@genome-spy/core 0.65.0 → 0.66.1
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.
- package/dist/bundle/browser-BRemItdO.js +138 -0
- package/dist/bundle/{index-CD7FLu9x.js → index-BatuyGAI.js} +23 -21
- package/dist/bundle/{index-C0llXMqm.js → index-ByuE8dvu.js} +140 -88
- package/dist/bundle/index-Cq3QFUxX.js +1781 -0
- package/dist/bundle/index-D28m8tSW.js +1607 -0
- package/dist/bundle/index-DbJ0oeYM.js +631 -0
- package/dist/bundle/index.es.js +17587 -16593
- package/dist/bundle/index.js +214 -212
- package/dist/bundle/{inflate-DRgHi_KK.js → inflate-GtwLkvSP.js} +222 -224
- package/dist/bundle/unzip-NywezaRR.js +1492 -0
- package/dist/schema.json +13 -3
- package/dist/src/config/scaleDefaults.d.ts +8 -0
- package/dist/src/config/scaleDefaults.d.ts.map +1 -0
- package/dist/src/config/scaleDefaults.js +45 -0
- package/dist/src/data/flowInit.js +2 -2
- package/dist/src/data/sources/lazy/axisTickSource.js +1 -1
- package/dist/src/data/sources/lazy/singleAxisLazySource.d.ts +1 -1
- package/dist/src/data/sources/lazy/singleAxisLazySource.d.ts.map +1 -1
- package/dist/src/data/sources/lazy/singleAxisLazySource.js +10 -3
- package/dist/src/data/sources/lazy/singleAxisWindowedSource.d.ts.map +1 -1
- package/dist/src/data/sources/lazy/singleAxisWindowedSource.js +5 -1
- package/dist/src/data/transforms/filterScoredLabels.d.ts +1 -1
- package/dist/src/data/transforms/filterScoredLabels.d.ts.map +1 -1
- package/dist/src/data/transforms/filterScoredLabels.js +1 -1
- package/dist/src/data/transforms/linearizeGenomicCoordinate.d.ts.map +1 -1
- package/dist/src/data/transforms/linearizeGenomicCoordinate.js +2 -1
- package/dist/src/encoder/encoder.d.ts +1 -1
- package/dist/src/encoder/encoder.d.ts.map +1 -1
- package/dist/src/encoder/encoder.js +1 -1
- package/dist/src/genome/scaleLocus.d.ts +39 -0
- package/dist/src/genome/scaleLocus.d.ts.map +1 -1
- package/dist/src/genome/scaleLocus.js +76 -0
- package/dist/src/genomeSpy/canvasExport.d.ts +19 -0
- package/dist/src/genomeSpy/canvasExport.d.ts.map +1 -0
- package/dist/src/genomeSpy/canvasExport.js +66 -0
- package/dist/src/genomeSpy/containerUi.d.ts +17 -0
- package/dist/src/genomeSpy/containerUi.d.ts.map +1 -0
- package/dist/src/genomeSpy/containerUi.js +78 -0
- package/dist/src/genomeSpy/eventListenerRegistry.d.ts +19 -0
- package/dist/src/genomeSpy/eventListenerRegistry.d.ts.map +1 -0
- package/dist/src/genomeSpy/eventListenerRegistry.js +38 -0
- package/dist/src/genomeSpy/inputBindingManager.d.ts +14 -0
- package/dist/src/genomeSpy/inputBindingManager.d.ts.map +1 -0
- package/dist/src/genomeSpy/inputBindingManager.js +63 -0
- package/dist/src/genomeSpy/interactionController.d.ts +40 -0
- package/dist/src/genomeSpy/interactionController.d.ts.map +1 -0
- package/dist/src/genomeSpy/interactionController.js +371 -0
- package/dist/src/genomeSpy/keyboardListenerManager.d.ts +10 -0
- package/dist/src/genomeSpy/keyboardListenerManager.d.ts.map +1 -0
- package/dist/src/genomeSpy/keyboardListenerManager.js +31 -0
- package/dist/src/genomeSpy/loadingIndicatorManager.d.ts +15 -0
- package/dist/src/genomeSpy/loadingIndicatorManager.d.ts.map +1 -0
- package/dist/src/genomeSpy/loadingIndicatorManager.js +92 -0
- package/dist/src/genomeSpy/renderCoordinator.d.ts +22 -0
- package/dist/src/genomeSpy/renderCoordinator.d.ts.map +1 -0
- package/dist/src/genomeSpy/renderCoordinator.js +118 -0
- package/dist/src/genomeSpy/viewContextFactory.d.ts +18 -0
- package/dist/src/genomeSpy/viewContextFactory.d.ts.map +1 -0
- package/dist/src/genomeSpy/viewContextFactory.js +79 -0
- package/dist/src/genomeSpy/viewDataInit.d.ts +12 -0
- package/dist/src/genomeSpy/viewDataInit.d.ts.map +1 -0
- package/dist/src/genomeSpy/viewDataInit.js +41 -0
- package/dist/src/genomeSpy/viewHierarchyConfig.d.ts +14 -0
- package/dist/src/genomeSpy/viewHierarchyConfig.d.ts.map +1 -0
