@jbrowse/cli 3.7.0 → 4.0.1

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Files changed (58) hide show
  1. package/README.md +4 -0
  2. package/bin/run +0 -0
  3. package/bundle/index.js +2280 -2722
  4. package/dist/bin.js +2 -2
  5. package/dist/commands/{add-assembly.js → add-assembly/index.js} +10 -10
  6. package/dist/commands/{assembly-utils.js → add-assembly/utils.js} +69 -105
  7. package/dist/commands/add-connection.js +10 -15
  8. package/dist/commands/add-track-json.js +26 -31
  9. package/dist/commands/add-track-utils/track-config.js +3 -15
  10. package/dist/commands/add-track-utils/validators.js +4 -9
  11. package/dist/commands/add-track.js +23 -25
  12. package/dist/commands/{admin-server.js → admin-server/index.js} +9 -9
  13. package/dist/commands/{admin-server-utils.js → admin-server/utils.js} +7 -16
  14. package/dist/commands/create.js +8 -8
  15. package/dist/commands/{make-pif.js → make-pif/index.js} +11 -17
  16. package/dist/commands/{make-pif-utils → make-pif}/pif-generator.js +6 -6
  17. package/dist/commands/{sort-bed-utils/process-utils.js → process-utils.js} +0 -10
  18. package/dist/commands/remove-track.js +6 -11
  19. package/dist/commands/set-default-session.js +8 -12
  20. package/dist/commands/shared/config-operations.js +37 -0
  21. package/dist/commands/shared/sort-utils.js +57 -0
  22. package/dist/commands/shared/validators.js +18 -0
  23. package/dist/commands/sort-bed.js +13 -24
  24. package/dist/commands/sort-gff.js +13 -24
  25. package/dist/commands/text-index/adapter-utils.js +43 -0
  26. package/dist/commands/text-index/aggregate.js +52 -0
  27. package/dist/commands/{text-index.js → text-index/command.js} +13 -6
  28. package/dist/commands/text-index/config-utils.js +134 -0
  29. package/dist/commands/{text-index-utils → text-index}/file-list.js +12 -15
  30. package/dist/commands/text-index/index.js +11 -0
  31. package/dist/commands/{text-index-utils → text-index}/indexing-utils.js +30 -20
  32. package/dist/commands/text-index/per-track.js +54 -0
  33. package/dist/commands/track-utils.js +33 -33
  34. package/dist/commands/upgrade.js +8 -8
  35. package/dist/index.js +39 -27
  36. package/dist/types/common.js +9 -8
  37. package/dist/types/gff3Adapter.js +17 -48
  38. package/dist/types/streamUtils.js +66 -0
  39. package/dist/types/vcfAdapter.js +17 -54
  40. package/dist/util.js +14 -7
  41. package/dist/utils.js +10 -5
  42. package/package.json +14 -17
  43. package/dist/commands/make-pif-utils/validators.js +0 -22
  44. package/dist/commands/sort-bed-utils/constants.js +0 -12
  45. package/dist/commands/sort-bed-utils/sort-utils.js +0 -24
  46. package/dist/commands/sort-bed-utils/validators.js +0 -22
  47. package/dist/commands/sort-gff-utils/constants.js +0 -13
  48. package/dist/commands/sort-gff-utils/process-utils.js +0 -23
  49. package/dist/commands/sort-gff-utils/sort-utils.js +0 -55
  50. package/dist/commands/sort-gff-utils/validators.js +0 -21
  51. package/dist/commands/text-index-utils/adapter-utils.js +0 -63
  52. package/dist/commands/text-index-utils/aggregate.js +0 -87
  53. package/dist/commands/text-index-utils/config-utils.js +0 -59
  54. package/dist/commands/text-index-utils/index.js +0 -9
  55. package/dist/commands/text-index-utils/per-track.js +0 -65
  56. /package/dist/commands/{make-pif-utils → make-pif}/cigar-utils.js +0 -0
  57. /package/dist/commands/{make-pif-utils → make-pif}/file-utils.js +0 -0
  58. /package/dist/commands/{text-index-utils → text-index}/validators.js +0 -0
package/README.md CHANGED
@@ -235,6 +235,7 @@ Usage: jbrowse text-index [options]
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  Options:
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  -h, --help Show CLI help
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  , --tracks Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks
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+ , --excludeTracks Specific tracks to exclude from indexing, formatted as comma separated trackIds
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  , --target Path to config file in JB2 installation directory to read from.
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  , --out Synonym for target
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  , --attributes Comma separated list of attributes to index
@@ -254,6 +255,9 @@ $ jbrowse text-index
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  # indexes specific trackIds that it can find in the current directory's config.json
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  $ jbrowse text-index --tracks=track1,track2,track3
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+ # indexes all tracks except specific trackIds
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+ $ jbrowse text-index --exclude-tracks=track1,track2,track3
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+
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  # indexes all tracks in a directory's config.json or in a specific config file
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  $ jbrowse text-index --out /path/to/jb2/
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package/bin/run CHANGED
File without changes