEAAyE;QACzE,SAAS;QACT,IAAI,IAAI,CAAC,GAAG,KAAK,8BAA8B,IAAI,IAAI,CAAC,GAAG,KAAK,EAAE,EAAE;YAClE,MAAM,IAAI,GAAG,IAAA,iBAAY,EAAC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;YACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CACA,KAAK,CAAC,YAAY,EACnB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,EAC5B,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACvC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAA;YACxB,CAAC,CAAC,CACL,CAAA;SACF;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAiBM,KAAK,CAAC,WAAW;QACtB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;SACnC;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;IACvC,CAAC;IAEM,KAAK,CAAC,UAAU;QACrB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;gBACjD,OAAO;gBACP,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,cAAc,CAAC,OAAO,CAAC;aAC7B,CAAC,CAAC,CAAA;SACJ;QACD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;QACrD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAED;;;;OAIG;IACI,WAAW,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAoB;QAC1D,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;YACpE,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AAhGD,gCAgGC"}
1
+ {"version":3,"file":"TwoBitAdapter.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/TwoBitAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAA6E;AAE7E,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,yCAAyC;AACzC,+DAA4D;AAK5D,MAAqB,aAAc,SAAQ,iCAAmB;IAOpD,KAAK,CAAC,cAAc;QAC1B,MAAM,IAAI,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC9D,2EAA2E;QAC3E,yEAAyE;QACzE,SAAS;QACT,IAAI,IAAI,CAAC,GAAG,KAAK,8BAA8B,IAAI,IAAI,CAAC,GAAG,KAAK,EAAE,EAAE;YAClE,MAAM,IAAI,GAAG,IAAA,iBAAY,EAAC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;YACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CACA,KAAK,CAAC,YAAY,EACnB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,EAC5B,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACvC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAA;YACxB,CAAC,CAAC,CACL,CAAA;SACF;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAC3C,IAAI,CAAC,MAAM,GAAG,IAAI,mBAAU,CAAC;YAC3B,UAAU,EAAE,IAAA,iBAAY,EACtB,IAAA,8BAAc,EAAC,MAAM,EAAE,gBAAgB,CAAC,EACxC,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;IACJ,CAAC;IAEM,KAAK,CAAC,WAAW;QACtB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;SACnC;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;IACvC,CAAC;IAEM,KAAK,CAAC,UAAU;QACrB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;gBACjD,OAAO;gBACP,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,cAAc,CAAC,OAAO,CAAC;aAC7B,CAAC,CAAC,CAAA;SACJ;QACD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;QACrD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAED;;;;OAIG;IACI,WAAW,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAoB;QAC1D,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;YACpE,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AAhGD,gCAgGC"}
package/dist/index.js CHANGED
@@ -9,7 +9,6 @@ const DivSequenceRenderer_1 = __importDefault(require("./DivSequenceRenderer"));
9
9
  const BgzipFastaAdapter_1 = __importDefault(require("./BgzipFastaAdapter"));
10
10
  const ChromSizesAdapter_1 = __importDefault(require("./ChromSizesAdapter"));
11
11
  const IndexedFastaAdapter_1 = __importDefault(require("./IndexedFastaAdapter"));
12
- const GCContentAdapter_1 = __importDefault(require("./GCContentAdapter"));
13
12
  const SequenceSearchAdapter_1 = __importDefault(require("./SequenceSearchAdapter"));
14
13
  const ReferenceSequenceTrack_1 = __importDefault(require("./ReferenceSequenceTrack"));
15
14
  const LinearReferenceSequenceDisplay_1 = __importDefault(require("./LinearReferenceSequenceDisplay"));
@@ -25,7 +24,6 @@ class SequencePlugin extends Plugin_1.default {
25
24
  (0, BgzipFastaAdapter_1.default)(pluginManager);
26
25
  (0, ChromSizesAdapter_1.default)(pluginManager);
27
26
  (0, IndexedFastaAdapter_1.default)(pluginManager);
28
- (0, GCContentAdapter_1.default)(pluginManager);
29
27
  (0, SequenceSearchAdapter_1.default)(pluginManager);
30
28
  (0, ReferenceSequenceTrack_1.default)(pluginManager);
31
29
  (0, LinearReferenceSequenceDisplay_1.default)(pluginManager);
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;AAAA,kEAAyC;AAGzC,oEAA4C;AAC5C,gFAAwD;AACxD,4EAAoD;AACpD,4EAAoD;AACpD,gFAAwD;AACxD,0EAAkD;AAClD,oFAA4D;AAC5D,sFAA8D;AAC9D,sGAA8E;AAC9E,oFAA2D;AAE3D,MAAqB,cAAe,SAAQ,gBAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAczB,CAAC;IAZC,OAAO,CAAC,aAA4B;QAClC,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;QACnC,IAAA,uBAAc,EAAC,aAAa,CAAC,CAAA;QAC7B,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;QACnC,IAAA,0BAAiB,EAAC,aAAa,CAAC,CAAA;QAChC,IAAA,+BAAsB,EAAC,aAAa,CAAC,CAAA;QACrC,IAAA,gCAAuB,EAAC,aAAa,CAAC,CAAA;QACtC,IAAA,wCAA+B,EAAC,aAAa,CAAC,CAAA;QAC9C,IAAA,+BAAqB,EAAC,aAAa,CAAC,CAAA;IACtC,CAAC;CACF;AAfD,iCAeC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;AAAA,kEAAyC;AAGzC,oEAA4C;AAC5C,gFAAwD;AACxD,4EAAoD;AACpD,4EAAoD;AACpD,gFAAwD;AACxD,oFAA4D;AAC5D,sFAA8D;AAC9D,sGAA8E;AAC9E,oFAA2D;AAE3D,MAAqB,cAAe,SAAQ,gBAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAazB,CAAC;IAXC,OAAO,CAAC,aAA4B;QAClC,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;QACnC,IAAA,uBAAc,EAAC,aAAa,CAAC,CAAA;QAC7B,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;QACnC,IAAA,+BAAsB,EAAC,aAAa,CAAC,CAAA;QACrC,IAAA,gCAAuB,EAAC,aAAa,CAAC,CAAA;QACtC,IAAA,wCAA+B,EAAC,aAAa,CAAC,CAAA;QAC9C,IAAA,+BAAqB,EAAC,aAAa,CAAC,CAAA;IACtC,CAAC;CACF;AAdD,iCAcC"}
package/esm/IndexedFastaAdapter/IndexedFastaAdapter.d.ts CHANGED
@@ -2,15 +2,11 @@ import { IndexedFasta } from '@gmod/indexedfasta';
2
2
  import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
3
3
  import { NoAssemblyRegion } from '@jbrowse/core/util/types';
4
4
  import { Feature } from '@jbrowse/core/util';
5
- import { AnyConfigurationModel } from '@jbrowse/core/configuration';
6
- import PluginManager from '@jbrowse/core/PluginManager';
7
- import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