- package/dist/src/genomeSpy/viewHierarchyConfig.js +24 -0
- package/dist/src/genomeSpy/viewHighlight.d.ts +5 -0
- package/dist/src/genomeSpy/viewHighlight.d.ts.map +1 -0
- package/dist/src/genomeSpy/viewHighlight.js +30 -0
- package/dist/src/genomeSpy.d.ts +16 -71
- package/dist/src/genomeSpy.d.ts.map +1 -1
- package/dist/src/genomeSpy.js +179 -745
- package/dist/src/gl/glslScaleGenerator.d.ts +1 -1
- package/dist/src/gl/webGLHelper.d.ts +2 -2
- package/dist/src/gl/webGLHelper.d.ts.map +1 -1
- package/dist/src/gl/webGLHelper.js +4 -4
- package/dist/src/index.d.ts.map +1 -1
- package/dist/src/index.js +2 -12
- package/dist/src/marks/mark.d.ts.map +1 -1
- package/dist/src/marks/mark.js +4 -2
- package/dist/src/{view → scales}/axisResolution.d.ts +9 -16
- package/dist/src/scales/axisResolution.d.ts.map +1 -0
- package/dist/src/{view → scales}/axisResolution.js +29 -18
- package/dist/src/scales/axisResolution.test.d.ts.map +1 -0
- package/dist/src/scales/scaleDomainAggregator.d.ts +57 -0
- package/dist/src/scales/scaleDomainAggregator.d.ts.map +1 -0
- package/dist/src/scales/scaleDomainAggregator.js +162 -0
- package/dist/src/scales/scaleDomainAggregator.test.d.ts +2 -0
- package/dist/src/scales/scaleDomainAggregator.test.d.ts.map +1 -0
- package/dist/src/scales/scaleInstanceManager.d.ts +40 -0
- package/dist/src/scales/scaleInstanceManager.d.ts.map +1 -0
- package/dist/src/scales/scaleInstanceManager.js +313 -0
- package/dist/src/scales/scaleInstanceManager.test.d.ts +2 -0
- package/dist/src/scales/scaleInstanceManager.test.d.ts.map +1 -0
- package/dist/src/scales/scaleInteractionController.d.ts +73 -0
- package/dist/src/scales/scaleInteractionController.d.ts.map +1 -0
- package/dist/src/scales/scaleInteractionController.js +336 -0
- package/dist/src/scales/scaleInteractionController.test.d.ts +2 -0
- package/dist/src/scales/scaleInteractionController.test.d.ts.map +1 -0
- package/dist/src/scales/scalePropsResolver.d.ts +23 -0
- package/dist/src/scales/scalePropsResolver.d.ts.map +1 -0
- package/dist/src/scales/scalePropsResolver.js +74 -0
- package/dist/src/{view → scales}/scaleResolution.d.ts +52 -35
- package/dist/src/scales/scaleResolution.d.ts.map +1 -0
- package/dist/src/scales/scaleResolution.js +658 -0
- package/dist/src/scales/scaleResolution.test.d.ts.map +1 -0
- package/dist/src/scales/scaleResolutionConstants.d.ts +6 -0
- package/dist/src/scales/scaleResolutionConstants.d.ts.map +1 -0
- package/dist/src/scales/scaleResolutionConstants.js +5 -0
- package/dist/src/scales/scaleRules.d.ts +16 -0
- package/dist/src/scales/scaleRules.d.ts.map +1 -0
- package/dist/src/scales/scaleRules.js +103 -0
- package/dist/src/scales/scaleRules.test.d.ts +2 -0
- package/dist/src/scales/scaleRules.test.d.ts.map +1 -0
- package/dist/src/spec/channel.d.ts +13 -18
- package/dist/src/spec/scale.d.ts +6 -0
- package/dist/src/types/embedApi.d.ts +5 -0
- package/dist/src/types/scaleResolutionApi.d.ts +1 -1
- package/dist/src/view/concatView.d.ts +18 -0
- package/dist/src/view/concatView.d.ts.map +1 -1
- package/dist/src/view/concatView.js +73 -0
- package/dist/src/view/concatView.test.d.ts +2 -0
- package/dist/src/view/concatView.test.d.ts.map +1 -0
- package/dist/src/view/containerMutationHelper.d.ts +74 -0
- package/dist/src/view/containerMutationHelper.d.ts.map +1 -0
- package/dist/src/view/containerMutationHelper.js +114 -0
- package/dist/src/view/containerView.d.ts +0 -7
- package/dist/src/view/containerView.d.ts.map +1 -1
- package/dist/src/view/containerView.js +0 -10
- package/dist/src/view/facetView.d.ts.map +1 -1
- package/dist/src/view/facetView.js +0 -15
- package/dist/src/view/gridView/gridChild.d.ts +11 -0
- package/dist/src/view/gridView/gridChild.d.ts.map +1 -1
- package/dist/src/view/gridView/gridChild.js +32 -6
- package/dist/src/view/gridView/gridView.d.ts +39 -1
