@jbrowse/cli 3.5.1 → 3.6.1

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 (72) hide show
  1. package/README.md +291 -607
  2. package/bin/run +1 -6
  3. package/bundle/index.js +4459 -0
  4. package/dist/base.js +5 -0
  5. package/dist/bin.js +3 -0
  6. package/dist/commands/add-assembly.js +143 -0
  7. package/dist/commands/add-connection.js +177 -0
  8. package/dist/commands/add-track-json.js +81 -0
  9. package/dist/commands/add-track-utils/adapter-utils.js +304 -0
  10. package/dist/commands/add-track-utils/file-operations.js +36 -0
  11. package/dist/commands/add-track-utils/track-config.js +63 -0
  12. package/dist/commands/add-track-utils/validators.js +74 -0
  13. package/dist/commands/add-track.js +193 -0
  14. package/dist/commands/admin-server-utils.js +238 -0
  15. package/dist/commands/admin-server.js +51 -0
  16. package/dist/commands/assembly-utils.js +410 -0
  17. package/dist/commands/create.js +121 -0
  18. package/dist/commands/make-pif-utils/cigar-utils.js +29 -0
  19. package/dist/commands/make-pif-utils/file-utils.js +38 -0
  20. package/dist/commands/make-pif-utils/pif-generator.js +64 -0
  21. package/dist/commands/make-pif-utils/validators.js +22 -0
  22. package/dist/commands/make-pif.js +58 -0
  23. package/dist/commands/remove-track.js +58 -0
  24. package/dist/commands/set-default-session.js +104 -0
  25. package/dist/commands/sort-bed-utils/constants.js +12 -0
  26. package/dist/commands/sort-bed-utils/process-utils.js +23 -0
  27. package/dist/commands/sort-bed-utils/sort-utils.js +24 -0
  28. package/dist/commands/sort-bed-utils/validators.js +22 -0
  29. package/dist/commands/sort-bed.js +49 -0
  30. package/dist/commands/sort-gff-utils/constants.js +13 -0
  31. package/dist/commands/sort-gff-utils/process-utils.js +23 -0
  32. package/dist/commands/sort-gff-utils/sort-utils.js +55 -0
  33. package/dist/commands/sort-gff-utils/validators.js +21 -0
  34. package/dist/commands/sort-gff.js +49 -0
  35. package/dist/commands/text-index-utils/adapter-utils.js +63 -0
  36. package/dist/commands/text-index-utils/aggregate.js +87 -0
  37. package/dist/commands/text-index-utils/config-utils.js +59 -0
  38. package/dist/commands/text-index-utils/file-list.js +31 -0
  39. package/dist/commands/text-index-utils/index.js +9 -0
  40. package/dist/commands/text-index-utils/indexing-utils.js +84 -0
  41. package/dist/commands/text-index-utils/per-track.js +65 -0
  42. package/dist/commands/text-index-utils/validators.js +20 -0
  43. package/dist/commands/text-index.js +113 -0
  44. package/dist/commands/track-utils.js +85 -0
  45. package/dist/commands/upgrade.js +122 -0
  46. package/dist/index.js +119 -0
  47. package/dist/utils.js +154 -0
  48. package/package.json +13 -38
  49. package/bin/dev +0 -17
  50. package/bin/dev.cmd +0 -3
  51. package/bin/run.cmd +0 -3
  52. package/lib/base.js +0 -157
  53. package/lib/commands/add-assembly.js +0 -491
  54. package/lib/commands/add-connection.js +0 -170
  55. package/lib/commands/add-track-json.js +0 -67
  56. package/lib/commands/add-track.js +0 -564
  57. package/lib/commands/admin-server.js +0 -153
  58. package/lib/commands/create.js +0 -111
  59. package/lib/commands/make-pif.js +0 -116
  60. package/lib/commands/remove-track.js +0 -37
  61. package/lib/commands/set-default-session.js +0 -98
  62. package/lib/commands/sort-bed.js +0 -45
  63. package/lib/commands/sort-gff.js +0 -45
  64. package/lib/commands/text-index.js +0 -380
  65. package/lib/commands/upgrade.js +0 -109
  66. package/lib/index.js +0 -6
  67. package/oclif.manifest.json +0 -1169
  68. /package/{lib → dist}/fetchWithProxy.js +0 -0
  69. /package/{lib → dist}/types/common.js +0 -0
  70. /package/{lib → dist}/types/gff3Adapter.js +0 -0
  71. /package/{lib → dist}/types/vcfAdapter.js +0 -0
  72. /package/{lib → dist}/util.js +0 -0
/package/{lib → dist}/fetchWithProxy.js RENAMED
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/package/{lib → dist}/types/common.js RENAMED
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/package/{lib → dist}/types/gff3Adapter.js RENAMED
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/package/{lib → dist}/types/vcfAdapter.js RENAMED
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/package/{lib → dist}/util.js RENAMED
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