8
5
  export default class extends BaseSequenceAdapter {
9
6
  protected setupP?: Promise<{
10
7
  fasta: IndexedFasta;
11
8
  }>;
12
9
  private seqCache;
13
- constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
14
10
  getRefNames(opts?: BaseOptions): Promise<string[]>;
15
11
  getRegions(opts?: BaseOptions): Promise<{
16
12
  refName: string;
package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js CHANGED
@@ -6,8 +6,8 @@ import { SimpleFeature } from '@jbrowse/core/util';
6
6
  import AbortablePromiseCache from 'abortable-promise-cache';
7
7
  import QuickLRU from '@jbrowse/core/util/QuickLRU';
8
8
  export default class extends BaseSequenceAdapter {
9
- constructor(config, getSubAdapter, pluginManager) {
10
- super(config, getSubAdapter, pluginManager);
9
+ constructor() {
10
+ super(...arguments);
11
11
  this.seqCache = new AbortablePromiseCache({
12
12
  cache: new QuickLRU({ maxSize: 200 }),
13
13
  fill: async (args, signal) => {
package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/TwoBitAdapter/TwoBitAdapter.js CHANGED
@@ -5,13 +5,6 @@ import SimpleFeature from '@jbrowse/core/util/simpleFeature';
5
5
  import { TwoBitFile } from '@gmod/twobit';
6
6
  import { readConfObject } from '@jbrowse/core/configuration';
7
7
  export default class TwoBitAdapter extends BaseSequenceAdapter {
8
- constructor(config, getSubAdapter, pluginManager) {
9
- super(config, getSubAdapter, pluginManager);
10
- this.chromSizesData = this.initChromSizes();
11
- this.twobit = new TwoBitFile({
12
- filehandle: openLocation(readConfObject(config, 'twoBitLocation'), this.pluginManager),
13
- });
14
- }
15
8
  async initChromSizes() {
16
9
  const conf = readConfObject(this.config, 'chromSizesLocation');
17
10
  // check against default and empty in case someone makes the field blank in
@@ -27,6 +20,13 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
27
20
  }
28
21
  return undefined;
29
22
  }
23
+ constructor(config, getSubAdapter, pluginManager) {
24
+ super(config, getSubAdapter, pluginManager);
25
+ this.chromSizesData = this.initChromSizes();
26
+ this.twobit = new TwoBitFile({
27
+ filehandle: openLocation(readConfObject(config, 'twoBitLocation'), this.pluginManager),
28
+ });
29
+ }
30
30
  async getRefNames() {
31
31
  const chromSizesData = await this.chromSizesData;
32
32
  if (chromSizesData) {
package/esm/TwoBitAdapter/TwoBitAdapter.js.map CHANGED
@@ -1 +1 @@
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package/esm/index.js CHANGED
@@ -4,7 +4,6 @@ import DivSequenceRendererF from './DivSequenceRenderer';
4
4
  import BgzipFastaAdapterF from './BgzipFastaAdapter';
5
5
  import ChromSizesAdapterF from './ChromSizesAdapter';
6
6
  import IndexedFastaAdapterF from './IndexedFastaAdapter';
7
- import GCContentAdapterF from './GCContentAdapter';
8
7
  import SequenceSearchAdapterF from './SequenceSearchAdapter';
9
8
  import ReferenceSequenceTrackF from './ReferenceSequenceTrack';
10
9
  import LinearReferenceSequenceDisplayF from './LinearReferenceSequenceDisplay';
@@ -20,7 +19,6 @@ export default class SequencePlugin extends Plugin {
20
19
  BgzipFastaAdapterF(pluginManager);
21
20
  ChromSizesAdapterF(pluginManager);
22
21
  IndexedFastaAdapterF(pluginManager);
23
- GCContentAdapterF(pluginManager);
24
22
  SequenceSearchAdapterF(pluginManager);
25
23
  ReferenceSequenceTrackF(pluginManager);
26
24
  LinearReferenceSequenceDisplayF(pluginManager);
package/esm/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,sBAAsB,MAAM,yBAAyB,CAAA;AAC5D,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,+BAA+B,MAAM,kCAAkC,CAAA;AAC9E,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAE3D,MAAM,CAAC,OAAO,OAAO,cAAe,SAAQ,MAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAczB,CAAC;IAZC,OAAO,CAAC,aAA4B;QAClC,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,iBAAiB,CAAC,aAAa,CAAC,CAAA;QAChC,sBAAsB,CAAC,aAAa,CAAC,CAAA;QACrC,uBAAuB,CAAC,aAAa,CAAC,CAAA;QACtC,+BAA+B,CAAC,aAAa,CAAC,CAAA;QAC9C,qBAAqB,CAAC,aAAa,CAAC,CAAA;IACtC,CAAC;CACF"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,sBAAsB,MAAM,yBAAyB,CAAA;AAC5D,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,+BAA+B,MAAM,kCAAkC,CAAA;AAC9E,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAE3D,MAAM,CAAC,OAAO,OAAO,cAAe,SAAQ,MAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAazB,CAAC;IAXC,OAAO,CAAC,aAA4B;QAClC,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,sBAAsB,CAAC,aAAa,CAAC,CAAA;QACrC,uBAAuB,CAAC,aAAa,CAAC,CAAA;QACtC,+BAA+B,CAAC,aAAa,CAAC,CAAA;QAC9C,qBAAqB,CAAC,aAAa,CAAC,CAAA;IACtC,CAAC;CACF"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-sequence",
3
- "version": "2.2.0",
3
+ "version": "2.2.1",
4
4
  "description": "JBrowse 2 sequence adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -59,5 +59,5 @@
59
59
  "distModule": "esm/index.js",
60
60
  "srcModule": "src/index.ts",
61
61
  "module": "esm/index.js",
62
- "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
62
+ "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
63
63
  }
package/src/BgzipFastaAdapter/__snapshots__/BgzipFastaAdapter.test.ts.snap CHANGED
@@ -1,8 +1,8 @@
1
1
  // Jest Snapshot v1, https://goo.gl/fbAQLP
2
2
 
3
3
  exports[`can use a indexed fasta with gzi 1`] = `
4
- Array [
5
- Object {
4
+ [
5
+ {
6
6
  "end": 20000,
7
7
  "refName": "ctgA",
8
8