- package/dist/src/view/gridView/gridView.d.ts.map +1 -1
- package/dist/src/view/gridView/gridView.js +106 -48
- package/dist/src/view/gridView/gridView.test.d.ts +2 -0
- package/dist/src/view/gridView/gridView.test.d.ts.map +1 -0
- package/dist/src/view/gridView/scrollbar.d.ts +39 -8
- package/dist/src/view/gridView/scrollbar.d.ts.map +1 -1
- package/dist/src/view/gridView/scrollbar.js +184 -69
- package/dist/src/view/layerView.d.ts +14 -0
- package/dist/src/view/layerView.d.ts.map +1 -1
- package/dist/src/view/layerView.js +66 -0
- package/dist/src/view/layerView.test.d.ts +2 -0
- package/dist/src/view/layerView.test.d.ts.map +1 -0
- package/dist/src/view/testUtils.d.ts.map +1 -1
- package/dist/src/view/testUtils.js +2 -1
- package/dist/src/view/unitView.d.ts.map +1 -1
- package/dist/src/view/unitView.js +24 -34
- package/dist/src/view/view.d.ts +6 -6
- package/dist/src/view/view.d.ts.map +1 -1
- package/dist/src/view/view.js +4 -4
- package/package.json +2 -2
- package/dist/bundle/browser-txUcLy2H.js +0 -123
- package/dist/bundle/index-BQpbYrv4.js +0 -1712
- package/dist/bundle/index-BhtHKLUo.js +0 -73
- package/dist/bundle/index-CCe8rnZz.js +0 -716
- package/dist/bundle/index-DhcU-Gk-.js +0 -1487
- package/dist/src/data/collector.test.js +0 -138
- package/dist/src/data/dataFlow.test.js +0 -38
- package/dist/src/data/flow.test.js +0 -81
- package/dist/src/data/flowInit.test.js +0 -413
- package/dist/src/data/flowNode.test.js +0 -50
- package/dist/src/data/flowOptimizer.test.js +0 -209
- package/dist/src/data/formats/fasta.test.js +0 -27
- package/dist/src/data/sources/inlineSource.test.js +0 -63
- package/dist/src/data/sources/sequenceSource.test.js +0 -81
- package/dist/src/data/transforms/aggregate.test.js +0 -134
- package/dist/src/data/transforms/clone.test.js +0 -11
- package/dist/src/data/transforms/coverage.test.js +0 -238
- package/dist/src/data/transforms/filter.test.js +0 -20
- package/dist/src/data/transforms/flatten.test.js +0 -96
- package/dist/src/data/transforms/flattenDelimited.test.js +0 -90
- package/dist/src/data/transforms/flattenSequence.test.js +0 -34
- package/dist/src/data/transforms/formula.test.js +0 -25
- package/dist/src/data/transforms/identifier.test.js +0 -92
- package/dist/src/data/transforms/pileup.test.js +0 -70
- package/dist/src/data/transforms/project.test.js +0 -32
- package/dist/src/data/transforms/regexExtract.test.js +0 -70
- package/dist/src/data/transforms/regexFold.test.js +0 -201
- package/dist/src/data/transforms/sample.test.js +0 -38
- package/dist/src/data/transforms/stack.test.js +0 -91
- package/dist/src/encoder/accessor.test.js +0 -162
- package/dist/src/encoder/encoder.test.js +0 -105
- package/dist/src/genome/genome.test.js +0 -268
- package/dist/src/genome/genomes.test.js +0 -8
- package/dist/src/genome/scaleIndex.test.js +0 -78
- package/dist/src/genome/scaleLocus.test.js +0 -4
- package/dist/src/scale/scale.test.js +0 -326
- package/dist/src/scale/ticks.test.js +0 -46
- package/dist/src/selection/selection.test.js +0 -14
- package/dist/src/utils/addBaseUrl.test.js +0 -30
- package/dist/src/utils/binnedIndex.test.js +0 -201
- package/dist/src/utils/cloner.test.js +0 -35
- package/dist/src/utils/coalesce.test.js +0 -16
- package/dist/src/utils/concatIterables.test.js +0 -8
- package/dist/src/utils/domainArray.test.js +0 -130
- package/dist/src/utils/indexer.test.js +0 -49
- package/dist/src/utils/interactionEvent.test.js +0 -35
- package/dist/src/utils/iterateNestedMaps.test.js +0 -33
- package/dist/src/utils/kWayMerge.test.js +0 -30
- package/dist/src/utils/mergeObjects.test.js +0 -42
- package/dist/src/utils/numberExtractor.test.js +0 -6
- package/dist/src/utils/propertyCacher.test.js +0 -89
- package/dist/src/utils/propertyCoalescer.test.js +0 -25
- package/dist/src/utils/radixSort.test.js +0 -51
- package/dist/src/utils/reservationMap.test.js +0 -20
