@jbrowse/plugin-bed 4.3.0 → 5.0.0-beta.2

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Files changed (56) hide show
  1. package/esm/BedAdapter/BedAdapter.d.ts +4 -19
  2. package/esm/BedAdapter/BedAdapter.js +31 -88
  3. package/esm/BedAdapter/configSchema.d.ts +89 -40
  4. package/esm/BedAdapter/configSchema.js +65 -13
  5. package/esm/BedAdapter/index.js +4 -2
  6. package/esm/BedGraphAdapter/BedGraphAdapter.d.ts +4 -9
  7. package/esm/BedGraphAdapter/BedGraphAdapter.js +31 -85
  8. package/esm/BedGraphAdapter/configSchema.d.ts +35 -9
  9. package/esm/BedGraphAdapter/configSchema.js +47 -12
  10. package/esm/BedGraphAdapter/index.js +3 -2
  11. package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.d.ts +5 -5
  12. package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js +62 -57
  13. package/esm/BedGraphTabixAdapter/configSchema.d.ts +48 -19
  14. package/esm/BedGraphTabixAdapter/configSchema.js +42 -34
  15. package/esm/BedGraphTabixAdapter/index.js +3 -2
  16. package/esm/BedTabixAdapter/BedTabixAdapter.d.ts +34 -38
  17. package/esm/BedTabixAdapter/BedTabixAdapter.js +82 -71
  18. package/esm/BedTabixAdapter/configSchema.d.ts +73 -31
  19. package/esm/BedTabixAdapter/configSchema.js +53 -35
  20. package/esm/BedTabixAdapter/index.js +4 -2
  21. package/esm/BedpeAdapter/BedpeAdapter.d.ts +4 -10
  22. package/esm/BedpeAdapter/BedpeAdapter.js +28 -69
  23. package/esm/BedpeAdapter/configSchema.d.ts +33 -10
  24. package/esm/BedpeAdapter/configSchema.js +45 -12
  25. package/esm/BedpeAdapter/index.js +4 -2
  26. package/esm/BedpeAdapter/util.js +22 -23
  27. package/esm/BigBedAdapter/BigBedAdapter.d.ts +8 -7
  28. package/esm/BigBedAdapter/BigBedAdapter.js +100 -107
  29. package/esm/BigBedAdapter/configSchema.d.ts +52 -17
  30. package/esm/BigBedAdapter/configSchema.js +53 -12
  31. package/esm/BigBedAdapter/index.js +3 -2
  32. package/esm/StarFusionAdapter/StarFusionAdapter.d.ts +15 -0
  33. package/esm/StarFusionAdapter/StarFusionAdapter.js +121 -0
  34. package/esm/StarFusionAdapter/configSchema.d.ts +31 -0
  35. package/esm/StarFusionAdapter/configSchema.js +52 -0
  36. package/esm/StarFusionAdapter/index.d.ts +2 -0
  37. package/esm/StarFusionAdapter/index.js +12 -0
  38. package/esm/adapterUtil.d.ts +5 -0
  39. package/esm/adapterUtil.js +28 -0
  40. package/esm/bedGraphUtil.d.ts +10 -0
  41. package/esm/bedGraphUtil.js +18 -0
  42. package/esm/generateBedMethylFeature.d.ts +1 -1
  43. package/esm/generateBedMethylFeature.js +19 -6
  44. package/esm/generateRastairMethylFeature.d.ts +28 -0
  45. package/esm/generateRastairMethylFeature.js +38 -0
  46. package/esm/generateRepeatMaskerFeature.d.ts +4 -51
  47. package/esm/generateRepeatMaskerFeature.js +28 -41
  48. package/esm/generateUcscTranscript.d.ts +15 -7
  49. package/esm/generateUcscTranscript.js +58 -28
  50. package/esm/index.d.ts +2 -0
  51. package/esm/index.js +10 -8
  52. package/esm/util.d.ts +32 -27
  53. package/esm/util.js +127 -97
  54. package/package.json +9 -13
  55. package/esm/GuessAdapter/index.d.ts +0 -2
  56. package/esm/GuessAdapter/index.js +0 -71
package/esm/GuessAdapter/index.js DELETED
@@ -1,71 +0,0 @@
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- import { testAdapter } from '@jbrowse/core/util';
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- import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
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- export default function GuessAdapterF(pluginManager) {
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- pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
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- return (file, index, adapterHint) => {
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- const fileName = getFileName(file);
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- const indexName = index && getFileName(index);
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- if (testAdapter(fileName, /\.bedpe(\.gz)?$/i, adapterHint, 'BedpeAdapter')) {
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- return {
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- type: 'BedpeAdapter',
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- bedpeLocation: file,
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- };
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- }
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- else if (testAdapter(fileName, /\.bb$/i, adapterHint, 'BigBedAdapter') ||
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- testAdapter(fileName, /\.bigbed$/i, adapterHint, 'BigBedAdapter')) {
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- return {
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- type: 'BigBedAdapter',
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- bigBedLocation: file,
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- };
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- }
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- else if (testAdapter(fileName, /\.bed$/i, adapterHint, 'BedAdapter')) {
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- return {
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- type: 'BedAdapter',
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- bedLocation: file,
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- };
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- }
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- else if (testAdapter(fileName, /\.bg$/i, adapterHint, 'BedGraphAdapter')) {
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- return {
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- type: 'BedGraphAdapter',
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- bedGraphLocation: file,
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- };
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- }
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- else if (testAdapter(fileName, /\.bg(\.gz)?$/i, adapterHint, 'BedGraphTabixAdapter')) {
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- return {
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- type: 'BedGraphTabixAdapter',
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- bedGraphGzLocation: file,
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- index: {
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- location: index || makeIndex(file, '.tbi'),
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- indexType: makeIndexType(indexName, 'CSI', 'TBI'),
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- },
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- };
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- }
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- else if (testAdapter(fileName, /\.bedmethyl\.gz$/i, adapterHint, 'BedTabixAdapter') ||
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- testAdapter(fileName, /\.bed\.gz$/i, adapterHint, 'BedTabixAdapter')) {
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- return {
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- type: 'BedTabixAdapter',
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- bedGzLocation: file,
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- index: {
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- location: index || makeIndex(file, '.tbi'),
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- indexType: makeIndexType(indexName, 'CSI', 'TBI'),
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- },
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- };
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- }
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- else {
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- return adapterGuesser(file, index, adapterHint);
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- }
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- };
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- });
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- pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName, file) => {
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- if (adapterName === 'BedTabixAdapter' &&
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- file &&
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- /\.bedmethyl\.gz$/i.test(getFileName(file))) {
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- return 'MultiQuantitativeTrack';
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- }
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- return ({
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- BedpeAdapter: 'VariantTrack',
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- BedGraphAdapter: 'QuantitativeTrack',
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- BedGraphTabixAdapter: 'QuantitativeTrack',
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- }[adapterName] || trackTypeGuesser(adapterName, file));
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- });
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- }