  "seq": "cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgattatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctgaattgagaactcgagcgggggctaggcaaattctgattcagcctgacttctcttggaaccctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagaccaacctgaccaccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctccttggtcgctccgttgtacccaggctactttgaaagagcgcagaatacttagacggtatcgatcatggtagcatagcattctgataacatgtatggagttcgaacatccgtctggggccggacggtccgtttgaggttggttgatctgggtgatagtcagcaagatagacgttagataacaaattaaaggattttaccttagattgcgactagtacaacggtacatcggtgattcgcgctctactagatcacgctatgggtaccataaacaaacggtggaccttctcaagctggttgacgcctcagcaacataggcttcctcctccacgcatctcagcataaaaggcttataaactgcttctttgtgccagagcaactcaattaagcccttggtaccgtgggcacgcattctgtcacggtgaccaactgttcatcctgaatcgccgaatgggactatttggtacaggaatcaagcggatggcactactgcagcttatttacgacggtattcttaaagtttttaagacaatgtatttcatgggtagttcggtttgttttattgctacacaggctcttgtagacgacctacttagcactacggccgagcgcaataacccccggaaagcacttgctactgggaggcgggtttatccatcggcaataggggttatcagtactaccaagaagattgtgaagatattaacagcattgaaaaaagttcggactgggcatgaaacgtgtgtcagagttagagtccttgagggactgaatgggtttgtcccaggcccaagcttgaggtggatgtcacctcgggtactgcctctattacagaggtatcttaatggcgcatccagccttgtggctgggtctacgtacgcgtgggcaccatacgtatgttggcaggaaaggtcaatcatgcttgtttcctcgtcgcagaaacgttcacactattggctcgcgggatcgaacgggcctgattatttttccagctcctgcgttcctatcacgccaactgtcgctaataaaatgttatatagagataacccattgctatgcaaggatggagaaaccgcttcacaacaccctagaattacttcagcactaacatctaagataccgggaaaaccgtaggtgccacttggttttgagggcaatgcctcttgcactggcgattcgtggagtaaccttgctaccgatttccaccttttctaggtatgattacatgcgatcgccattgtcagtcgtcgtacgaaatccaggaaggaattcgaatacatgaccgaaagctatggcatcataagcgtggctctttactaaggacacgtgtagtcggctgatttcgcgcagaacttcgctcaccggacagtgactgctgtccgaacttgggggcagcgtagattctagctagagaccgcagcgaaaatgccactcgctaggtggctatggacgtccagctataggcccccacattcgtatgtatactccggtaattgagtctacctttcgaaagatcaaagttcacaaaccttctctcacgttaacatagatgctcgcacatagctagtccggtgataaagcggccgtgcatgcgagtatttagcgcacggaacagatattaggctgcgaaataccctcatatgctacagcgcaggtaacagacggttgatctccccgtagaattccctcaaggccggatcgttctcatgagtagcctttgtctgacatttcctctcaatagattgcagactcctgtgtcgtgggaaaacttcgcggaatcgctgtcgttacataaatctaaacagtgcagtccaagctatttactaccacgtatcataatgaacatctctttgtgaaatacgccggtacgccgagagatcgcccacattgcgtgtcaccaagacccagtgtctattgggcgcgctggttatagtatgcggaggcacccgatgtgctgctaatcactacaaactcgacaccaagaggcgaccgcgtgcgggagggctagaacgcgagagccacgtcaacgtggtggtaccgctcctgatgatacgagcactgtgctggcaccgctgccctatgtccagctaacaggtgtcacataatatcgcatctatagttgagtatcttatcgctagcgttacttgtgagttctcgggtagaatcgtcgtagcattctagtccttagcgtaagcaacgatatcgccgatattataggggcaataggtctcacccaccacgggtgtatatttaacgccctaagtagttaacggagactattaaacaattatgcacgtgaaagattagggtactgcacacgtgtcacgttgacgatgtaaacaccataaaggttgttctgtgatgcgatgcccatacctgcggtgcaacgtcctaaacttatgcggatcaccttctaattcagccgacgttgagaacgccagctatactctgtgagtacaaggtgaaagccccagatcaaaatattggagtcttgtccgtagctcttgggtggagagtgtgaccacgtttatcccttaatactgagactcttctcgttccacgccccggacattcgcgatacagcctagtttgataggtggctacaagggctctatccgaatagcacaaaactcagtcctagtgcgtataggtcgtgctctgcggttatacgctccacagaagaaagtacccactgcagtttgtcggtgggacttagcaaaacctgtaaccaaaaccgcacatggactctgttttggtggcgtggagtgtgcccgccgcctttatgctgggtcaaaatactatatgatttgttgtggtcgggcgcgacattggctcttatggtttataactattattcggtgcacagaaccgacttatgccccgattttgcacctcccgagagaaatggtactagtcattgtctcggggttttacaactcaaggataatctgccagcggtaccccgaaaaatcccatcccgaacggctggtacctatgctggagaccgaaatggagccagtgctatgcaaaccctcgctctttctatttggcccgaccagctgcgagagtcattcgacatacattgcgatggctggttcatctctctgcttcggattccgatcctgctgcctatggccacaacacgaaagagatcttggatacgtcctcaccatagtccaacggacaaatatggaggtgtacgcgcacggatacgagtacgacgggccgcccaatgctggtccttcgtgttatactgtttacttgcctccggtaagagtgtacagcttgtacccacgcggtggaggaccttacgcgtcgtccgcaggtgtggagatttcgctacctgttgcattggggcctcgccttacgtttttttcgacggaggcccgacccgccaggccagaccctcatcattgggatttttactgccttggacggcagattctgatgctggtaacgcgcttggcacacaccctggtcgtaattacgtactatcacctctattttaccaggggcgggccccgcctcaacgatcggtagtctcgttagaacagttgcttatactccgttagcactcacaactcggagaatgagcttacacagtccgtaatagtctccacagcttcccctggaaggttcgtacaggggccctggggtctaatgtgctaccgcctaacttcgttagtgtaaggtctcgtgtgcacctccaataacgctgcatttttgtatagaactcctttataggcctgactcttcggaacagcccactaattgacgtgcacgatgctgcatatacccttctcaatgacgcataccggtgactaaatcctgtggctggttgacactttgcataacccaccacgaaaacgcggtttgcacgtggttggaagcgagtaccggttaagggaagttacgtaaacccaacatagtgagcgatgcttaaaacactgcatgcgaacaacgaccggaacgagagcctaatagaaccaaatggataggtggttacgaaatccgcgcacaagtgtcgtgccactctcgtaaagaatgattgcttgcttatctatgagaaacctaataggcacgcacgtgtcgccagggaaaaaccaccatccgacaagacgctgaaaatcgagatagatgcagcccgcgcgtactttaagcacgatagccatcttgagcgcgacgattcagcttacggagattacttctcaaagcggacacctcgacgctgaagctctctatcgatgcacttgcatgtccatctacggcttgagcgaaccatgcttaacgcttggatgacgttgttagtcggattcgatcgtaccatactgtcctatccatcataacttcccgaattaaaactcattttctaccctcatttgtttcattggcgcatatgagcgccccatgggcgctgatcgacacaggcttgtagcgcacggctcgtcttgcagtagataaccatagtctttacgtcgcatatattaatatatcctcagacttccactgcggtattttggatcgtggcgtctgggacagtcacactctttaacgggagcgcgttcaatgtctgagtccatccgtgcagttcggtgcgatttta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accacattcagctctcggtaacatgggaggcttgtggttgcaccgtaaaagggggatagcccatccatcctgtaaacctacaatcgcgcgtagcttaatacgctcacattagacattcgatcgagagacctggtttcaagagccttcccttttgctttagtgggccaaatcgcaaccctgctcccctcccttacgccttatacacttcagtgcaaattcatgcgttcagcgaacaactggacttctgttgtacgtagtccacgggggcttattcattatagaaagccccctactgtcaccgttatatggttcacacatgagctgatcacctagagagtcgtcatgcacattcgcctaacaaggacatatgagtaaccgggaggggatatcttcgatttgcagcaccaatcgacgttgtactggtctattgtcggttaggtccgattatccgaccggcaatgaggcaagcccatctattcaggaaacttaggcagttccctgtgctggcccgacgtcgatgagttaagtctatacaggccggccgcgagtagttaacgagaccaacatagaactatcatactagccggcaatgatcaatagggtcttagtgccactgtccttcgagccctcgcctaatttagcgcgaccggtttcctattggcctgtggggttgcgggcgcgtccgctttaagaatggtccttaacacctacccggagatccattgcatagcacactctccccattagcctagacacgtcgtcgcccgtcgactttggctggaatttaatcgccggggatatcgaactttcacgccctttaacgacgaggaaacctaccgtcgcctggctggtaaatgggtgccttacggggactcacgatgctgtgaaccgcccgccagtctctggggctcccaaaatccaggttggaattacggacctccgccggtactacgcattacggggtggaaagtcctaagataggtgaatgaaagggcttcgctaaaccagtaagtcattaacaggacatcggcgtcacgtctcgcgggtttacacggcgcacaaatcctattcccatgataaacaccttatgccaatccacatccctcgctgcctaataaaattgtcacacctgcgctactgactaacgtttacgcaatgagagatgaattccgacacccacgcttgttgcaagcacagccgtatgggttctcgggtaaggtaacacgaggcacactccggcgcggccacttcggcccctccctgacgatgaccctcattggtcaagcatcagtcgaatgattcgtaacaaggagcaaccgactcagtagagagggtgaatctcacgcgctagcctgaggaccgcctaagtgcttgctgtgcgtcgcggcagtcgcgaggtgcgggctaaagtaaataattactggtcttacctaattaaagttggtggttagggacaacgttaccactaccagggtgcgcccctgaattcgggtatcggactatccagggcgccttttgcggccttaaatacctttttaatcacgctggagctagaaggccatcgggatagacggggttctaggtactcgaaaaaacaggcctaataactttattgcgcttggactaacctatgtacaacacgttgtagcatactatggaatgttactgacctacacggatagcatttgttcgggagcgtcattgacctcccagaccctatgccgatctgcaccattcagtgaccatccacaagtctctaggtttagccaaaggtgacaggtcaagcacttgcgcatgtccactagtcgattatgcaacgtctctgaacagttagcacttatctcccgccgtgtgactcacgcagtgaacttacctatagcatacgcctactattgaatgttcgttgttctaacacagcgctaatacctcactggcagaggtgcgcacgctcctagtatgggagggagtcaggtcagagtgtatgagactgatttttattcccgataggggttcagtgaaatcgacctctcaaaagagaggcgcagaattcgctgataagctctgctacgatcgctaaggcacgataagcagggcggtgaaggttggagcaagataatatcacccggacgcgggtcctgtcgcaacgagcggccgtgagacctggtgcgcaccgtgtctcgatcggccgaatatcggaacccactgcgtgactcaaatgatatttttgctatctgtgggggatttatgtcccggtagaactctgcttctagcagaggataaactttacaaggacggcgaatatggtgtcagagcgccctaatgatcccgtgctattccgcgggccaccggccgttaatggacttcgggttagaaggatgggttattcatcttccacagaaacgcccagccgcaatcgtgggtttactcgaccgcggttatctgcctacttagctgcattcctaaaacaggattaaaaaggccgcgagggttgcgaacctatggttgagaacagagtcatagagtcagatgcgcagggacggcacggatccacatggcagttaactaatattaatacccccttagcctcgtatatgggcgtgtgcagtcttgtccactcgcggacgcgtatccgagcgattctgtcttccaacgctattcgttaccactttggcacctctttgctaagcaggatgagaacatctcactcactacgagccttgactttcagcacgcggtacgagggcactgggcttctcgtcctttgctagatgtaggtgccttcccgccctcatgacgatgtcacgtctatcggtttattaaggtcggggaccattacgagattaccccgcgaccttcgtccaaatgggatcacggcaacgttccacgaggggcgcgttgcctgagccactcgggtatccccttccgatatccgcagaagtctagctaggagcaccgccaagcattacccgattaagcaaagcctactcatcgcatacacggttcttggggtttgcgtcagatagcaacttccggcggcagtagagatgatattttatccgattgagcttgcccagcgcaccctcgggccccgtggctcttctcttaaatgtgccctgcacgatgttagcggttcctactcctccccgagccctatgggtggacagactcgccctctgaggctgcgtgttcaactggttccaagtccggcgcctgtggatctacgacgcgaccagcaacattataccaatgtctaggcttagctcgaaaactagtaagccttagaactagggtcgtagcttcttctaaatgaagggcagcgtcatagccatccacgttagcgcttactcaatcgcctgtcggctgtcatgttaccgctgccgtaagttcgtgaacataaaatacaacacattttaggtttaacaaggattgtttaccgccacgtactggtgccggtagtgaaacgaaaaacctcagcatcgggaggaggagaacggaatccctaccaatcttatctctacttaaagaacaaagcgcgcggtacatggcgcagacgagaatgaatccccgaacgggccgagttagactcctcaacctgtcgaaaagttgcgatccgctagatcgtagagtacggacttaaaaaagaaaagaaggtctctacccgagcggtgagcccaaccagttccaggttgctgccggattcttccacacggcggtgccatatggacgaccccgtactttgggcattctaggctacctactgcgaacgcctcgcgttcatgcgcaaagttttctctagataggcgcgctttggtaagcatagtaataggttcttcagcgtctaaagcccgcccattaggcctggcgactctgctttagtggtaaagagatagcatcgatgtacatcgatggagagagtattttcacgaaagtgcgcgccgtacactatttatcggcatgcgcgctaaactggagggtctaataaccagatcacgcaacgaggtcccatgtacggttcgcattgcgaaagtatgggatactagaggttttatcgggcctcgcttgaggtctgtctgggactggcgcacatcgctcgtcgcccagtcgatagcggggtgattaaataagaaatatgttagtgcccggatttggaaccaaccagtcccggtagcggtacaaaaagcctttcctgctagttctatgcttaaagcgtactcctgttacaatccgtaggcaacctgaagaggcaacctggttttcctttatttcgactttgtttgccatttccaatgtgatactgtgcggcgaccttaatgctttttggtaaaaccataccgagatccagcgcacgcgacattcagaccggtcccggtttggcggtcaacctcgtactctgcactgttcagctagaggggtctcctatcccgaggtaccggtcgtctaacgggtggttacaggggctggtcctactctaccaacagttaaggagggcaacaagttcgatggggcatcgtataacttgaatgccattggacaaataataattgctccacgtcccaaacctcaactgaccttgtacgcataggtgccacctgcacgcaaccgagctcgttcaagtgtccttcttagctggcgccgagtgaacctgcatctgagagtctacccaacgatctagtatcataatgtctgtagccagcgactatgacacttagagagccgcctaagaaagtgtttgcggctcctgccccggtgcgcttgttcggtgggaggtcgttatatagaaccatggggatataatgaatggtaacatatctgccacgttgacaagccgctattatgaattcagggttggatactattatggcccttcacggtcacttgtaggacggccccaaacaggattagtaaagtcggtggtctaagtgtaagcgataggcaaactgcggttattcgcgtagaccgcttgatgatgtaaaataacagttttcatgtctttgcaattac",
@@ -12,4 +12,4 @@ Array [
12
12
  ]
13
13
  `;
14
14
 
15
- exports[`can use a indexed fasta with gzi 2`] = `Array []`;
15
+ exports[`can use a indexed fasta with gzi 2`] = `[]`;
package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts CHANGED
@@ -7,11 +7,8 @@ import { FileLocation, NoAssemblyRegion } from '@jbrowse/core/util/types'
7
7
  import { openLocation } from '@jbrowse/core/util/io'
8
8
  import { ObservableCreate } from '@jbrowse/core/util/rxjs'
9
9
  import { SimpleFeature, Feature } from '@jbrowse/core/util'
10
- import { AnyConfigurationModel } from '@jbrowse/core/configuration'
11
10
  import AbortablePromiseCache from 'abortable-promise-cache'
12
11
  import QuickLRU from '@jbrowse/core/util/QuickLRU'
13
- import PluginManager from '@jbrowse/core/PluginManager'
14
- import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
15
12
 
16
13
  type T = { refName: string; start: number; end: number; fasta: IndexedFasta }
17
14
 
@@ -26,14 +23,6 @@ export default class extends BaseSequenceAdapter {
26
23
  },
27
24
  })
28
25
 
29
- public constructor(
30
- config: AnyConfigurationModel,
31
- getSubAdapter?: getSubAdapterType,
32
- pluginManager?: PluginManager,
33
- ) {
34
- super(config, getSubAdapter, pluginManager)
35
- }
36
-
37
26
  public async getRefNames(opts?: BaseOptions) {
38
27
  const { fasta } = await this.setup()
39
28
  return fasta.getSequenceNames(opts)
package/src/IndexedFastaAdapter/__snapshots__/IndexedFastaAdapter.test.ts.snap CHANGED
@@ -1,8 +1,8 @@
1
1
  // Jest Snapshot v1, https://goo.gl/fbAQLP
2
2
 
3
3
  exports[`adapter can fetch sequence from volvox.fa 1`] = `
4
- Array [
5
- Object {
4
+ [
5
+ {
6
6
  "end": 20000,
7
7
  "refName": "ctgA",
8
8
  "seq": 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c",
@@ -12,4 +12,4 @@ Array [
12
12
  ]
13
13
  `;
14
14
 
15
- exports[`adapter can fetch sequence from volvox.fa 2`] = `Array []`;
15
+ exports[`adapter can fetch sequence from volvox.fa 2`] = `[]`;
package/src/TwoBitAdapter/__snapshots__/TwoBitAdapter.test.ts.snap CHANGED
@@ -1,8 +1,8 @@
1
1
  // Jest Snapshot v1, https://goo.gl/fbAQLP
2
2
 
3
3
  exports[`adapter can fetch features from volvox.2bit 1`] = `
4
- Array [
5
- Object {
4
+ [
5
+ {
6
6
  "end": 20000,
7
7
  "refName": "ctgA",
8
8