- package/dist/src/utils/ringBuffer.test.js +0 -39
- package/dist/src/utils/topK.test.js +0 -54
- package/dist/src/utils/trees.test.js +0 -135
- package/dist/src/utils/url.test.js +0 -28
- package/dist/src/utils/variableTools.test.js +0 -13
- package/dist/src/view/axisResolution.d.ts.map +0 -1
- package/dist/src/view/axisResolution.test.d.ts.map +0 -1
- package/dist/src/view/axisResolution.test.js +0 -206
- package/dist/src/view/flowBuilder.test.js +0 -125
- package/dist/src/view/gridView/selectionRect.test.js +0 -87
- package/dist/src/view/layout/flexLayout.test.js +0 -323
- package/dist/src/view/layout/grid.test.js +0 -71
- package/dist/src/view/layout/rectangle.test.js +0 -192
- package/dist/src/view/paramMediator.test.js +0 -282
- package/dist/src/view/scaleResolution.d.ts.map +0 -1
- package/dist/src/view/scaleResolution.js +0 -1059
- package/dist/src/view/scaleResolution.test.d.ts.map +0 -1
- package/dist/src/view/scaleResolution.test.js +0 -645
- package/dist/src/view/view.test.js +0 -245
- package/dist/src/view/viewDispose.test.js +0 -110
- package/dist/src/view/viewFactory.test.js +0 -25
- package/dist/src/view/viewUtils.test.js +0 -87
- /package/dist/src/{view → scales}/axisResolution.test.d.ts +0 -0
- /package/dist/src/{view → scales}/scaleResolution.test.d.ts +0 -0
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|
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|
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|
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import { LocalFile as d } from "./browser-
|
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import { I as b, Z as F } from "./inflate-
|
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import { LocalFile as d } from "./browser-BRemItdO.js";
|
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|
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import { I as b, Z as F } from "./inflate-GtwLkvSP.js";
|
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6
|
const w = 65536, S = w * w;
|
|
7
7
|
function g(r, e = 0) {
|
|
8
8
|
const t = r[e] | r[e + 1] << 8 | r[e + 2] << 16 | r[e + 3] << 24;
|
|
@@ -30,7 +30,7 @@ class B {
|
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|
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|
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|
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|
|
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const s = 16 * t;
|
|
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34
|
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|
|
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throw new TypeError("integer overflow");
|
|
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const i = await this.filehandle.read(s, 8);
|
|
@@ -58,20 +58,20 @@ class B {
|
|
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|
return i[i.length - 1][u] < n && i.push([]), i;
|
|
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|
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|
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|
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|
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|
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|
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|
|
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|
|
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|
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|
|
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|
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|
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|
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function
|
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|
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const t = new Uint8Array(e ??
