@jbrowse/plugin-legacy-jbrowse 1.7.7 → 1.7.8

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Files changed (4) hide show
  1. package/dist/JBrowse1Connection/jb1ToJb2.d.ts +2 -0
  2. package/dist/JBrowse1Connection/jb1ToJb2.js +20 -2
  3. package/package.json +2 -2
  4. package/src/JBrowse1Connection/jb1ToJb2.ts +18 -10
package/dist/JBrowse1Connection/jb1ToJb2.d.ts CHANGED
@@ -21,7 +21,9 @@ interface Jb2Adapter {
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  bigWigLocation?: Jb2Location;
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  bigBedLocation?: Jb2Location;
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  vcfGzLocation?: Jb2Location;
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+ gffLocation?: Jb2Location;
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  gffGzLocation?: Jb2Location;
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+ gtfLocation?: Jb2Location;
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  bedGzLocation?: Jb2Location;
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  index?: {
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  location: Jb2Location;
package/dist/JBrowse1Connection/jb1ToJb2.js CHANGED
@@ -199,7 +199,16 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
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  }
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  if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {
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- return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "GFF3 (".concat(urlTemplate, ")"), jb2TrackConfig.category);
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+ return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
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+ type: 'FeatureTrack',
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+ adapter: {
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+ type: 'Gff3Adapter',
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+ gffLocation: {
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+ uri: urlTemplate,
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+ locationType: 'UriLocation'
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+ }
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+ }
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+ });
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  }
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  if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {
@@ -298,7 +307,16 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
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  }
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  if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {
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- return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "GTF (".concat(urlTemplate, ")"), jb2TrackConfig.category);
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+ return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
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+ type: 'FeatureTrack',
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+ adapter: {
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+ type: 'GtfAdapter',
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+ gtfLocation: {
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+ uri: urlTemplate,
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+ locationType: 'UriLocation'
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+ }
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+ }
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+ });
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  }
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  if (storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' || storeClass === 'JBrowse/Store/Sequence/StaticChunked') {
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-legacy-jbrowse",
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- "version": "1.7.7",
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+ "version": "1.7.8",
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  "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
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  "keywords": [
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  "jbrowse",
@@ -48,5 +48,5 @@
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  "publishConfig": {
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  "access": "public"
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  },
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- "gitHead": "2c26e04ae942c380bf2f5b79ef7a49cc32b7bfed"
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+ "gitHead": "b429fa2bb5734fc8a5380988f6dfdd3f7a41a39f"
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  }
package/src/JBrowse1Connection/jb1ToJb2.ts CHANGED
@@ -33,7 +33,9 @@ interface Jb2Adapter {
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  bigWigLocation?: Jb2Location
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  bigBedLocation?: Jb2Location
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  vcfGzLocation?: Jb2Location
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+ gffLocation?: Jb2Location
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  gffGzLocation?: Jb2Location
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+ gtfLocation?: Jb2Location
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  bedGzLocation?: Jb2Location
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  index?: { location: Jb2Location; indexType?: string }
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  rootUrlTemplate?: Jb2Location
@@ -224,11 +226,14 @@ export function convertTrackConfig(
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  )
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  }
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  if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {
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- return generateUnsupportedTrackConf(
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- jb2TrackConfig.name,
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- `GFF3 (${urlTemplate})`,
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- jb2TrackConfig.category,
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- )
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+ return {
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+ ...jb2TrackConfig,
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+ type: 'FeatureTrack',
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+ adapter: {
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+ type: 'Gff3Adapter',
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+ gffLocation: { uri: urlTemplate, locationType: 'UriLocation' },
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+ },
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+ }
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  }
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  if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {
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  return {
@@ -310,11 +315,14 @@ export function convertTrackConfig(
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  }
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  }
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  if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {
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- return generateUnsupportedTrackConf(
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- jb2TrackConfig.name,
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- `GTF (${urlTemplate})`,
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- jb2TrackConfig.category,
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- )
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+ return {
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+ ...jb2TrackConfig,
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+ type: 'FeatureTrack',
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+ adapter: {
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+ type: 'GtfAdapter',
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+ gtfLocation: { uri: urlTemplate, locationType: 'UriLocation' },
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+ },
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+ }
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  }
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  if (
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  storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' ||