  "seq": "cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgattatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctgaattgagaactcgagcgggggctaggcaaattctgattcagcctgacttctcttggaaccctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagaccaacctgaccaccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctccttggtcgctccgttgtacccaggctactttgaaagagcgcagaatacttagacggtatcgatcatggtagcatagcattctgataacatgtatggagttcgaacatccgtctggggccggacggtccgtttgaggttggttgatctgggtgatagtcagcaagatagacgttagataacaaattaaaggattttaccttagattgcgactagtacaacggtacatcggtgattcgcgctctactagatcacgctatgggtaccataaacaaacggtggaccttctcaagctggttgacgcctcagcaacataggcttcctcctccacgcatctcagcataaaaggcttataaactgcttctttgtgccagagcaactcaattaagcccttggtaccgtgggcacgcattctgtcacggtgaccaactgttcatcctgaatcgccgaatgggactatttggtacaggaatcaagcggatggcactactgcagcttatttacgacggtattcttaaagtttttaagacaatgtatttcatgggtagttcggtttgttttattgctacacaggctcttgtagacgacctacttagcactacggccgagcgcaataacccccggaaagcacttgctactgggaggcgggtttatccatcggcaataggggttatcagtactaccaagaagattgtgaagatattaacagcattgaaaaaagttcggactgggcatgaaacgtgtgtcagagttagagtccttgagggactgaatgggtttgtcccaggcccaagcttgaggtggatgtcacctcgggtactgcctctattacagaggtatcttaatggcgcatccagccttgtggctgggtctacgtacgcgtgggcaccatacgtatgttggcaggaaaggtcaatcatgcttgtttcctcgtcgcagaaacgttcacactattggctcgcgggatcgaacgggcctgattatttttccagctcctgcgttcctatcacgccaactgtcgctaataaaatgttatatagagataacccattgctatgcaaggatggagaaaccgcttcacaacaccctagaattacttcagcactaacatctaagataccgggaaaaccgtaggtgccacttggttttgagggcaatgcctcttgcactggcgattcgtggagtaaccttgctaccgatttccaccttttctaggtatgattacatgcgatcgccattgtcagtcgtcgtacgaaatccaggaaggaattcgaatacatgaccgaaagctatggcatcataagcgtggctctttactaaggacacgtgtagtcggctgatttcgcgcagaacttcgctcaccggacagtgactgctgtccgaacttgggggcagcgtagattctagctagagaccgcagcgaaaatgccactcgctaggtggctatggacgtccagctataggcccccacattcgtatgtatactccggtaattgagtctacctttcgaaagatcaaagttcacaaaccttctctcacgttaacatagatgctcgcacatagctagtccggtgataaagcggccgtgcatgcgagtatttagcgcacggaacagatattaggctgcgaaataccctcatatgctacagcgcaggtaacagacggttgatctccccgtagaattccctcaaggccggatcgttctcatgagtagcctttgtctgacatttcctctcaatagattgcagactcctgtgtcgtgggaaaacttcgcggaatcgctgtcgttacataaatctaaacagtgcagtccaagctatttactaccacgtatcataatgaacatctctttgtgaaatacgccggtacgccgagagatcgcccacattgcgtgtcaccaagacccagtgtctattgggcgcgctggttatagtatgcggaggcacccgatgtgctgctaatcactacaaactcgacaccaagaggcgaccgcgtgcgggagggctagaacgcgagagccacgtcaacgtggtggtaccgctcctgatgatacgagcactgtgctggcaccgctgccctatgtccagctaacaggtgtcacataatatcgcatctatagttgagtatcttatcgctagcgttacttgtgagttctcgggtagaatcgtcgtagcattctagtccttagcgtaagcaacgatatcgccgatattataggggcaataggtctcacccaccacgggtgtatatttaacgccctaagtagttaacggagactattaaacaattatgcacgtgaaagattagggtactgcacacgtgtcacgttgacgatgtaaacaccataaaggttgttctgtgatgcgatgcccatacctgcggtgcaacgtcctaaacttatgcggatcaccttctaattcagccgacgttgagaacgccagctatactctgtgagtacaaggtgaaagccccagatcaaaatattggagtcttgtccgtagctcttgggtggagagtgtgaccacgtttatcccttaatactgagactcttctcgttccacgccccggacattcgcgatacagcctagtttgataggtggctacaagggctctatccgaatagcacaaaactcagtcctagtgcgtataggtcgtgctctgcggttatacgctccacagaagaaagtacccactgcagtttgtcggtgggacttagcaaaacctgtaaccaaaaccgcacatggactctgttttggtggcgtggagtgtgcccgccgcctttatgctgggtcaaaatactatatgatttgttgtggtcgggcgcgacattggctcttatggtttataactattattcggtgcacagaaccgacttatgccccgattttgcacctcccgagagaaatggtactagtcattgtctcggggttttacaactcaaggataatctgccagcggtaccccgaaaaatcccatcccgaacggctggtacctatgctggagaccgaaatggagccagtgctatgcaaaccctcgctctttctatttggcccgaccagctgcgagagtcattcgacatacattgcgatggctggttcatctctctgcttcggattccgatcctgctgcctatggccacaacacgaaagagatcttggatacgtcctcaccatagtccaacggacaaatatggaggtgtacgcgcacggatacgagtacgacgggccgcccaatgctggtccttcgtgttatactgtttacttgcctccggtaagagtgtacagcttgtacccacgcggtggaggaccttacgcgtcgtccgcaggtgtggagatttcgctacctgttgcattggggcctcgccttacgtttttttcgacggaggcccgacccgccaggccagaccctcatcattgggatttttactgccttggacggcagattctgatgctggtaacgcgcttggcacacaccctggtcgtaattacgtactatcacctctattttaccaggggcgggccccgcctcaacgatcggtagtctcgttagaacagttgcttatactccgttagcactcacaactcggagaatgagcttacacagtccgtaatagtctccacagcttcccctggaaggttcgtacaggggccctggggtctaatgtgctaccgcctaacttcgttagtgtaaggtctcgtgtgcacctccaataacgctgcatttttgtatagaactcctttataggcctgactcttcggaacagcccactaattgacgtgcacgatgctgcatatacccttctcaatgacgcataccggtgactaaatcctgtggctggttgacactttgcataacccaccacgaaaacgcggtttgcacgtggttggaagcgagtaccggttaagggaagttacgtaaacccaacatagtgagcgatgcttaaaacactgcatgcgaacaacgaccggaacgagagcctaatagaaccaaatggataggtggttacgaaatccgcgcacaagtgtcgtgccactctcgtaaagaatgattgcttgcttatctatgagaaacctaataggcacgcacgtgtcgccagggaaaaaccaccatccgacaagacgctgaaaatcgagatagatgcagcccgcgcgtactttaagcacgatagccatcttgagcgcgacgattcagcttacggagattacttctcaaagcggacacctcgacgctgaagctctctatcgatgcacttgcatgtccatctacggcttgagcgaaccatgcttaacgcttggatgacgttgttagtcggattcgatcgtaccatactgtcctatccatcataacttcccgaattaaaactcattttctaccctcatttgtttcattggcgcatatgagcgccccatgggcgctgatcgacacaggcttgtagcgcacggctcgtcttgcagtagataaccatagtctttacgtcgcatatattaatatatcctcagacttccactgcggtattttggatcgtggcgtctgggacagtcacactctttaacgggagcgcgttcaatgtctgagtccatccgtgcagttcggtgcgatttta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c",
@@ -12,16 +12,16 @@ Array [
12
12
  ]
13
13
  `;
14
14
 
15
- exports[`adapter can fetch features from volvox.2bit 2`] = `Array []`;
15
+ exports[`adapter can fetch features from volvox.2bit 2`] = `[]`;
16
16
 
17
17
  exports[`adapter can fetch regions from with chrom.sizes 1`] = `
18
- Array [
19
- Object {
18
+ [
19
+ {
20
20
  "end": 50001,
21
21
  "refName": "ctgA",
22
22
  "start": 0,
23
23
  },
24
- Object {
24
+ {
25
25
  "end": 6079,
26
26
  "refName": "ctgB",
27
27
  "start": 0,
package/src/__snapshots__/index.test.js.snap CHANGED
@@ -1,5 +1,5 @@
1
1
  // Jest Snapshot v1, https://goo.gl/fbAQLP
2
2
 
3
- exports[`plugin in a stock JBrowse 1`] = `Object {}`;
3
+ exports[`plugin in a stock JBrowse 1`] = `{}`;
4
4
 
5
- exports[`plugin in a stock JBrowse 2`] = `Object {}`;
5
+ exports[`plugin in a stock JBrowse 2`] = `{}`;
package/src/index.ts CHANGED
@@ -6,7 +6,6 @@ import DivSequenceRendererF from './DivSequenceRenderer'
6
6
  import BgzipFastaAdapterF from './BgzipFastaAdapter'
7
7
  import ChromSizesAdapterF from './ChromSizesAdapter'
8
8
  import IndexedFastaAdapterF from './IndexedFastaAdapter'
9
- import GCContentAdapterF from './GCContentAdapter'
10
9
  import SequenceSearchAdapterF from './SequenceSearchAdapter'
11
10
  import ReferenceSequenceTrackF from './ReferenceSequenceTrack'
12
11