|
|
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|
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|
|
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|
+
const t = new Uint8Array(e ?? E(r));
|
|
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|
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|
|
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|
|
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71
|
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|
|
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|
return t;
|
|
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|
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|
|
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|
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|
|
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|
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async function k(r) {
|
|
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75
|
try {
|
|
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|
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|
|
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77
|
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|
|
@@ -84,7 +84,7 @@ async function E(r) {
|
|
|
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84
|
const o = n.result;
|
|
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85
|
s.push(o), i += o.length;
|
|
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86
|
} while (e.avail_in);
|
|
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|
-
return
|
|
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|
+
return y(s, i);
|
|
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88
|
} catch (e) {
|
|
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89
|
throw /incorrect header check/.exec(`${e}`) ? new Error("problem decompressing block: incorrect gzip header check") : e;
|
|
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90
|
}
|
|
@@ -101,7 +101,7 @@ class p {
|
|
|
101
101
|
let n = t;
|
|
102
102
|
n || (n = (await this.filehandle.stat()).size);
|
|
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103
|
const s = n - e, i = await this.filehandle.read(s, e);
|
|
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|
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return
|
|
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|
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return k(i);
|
|
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105
|
}
|
|
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106
|
async read(e, t) {
|
|
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107
|
const n = await this.gzi.getRelevantBlocksForRead(e, t), s = [];
|
|
@@ -109,13 +109,13 @@ class p {
|
|
|
109
109
|
const a = await this._readAndUncompressBlock(n[i][0], n[i + 1][0]), [, o] = n[i], c = o >= t ? 0 : t - o, l = Math.min(t + e, o + a.length) - o;
|
|
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110
|
c >= 0 && c < a.length && s.push(a.subarray(c, l));
|
|
111
111
|
}
|
|
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|
-
return
|
|
112
|
+
return y(s);
|
|
113
113
|
}
|
|
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114
|
}
|
|
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|
-
function
|
|
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|
+
function x(r, e) {
|
|
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116
|
return r.offset + r.lineBytes * Math.floor(e / r.lineLength) + e % r.lineLength;
|
|
117
117
|
}
|
|
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|
-
async function
|
|
118
|
+
async function z(r, e = {}) {
|
|
119
119
|
const t = new TextDecoder("utf8");
|
|
120
120
|
return Object.fromEntries(t.decode(await r.readFile(e)).split(/\r?\n/).map((n) => n.trim()).filter((n) => !!n).map((n) => n.split(" ")).map((n) => {