  import LinearReferenceSequenceDisplayF from './LinearReferenceSequenceDisplay'
@@ -21,7 +20,6 @@ export default class SequencePlugin extends Plugin {
21
20
  BgzipFastaAdapterF(pluginManager)
22
21
  ChromSizesAdapterF(pluginManager)
23
22
  IndexedFastaAdapterF(pluginManager)
24
- GCContentAdapterF(pluginManager)
25
23
  SequenceSearchAdapterF(pluginManager)
26
24
  ReferenceSequenceTrackF(pluginManager)
27
25
  LinearReferenceSequenceDisplayF(pluginManager)
package/dist/GCContentAdapter/GCContentAdapter.d.ts DELETED
@@ -1,17 +0,0 @@
1
- import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
2
- import { Feature, Region } from '@jbrowse/core/util';
3
- export default class extends BaseFeatureDataAdapter {
4
- private windowSize;
5
- private windowDelta;
6
- private gcMode;
7
- static capabilities: string[];
8
- configure(): Promise<BaseFeatureDataAdapter>;
9
- getRefNames(): Promise<string[]>;
10
- getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
11
- /**
12
- * called to provide a hint that data tied to a certain region
13
- * will not be needed for the forseeable future and can be purged
14
- * from caches, etc
15
- */
16
- freeResources(): void;
17
- }
package/dist/GCContentAdapter/GCContentAdapter.js DELETED
@@ -1,89 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
4
- const rxjs_1 = require("@jbrowse/core/util/rxjs");
5
- const util_1 = require("@jbrowse/core/util");
6
- const operators_1 = require("rxjs/operators");
7
- class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
8
- constructor() {
9
- super(...arguments);
10
- this.windowSize = 1000;
11
- this.windowDelta = 1000;
12
- this.gcMode = 'content';
13
- }
14
- async configure() {
15
- var _a;
16
- const adapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, this.getConf('sequenceAdapter')));
17
- if (!adapter) {
18
- throw new Error('Error getting subadapter');
19
- }
20
- return adapter.dataAdapter;
21
- }
22
- async getRefNames() {
23
- const adapter = await this.configure();
24
- return adapter.getRefNames();
25
- }
26
- getFeatures(query, opts) {
27
- return (0, rxjs_1.ObservableCreate)(async (observer) => {
28
- var _a;
29
- const sequenceAdapter = await this.configure();
30
- const hw = this.windowSize === 1 ? 1 : this.windowSize / 2; // Half the window size
31
- const f = this.windowSize === 1;
32
- let { start: queryStart, end: queryEnd } = query;
33
- queryStart = Math.max(0, queryStart - hw);
34
- queryEnd += hw;
35
- if (queryEnd < 0 || queryStart > queryEnd) {
36
- observer.complete();
37
- return;
38
- }
39
- const ret = sequenceAdapter.getFeatures({
40
- ...query,
41
- start: queryStart,
42
- end: queryEnd,
43
- }, opts);
44
- const feats = await ret.pipe((0, operators_1.toArray)()).toPromise();
45
- const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
46
- for (let i = hw; i < residues.length - hw; i += this.windowDelta) {
47
- const r = f ? residues[i] : residues.slice(i - hw, i + hw);
48
- let nc = 0;
49
- let ng = 0;
50
- let len = 0;
51
- for (let j = 0; j < r.length; j++) {
52
- if (r[j] === 'c' || r[j] === 'C') {
53
- nc++;
54
- }
55
- else if (r[j] === 'g' || r[j] === 'G') {
56
- ng++;
57
- }
58
- if (r[j] !== 'N') {
59
- len++;
60
- }
61
- }
62
- const pos = queryStart;
63
- let score;
64
- if (this.gcMode === 'content') {
65
- score = (ng + nc) / (len || 1);
66
- }
67
- else if (this.gcMode === 'skew') {
68
- score = (ng - nc) / (ng + nc || 1);
69
- }
70
- observer.next(new util_1.SimpleFeature({
71
- uniqueId: `${this.id}_${pos + i}`,
72
- start: pos + i,
73
- end: pos + i + this.windowDelta,
74
- score,
75
- }));
76
- }
77
- observer.complete();
78
- });
79
- }
80
- /**
81
- * called to provide a hint that data tied to a certain region
82
- * will not be needed for the forseeable future and can be purged
83
- * from caches, etc
84
- */
85
- freeResources( /* { region } */) { }
86
- }
87
- exports.default = default_1;
88
- default_1.capabilities = ['hasLocalStats'];
89
- //# sourceMappingURL=GCContentAdapter.js.map
package/dist/GCContentAdapter/GCContentAdapter.js.map DELETED
@@ -1 +0,0 @@
1
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package/dist/GCContentAdapter/configSchema.d.ts DELETED
@@ -1,3 +0,0 @@
1
- import PluginManager from '@jbrowse/core/PluginManager';
2
- declare const GCContentAdapterF: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
3
- export default GCContentAdapterF;
package/dist/GCContentAdapter/configSchema.js DELETED
@@ -1,17 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- const configuration_1 = require("@jbrowse/core/configuration");
4
- /**
5
- * #config GCContentAdapter
6
- */
7
- function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
8
- const GCContentAdapterF = (pluginManager) => {
9
- return (0, configuration_1.ConfigurationSchema)('GCContentAdapter', {
10
- /**
11
- * #slot
12
- */
13
- sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
14
- }, { explicitlyTyped: true });
15
- };
16
- exports.default = GCContentAdapterF;
17
- //# sourceMappingURL=configSchema.js.map
package/dist/GCContentAdapter/configSchema.js.map DELETED
@@ -1 +0,0 @@
1
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package/dist/GCContentAdapter/index.d.ts DELETED
@@ -1,3 +0,0 @@
1
- import PluginManager from '@jbrowse/core/PluginManager';
2
- declare const _default: (pluginManager: PluginManager) => void;
3
- export default _default;
package/dist/GCContentAdapter/index.js DELETED
@@ -1,44 +0,0 @@
1
- "use strict";
2
- var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
3
- if (k2 === undefined) k2 = k;
4
- var desc = Object.getOwnPropertyDescriptor(m, k);
5
- if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
6
- desc = { enumerable: true, get: function() { return m[k]; } };
7
- }
8
- Object.defineProperty(o, k2, desc);
9
- }) : (function(o, m, k, k2) {
10
- if (k2 === undefined) k2 = k;
11
- o[k2] = m[k];
12
- }));
13
- var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
14
- Object.defineProperty(o, "default", { enumerable: true, value: v });
15
- }) : function(o, v) {
16
- o["default"] = v;
17
- });
18
- var __importStar = (this && this.__importStar) || function (mod) {
19
- if (mod && mod.__esModule) return mod;
20
- var result = {};
21
- if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
22
- __setModuleDefault(result, mod);
23
- return result;
24
- };
25
- var __importDefault = (this && this.__importDefault) || function (mod) {
26
- return (mod && mod.__esModule) ? mod : { "default": mod };
27
- };
28
- Object.defineProperty(exports, "__esModule", { value: true });
29
- const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
30
- const configSchema_1 = __importDefault(require("./configSchema"));
31
- exports.default = (pluginManager) => {
32
- pluginManager.addAdapterType(() => new AdapterType_1.default({
33
- name: 'GCContentAdapter',
34
- adapterMetadata: {
35
- category: null,
36
- hiddenFromGUI: true,
37
- displayName: null,
38
- description: null,
39
- },
40
- configSchema: (0, configSchema_1.default)(pluginManager),
41
- getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./GCContentAdapter'))).then(r => r.default),
42
- }));
43
- };
44
- //# sourceMappingURL=index.js.map
package/dist/GCContentAdapter/index.js.map DELETED
@@ -1 +0,0 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GCContentAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAA0C;AAE1C,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,kBAAkB;QACxB,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;YACjB,WAAW,EAAE,IAAI;SAClB;QACD,YAAY,EAAE,IAAA,sBAAa,EAAC,aAAa,CAAC;QAC1C,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,oBAAoB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
package/esm/GCContentAdapter/GCContentAdapter.d.ts DELETED
@@ -1,17 +0,0 @@
1
- import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
2
- import { Feature, Region } from '@jbrowse/core/util';
3
- export default class extends BaseFeatureDataAdapter {
4
- private windowSize;
5
- private windowDelta;
6
- private gcMode;
7
- static capabilities: string[];
8
- configure(): Promise<BaseFeatureDataAdapter>;
9
- getRefNames(): Promise<string[]>;
10
- getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
11
- /**
12
- * called to provide a hint that data tied to a certain region
13
- * will not be needed for the forseeable future and can be purged
14
- * from caches, etc
15
- */
16
- freeResources(): void;
17
- }
package/esm/GCContentAdapter/GCContentAdapter.js DELETED
@@ -1,86 +0,0 @@
1
- import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
2
- import { ObservableCreate } from '@jbrowse/core/util/rxjs';
3
- import { SimpleFeature } from '@jbrowse/core/util';
4
- import { toArray } from 'rxjs/operators';
5
- export default class default_1 extends BaseFeatureDataAdapter {
6
- constructor() {
7
- super(...arguments);
8
- this.windowSize = 1000;
9
- this.windowDelta = 1000;
10
- this.gcMode = 'content';
11
- }
12
- async configure() {
13
- var _a;
14
- const adapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, this.getConf('sequenceAdapter')));
15
- if (!adapter) {
16
- throw new Error('Error getting subadapter');
17
- }
18
- return adapter.dataAdapter;
19
- }
20
- async getRefNames() {
21
- const adapter = await this.configure();
22
- return adapter.getRefNames();
23
- }
24
- getFeatures(query, opts) {
25
- return ObservableCreate(async (observer) => {
26
- var _a;
27
- const sequenceAdapter = await this.configure();
28
- const hw = this.windowSize === 1 ? 1 : this.windowSize / 2; // Half the window size
29
- const f = this.windowSize === 1;
30
- let { start: queryStart, end: queryEnd } = query;
31
- queryStart = Math.max(0, queryStart - hw);
32
- queryEnd += hw;
33
- if (queryEnd < 0 || queryStart > queryEnd) {
34
- observer.complete();
35
- return;
36
- }
37
- const ret = sequenceAdapter.getFeatures({
38
- ...query,
39
- start: queryStart,
40
- end: queryEnd,
41
- }, opts);
42
- const feats = await ret.pipe(toArray()).toPromise();
43
- const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
44
- for (let i = hw; i < residues.length - hw; i += this.windowDelta) {
45
- const r = f ? residues[i] : residues.slice(i - hw, i + hw);
46
- let nc = 0;
47
- let ng = 0;
48
- let len = 0;
49
- for (let j = 0; j < r.length; j++) {
50
- if (r[j] === 'c' || r[j] === 'C') {
51
- nc++;
52
- }
53
- else if (r[j] === 'g' || r[j] === 'G') {
54
- ng++;
55
- }
56
- if (r[j] !== 'N') {
57
- len++;
58
- }
59
- }
60
- const pos = queryStart;
61
- let score;
62
- if (this.gcMode === 'content') {
63
- score = (ng + nc) / (len || 1);
64
- }
65
- else if (this.gcMode === 'skew') {
66
- score = (ng - nc) / (ng + nc || 1);
67
- }
68
- observer.next(new SimpleFeature({
69
- uniqueId: `${this.id}_${pos + i}`,
70
- start: pos + i,
71
- end: pos + i + this.windowDelta,
72
- score,
73
- }));
74
- }
75
- observer.complete();
76
- });
77
- }
78
- /**
79
- * called to provide a hint that data tied to a certain region
80
- * will not be needed for the forseeable future and can be purged
81
- * from caches, etc
82
- */
83
- freeResources( /* { region } */) { }
84
- }
85
- default_1.capabilities = ['hasLocalStats'];
86
- //# sourceMappingURL=GCContentAdapter.js.map
package/esm/GCContentAdapter/GCContentAdapter.js.map DELETED
@@ -1 +0,0 @@
1
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package/esm/GCContentAdapter/configSchema.d.ts DELETED
@@ -1,3 +0,0 @@
1
- import PluginManager from '@jbrowse/core/PluginManager';
2
- declare const GCContentAdapterF: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
3
- export default GCContentAdapterF;
package/esm/GCContentAdapter/configSchema.js DELETED
@@ -1,15 +0,0 @@
1
- import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
- /**
3
- * #config GCContentAdapter
4
- */
5
- function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
6
- const GCContentAdapterF = (pluginManager) => {
7
- return ConfigurationSchema('GCContentAdapter', {
8
- /**
9
- * #slot
10
- */
11
- sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