|
|
121
121
|
var s;
|
|
@@ -135,7 +135,7 @@ async function N(r, e = {}) {
|
|
|
135
135
|
];
|
|
136
136
|
}));
|
|
137
137
|
}
|
|
138
|
-
class
|
|
138
|
+
class N {
|
|
139
139
|
constructor({ fasta: e, fai: t, path: n, faiPath: s }) {
|
|
140
140
|
if (e)
|
|
141
141
|
this.fasta = e;
|
|
@@ -153,7 +153,7 @@ class A {
|
|
|
153
153
|
throw new Error("Need to pass filehandle for or path to localfile");
|
|
154
154
|
}
|
|
155
155
|
async _getIndexes(e) {
|
|
156
|
-
return this.indexes || (this.indexes =
|
|
156
|
+
return this.indexes || (this.indexes = z(this.fai, e).catch((t) => {
|
|
157
157
|
throw this.indexes = void 0, t;
|
|
158
158
|
})), this.indexes;
|
|
159
159
|
}
|
|
@@ -212,11 +212,13 @@ class A {
|
|
|
212
212
|
throw new TypeError("regionStart cannot be less than 0");
|
|
213
213
|
if ((i === void 0 || i > e.length) && (i = e.length), t >= i)
|
|
214
214
|
return "";
|
|
215
|
-
const a =
|
|
216
|
-
|
|
215
|
+
const a = x(e, t), o = x(e, i) - a, l = new TextDecoder("utf8").decode(await this.fasta.read(o, a, s)).replace(/\s+/g, "");
|
|
216
|
+
if (/[^\x20-\x7e]/.test(l.slice(0, 1e3)))
|
|
217
|
+
throw new Error("Non-ASCII characters detected in sequence. The file may be gzip compressed. Use BgzipIndexedFasta for bgzip files, or decompress the file.");
|
|
218
|
+
return l;
|
|
217
219
|
}
|
|
218
220
|
}
|
|
219
|
-
class O extends
|
|
221
|
+
class O extends N {
|
|
220
222
|
constructor({ fasta: e, path: t, fai: n, faiPath: s, gzi: i, gziPath: a }) {
|
|
221
223
|
super({ fasta: e, path: t, fai: n, faiPath: s }), e && i ? this.fasta = new p({
|
|
222
224
|
filehandle: e,
|
|
@@ -227,7 +229,7 @@ class O extends A {
|
|
|
227
229
|
}));
|
|
228
230
|
}
|
|
229
231
|
}
|
|
230
|
-
function
|
|
232
|
+
function A(r) {
|
|
231
233
|
return r.split(">").filter((e) => /\S/.test(e)).map((e) => {
|
|
232
234
|
const [t, ...n] = e.split(`
|
|
233
235
|
`), [s, ...i] = t.split(" "), a = n.join("").replace(/\s/g, "");
|
|
@@ -248,7 +250,7 @@ class R {
|
|
|
248
250
|
throw new Error("Need to pass fasta or path");
|
|
249
251
|
this.data = this.fasta.readFile().then((n) => {
|
|
250
252
|
const i = new TextDecoder("utf8").decode(n);
|
|
251
|
-
return
|
|
253
|
+
return A(i);
|
|
252
254
|
});
|
|
253
255
|
}
|
|
254
256
|
async fetch(e, t, n) {
|
|
@@ -264,6 +266,6 @@ class R {
|
|
|
264
266
|
export {
|
|
265
267
|
O as BgzipIndexedFasta,
|
|
266
268
|
R as FetchableSmallFasta,
|
|
267
|
-
|
|
268
|
-
|
|
269
|
+
N as IndexedFasta,
|
|
270
|
+
A as parseSmallFasta
|
|
269
271
|
};
|
|
@@ -1,11 +1,11 @@
|
|
|
1
1
|
var v = Object.defineProperty;
|
|
2
|
-
var
|
|
3
|
-
var
|
|
4
|
-
const
|
|
5
|
-
function
|
|
6
|
-
return n.includes("%") ? n.replaceAll(
|
|
2
|
+
var F = (n, e, t) => e in n ? v(n, e, { enumerable: !0, configurable: !0, writable: !0, value: t }) : n[e] = t;
|
|
3
|
+
var f = (n, e, t) => F(n, typeof e != "symbol" ? e + "" : e, t);
|
|
4
|
+
const y = /%([0-9A-Fa-f]{2})/g, R = /^\s*##\s*(\S+)\s*(.*)/, g = /\r?\n$/, b = /\s+/, C = /\D/g;
|
|
5
|
+
function p(n) {
|
|
6
|
+
return n.includes("%") ? n.replaceAll(y, (e, t) => String.fromCharCode(parseInt(t, 16))) : n;
|
|
7
7
|
}
|
|
8
|
-
function
|
|
8
|
+
function k(n) {
|
|
9
9
|
if (!n.length || n === ".")
|
|
10
10
|
return {};
|
|
11
11
|
const e = {};
|
|
@@ -20,78 +20,115 @@ function F(n) {
|
|
|
20
20
|
const c = r.slice(s + 1);
|
|
21
21
|
if (!c.length)
|
|
22
22
|
continue;
|
|
23
|
-
const
|
|
24
|
-
let
|
|
25
|
-
|
|
23
|
+
const i = r.slice(0, s).trim();
|
|
24
|
+
let o = e[i];
|
|
25
|
+
o || (o = [], e[i] = o);
|
|
26
26
|
for (const l of c.split(","))
|
|
27
|
-
|
|
27
|
+
o.push(p(l.trim()));
|
|
28
28
|
}
|
|
29
29
|
return e;
|
|
30
30
|
}
|
|
31
31
|
function I(n) {
|
|
32
|
-
|
|
32
|
+
if (!n.length || n === ".")