12
- }, { explicitlyTyped: true });
13
- };
14
- export default GCContentAdapterF;
15
- //# sourceMappingURL=configSchema.js.map
package/esm/GCContentAdapter/configSchema.js.map DELETED
@@ -1 +0,0 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/GCContentAdapter/configSchema.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,iBAAiB,GAAG,CAAC,aAA4B,EAAE,EAAE;IACzD,OAAO,mBAAmB,CACxB,kBAAkB,EAClB;QACE;;WAEG;QACH,eAAe,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;KACpE,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACH,CAAC,CAAA;AAED,eAAe,iBAAiB,CAAA"}
package/esm/GCContentAdapter/index.d.ts DELETED
@@ -1,3 +0,0 @@
1
- import PluginManager from '@jbrowse/core/PluginManager';
2
- declare const _default: (pluginManager: PluginManager) => void;
3
- export default _default;
package/esm/GCContentAdapter/index.js DELETED
@@ -1,16 +0,0 @@
1
- import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
2
- import configSchemaF from './configSchema';
3
- export default (pluginManager) => {
4
- pluginManager.addAdapterType(() => new AdapterType({
5
- name: 'GCContentAdapter',
6
- adapterMetadata: {
7
- category: null,
8
- hiddenFromGUI: true,
9
- displayName: null,
10
- description: null,
11
- },
12
- configSchema: configSchemaF(pluginManager),
13
- getAdapterClass: () => import('./GCContentAdapter').then(r => r.default),
14
- }));
15
- };
16
- //# sourceMappingURL=index.js.map
package/esm/GCContentAdapter/index.js.map DELETED
@@ -1 +0,0 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GCContentAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,kBAAkB;QACxB,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;YACjB,WAAW,EAAE,IAAI;SAClB;QACD,YAAY,EAAE,aAAa,CAAC,aAAa,CAAC;QAC1C,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,oBAAoB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
package/src/GCContentAdapter/GCContentAdapter.ts DELETED
@@ -1,99 +0,0 @@
1
- import {
2
- BaseFeatureDataAdapter,
3
- BaseOptions,
4
- } from '@jbrowse/core/data_adapters/BaseAdapter'
5
- import { ObservableCreate } from '@jbrowse/core/util/rxjs'
6
- import { SimpleFeature, Feature, Region } from '@jbrowse/core/util'
7
- import { toArray } from 'rxjs/operators'
8
-
9
- export default class extends BaseFeatureDataAdapter {
10
- private windowSize = 1000
11
-
12
- private windowDelta = 1000
13
-
14
- private gcMode = 'content'
15
-
16
- public static capabilities = ['hasLocalStats']
17
-
18
- public async configure() {
19
- const adapter = await this.getSubAdapter?.(this.getConf('sequenceAdapter'))
20
- if (!adapter) {
21
- throw new Error('Error getting subadapter')
22
- }
23
- return adapter.dataAdapter as BaseFeatureDataAdapter
24
- }
25
-
26
- public async getRefNames() {
27
- const adapter = await this.configure()
28
- return adapter.getRefNames()
29
- }
30
-
31
- public getFeatures(query: Region, opts: BaseOptions) {
32
- return ObservableCreate<Feature>(async observer => {
33
- const sequenceAdapter = await this.configure()
34
- const hw = this.windowSize === 1 ? 1 : this.windowSize / 2 // Half the window size
35
- const f = this.windowSize === 1
36
-
37
- let { start: queryStart, end: queryEnd } = query
38
- queryStart = Math.max(0, queryStart - hw)
39
- queryEnd += hw
40
-
41
- if (queryEnd < 0 || queryStart > queryEnd) {
42
- observer.complete()
43
- return
44
- }
45
-
46
- const ret = sequenceAdapter.getFeatures(
47
- {
48
- ...query,
49
- start: queryStart,
50
- end: queryEnd,
51
- },
52
- opts,
53
- )
54
- const feats = await ret.pipe(toArray()).toPromise()
55
- const residues = feats[0]?.get('seq') || ''
56
-
57
- for (let i = hw; i < residues.length - hw; i += this.windowDelta) {
58
- const r = f ? residues[i] : residues.slice(i - hw, i + hw)
59
- let nc = 0
60
- let ng = 0
61
- let len = 0
62
- for (let j = 0; j < r.length; j++) {
63
- if (r[j] === 'c' || r[j] === 'C') {
64
- nc++
65
- } else if (r[j] === 'g' || r[j] === 'G') {
66
- ng++
67
- }
68
- if (r[j] !== 'N') {
69
- len++
70
- }
71
- }
72
- const pos = queryStart
73
- let score
74
- if (this.gcMode === 'content') {
75
- score = (ng + nc) / (len || 1)
76
- } else if (this.gcMode === 'skew') {
77
- score = (ng - nc) / (ng + nc || 1)
78
- }
79
-
80
- observer.next(
81
- new SimpleFeature({
82
- uniqueId: `${this.id}_${pos + i}`,
83
- start: pos + i,
84
- end: pos + i + this.windowDelta,
85
- score,
86
- }),
87
- )
88
- }
89
- observer.complete()
90
- })
91
- }
92
-
93
- /**
94
- * called to provide a hint that data tied to a certain region
95
- * will not be needed for the forseeable future and can be purged
96
- * from caches, etc
97
- */
98
- public freeResources(/* { region } */) {}
99
- }
package/src/GCContentAdapter/configSchema.ts DELETED
@@ -1,22 +0,0 @@
1
- import PluginManager from '@jbrowse/core/PluginManager'
2
- import { ConfigurationSchema } from '@jbrowse/core/configuration'
3
-
4
- /**
5
- * #config GCContentAdapter
6
- */
7
- function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
8
-
9
- const GCContentAdapterF = (pluginManager: PluginManager) => {
10
- return ConfigurationSchema(
11
- 'GCContentAdapter',
12
- {
13
- /**
14
- * #slot
15
- */
16
- sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
17
- },
18
- { explicitlyTyped: true },
19
- )
20
- }
21
-
22
- export default GCContentAdapterF
package/src/GCContentAdapter/index.ts DELETED
@@ -1,22 +0,0 @@
1
- import PluginManager from '@jbrowse/core/PluginManager'
2
- import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
3
-
4
- import configSchemaF from './configSchema'
5
-
6
- export default (pluginManager: PluginManager) => {
7
- pluginManager.addAdapterType(
8
- () =>
9
- new AdapterType({
10
- name: 'GCContentAdapter',
11
- adapterMetadata: {
12
- category: null,
13
- hiddenFromGUI: true,
14
- displayName: null,
15
- description: null,
16
- },
17
- configSchema: configSchemaF(pluginManager),
18
- getAdapterClass: () =>
19
- import('./GCContentAdapter').then(r => r.default),
20
- }),
21
- )
22
- }