|
|
33
|
+
return {};
|
|
34
|
+
const e = {};
|
|
35
|
+
let t = n;
|
|
36
|
+
t.endsWith(`
|
|
37
|
+
`) && (t = t.slice(0, t.endsWith(`\r
|
|
38
|
+
`) ? -2 : -1));
|
|
39
|
+
for (const r of t.split(";")) {
|
|
40
|
+
const s = r.indexOf("=");
|
|
41
|
+
if (s === -1)
|
|
42
|
+
continue;
|
|
43
|
+
const c = r.slice(s + 1);
|
|
44
|
+
if (!c.length)
|
|
45
|
+
continue;
|
|
46
|
+
const i = r.slice(0, s).trim();
|
|
47
|
+
let o = e[i];
|
|
48
|
+
o || (o = [], e[i] = o);
|
|
49
|
+
for (const l of c.split(","))
|
|
50
|
+
o.push(l.trim());
|
|
51
|
+
}
|
|
52
|
+
return e;
|
|
53
|
+
}
|
|
54
|
+
function L(n) {
|
|
55
|
+
return _(n.split(" "));
|
|
33
56
|
}
|
|
34
|
-
function
|
|
57
|
+
function a(n) {
|
|
35
58
|
return n === "." || n === "" || n === void 0 ? null : n;
|
|
36
59
|
}
|
|
37
|
-
function
|
|
38
|
-
const e =
|
|
60
|
+
function _(n) {
|
|
61
|
+
const e = a(n[0]), t = a(n[1]), r = a(n[2]), s = a(n[3]), c = a(n[4]), i = a(n[5]), o = a(n[6]), l = a(n[7]), u = a(n[8]);
|
|
39
62
|
return {
|
|
40
|
-
seq_id: e ?
|
|
41
|
-
source: t ?
|
|
42
|
-
type: r ?
|
|
63
|
+
seq_id: e ? p(e) : null,
|
|
64
|
+
source: t ? p(t) : null,
|
|
65
|
+
type: r ? p(r) : null,
|
|
43
66
|
start: s === null ? null : parseInt(s, 10),
|
|
44
67
|
end: c === null ? null : parseInt(c, 10),
|
|
45
|
-
score:
|
|
46
|
-
strand:
|
|
68
|
+
score: i === null ? null : parseFloat(i),
|
|
69
|
+
strand: o,
|
|
47
70
|
phase: l,
|
|
48
|
-
attributes: u === null ? null :
|
|
71
|
+
attributes: u === null ? null : k(u)
|
|
49
72
|
};
|
|
50
73
|
}
|
|
51
|
-
function
|
|
52
|
-
|
|
53
|
-
|
|
74
|
+
function D(n) {
|
|
75
|
+
const e = a(n[0]), t = a(n[1]), r = a(n[2]), s = a(n[3]), c = a(n[4]), i = a(n[5]), o = a(n[6]), l = a(n[7]), u = a(n[8]);
|
|
76
|
+
return {
|
|
77
|
+
seq_id: e,
|
|
78
|
+
source: t,
|
|
79
|
+
type: r,
|
|
80
|
+
start: s === null ? null : parseInt(s, 10),
|
|
81
|
+
end: c === null ? null : parseInt(c, 10),
|
|
82
|
+
score: i === null ? null : parseFloat(i),
|
|
83
|
+
strand: o,
|
|
84
|
+
phase: l,
|
|
85
|
+
attributes: u === null ? null : I(u)
|
|
86
|
+
};
|
|
87
|
+
}
|
|
88
|
+
function A(n) {
|
|
89
|
+
var c, i;
|
|
90
|
+
const e = R.exec(n);
|
|
54
91
|
if (!e)
|
|
55
92
|
return null;
|
|
56
93
|
const [, t] = e;
|
|
57
94
|
let [, , r] = e;
|
|
58
95
|
const s = { directive: t };
|
|
59
96
|
if (r.length && (r = r.replace(g, ""), s.value = r), t === "sequence-region") {
|
|
60
|
-
const
|
|
97
|
+
const o = r.split(b, 3);
|
|
61
98
|
return {
|
|
62
99
|
...s,
|
|
63
|
-
seq_id:
|
|
64
|
-
start: (c =
|
|
65
|
-
end: (
|
|
100
|
+
seq_id: o[0],
|
|
101
|
+
start: (c = o[1]) == null ? void 0 : c.replaceAll(C, ""),
|
|
102
|
+
end: (i = o[2]) == null ? void 0 : i.replaceAll(C, "")
|
|
66
103
|
};
|
|
67
104
|
} else if (t === "genome-build") {
|
|
68
|
-
const [
|
|
105
|
+
const [o, l] = r.split(b, 2);
|
|
69
106
|
return {
|
|
70
107
|
...s,
|
|
71
|
-
source:
|
|
108
|
+
source: o,
|
|
72
109
|
buildName: l
|
|
73
110
|
};
|
|
74
111
|
}
|
|
75
112
|
return s;
|
|
76
113
|
}
|
|
77
|
-
const
|
|
78
|
-
class
|
|
114
|
+
const x = /^\s*[^#\s>]/, w = /^\s*(#+)(.*)/, S = /^\s*$/, E = /^\s*>/, P = /\r?\n?$/g;
|
|
115
|
+
class m {
|
|
79
116
|
constructor(e) {
|
|
80
|
-
|
|
81
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f(this, "featureCallback");
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f(this, "commentCallback");
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f(this, "errorCallback");
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f(this, "disableDerivesFromReferences");
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f(this, "directiveCallback");
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f(this, "bufferSize");
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f(this, "eof", !1);
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f(this, "lineNumber", 0);
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// might be referenced by something else
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f(this, "_underConstructionTopLevel", []);
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f(this, "_underConstructionById", {});
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this.featureCallback = e.featureCallback || t, this.endCallback = e.endCallback || t, this.commentCallback = e.commentCallback || t, this.errorCallback = e.errorCallback || t, this.directiveCallback = e.directiveCallback || t, this.disableDerivesFromReferences = e.disableDerivesFromReferences || !1, this.bufferSize = e.bufferSize === void 0 ? 1 / 0 : e.bufferSize;
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return;
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if (this.lineNumber += 1, x.test(e)) {
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c && (c.directive === "FASTA" ? (this._emitAllUnderConstructionFeatures(), this.eof = !0) : this._emitItem(c));
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_enforceBufferSizeLimit(e = 0) {
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r && Array.isArray(r) && ((c = (s = r[0].attributes) == null ? void 0 : s.ID) != null && c[0]) && (r[0].attributes.ID.forEach((
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}), r.forEach((
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r && Array.isArray(r) && ((c = (s = r[0].attributes) == null ? void 0 : s.ID) != null && c[0]) && (r[0].attributes.ID.forEach((o) => {
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delete this._underConstructionById[o], delete this._completedReferences[o];
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}), r.forEach((o) => {
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t(l);
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}),
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}), o.derived_features && o.derived_features.forEach((l) => {
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t(l);
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}));
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@@ -167,24 +204,24 @@ class p {
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throw new Error(`some features reference other features that do not exist in the file (or in the same '###' scope). ${e.join(",")}`);
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}
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_bufferLine(e) {
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this._bufferParsedLine(
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this._bufferParsedLine(L(e));
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}
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_bufferParsedLine(e) {
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var
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var o, l, u;
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|
t.child_features = [], t.derived_features = [];
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const r = ((
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const r = ((o = t.attributes) == null ? void 0 : o.ID) || [], s = ((l = t.attributes) == null ? void 0 : l.Parent) || [], c = this.disableDerivesFromReferences ? [] : ((u = t.attributes) == null ? void 0 : u.Derives_from) || [];
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|
if (!r.length && !s.length && !c.length) {
|
|
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215
|
this._emitItem([t]);
|
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216
|
return;
|
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217
|
}
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|
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let
|
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|
+
let i;
|
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|
r.forEach((d) => {
|
|
183
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|
const h = this._underConstructionById[d];
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|
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h ? (h[h.length - 1].type !== t.type && this._parseError(`multi-line feature "${d}" has inconsistent types: "${t.type}", "${h[h.length - 1].type}"`), h.push(t),
|
|
221
|
+
h ? (h[h.length - 1].type !== t.type && this._parseError(`multi-line feature "${d}" has inconsistent types: "${t.type}", "${h[h.length - 1].type}"`), h.push(t), i = h) : (i = [t], this._enforceBufferSizeLimit(1), !s.length && !c.length && this._underConstructionTopLevel.push(i), this._underConstructionById[d] = i, this._resolveReferencesTo(i, d));
|
|
185
222
|
}), this._resolveReferencesFrom(
|
|
186
223
|
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
|
|
187
|
-
|
|
224
|
+
i || [t],
|
|
188
225
|
{ Parent: s, Derives_from: c },
|
|
189
226
|
r
|
|
190
227
|
);
|
|
@@ -204,39 +241,39 @@ class p {
|
|
|
204
241
|
for (const s of t.Parent) {
|
|
205
242
|
const c = this._underConstructionById[s];
|
|
206
243
|
if (c) {
|
|
207
|
-
let
|
|
208
|
-
for (const
|
|
209
|
-
const l = `Parent,${s}`, u = this._completedReferences[
|
|
210
|
-
u[l] && (
|
|
244
|
+
let i = !1;
|
|
245
|
+
for (const o of r) {
|
|
246
|
+
const l = `Parent,${s}`, u = this._completedReferences[o] || (this._completedReferences[o] = {});
|
|
247
|
+
u[l] && (i = !0), u[l] = !0;
|
|
211
248
|
}
|
|
212
|
-
if (!
|
|
213
|
-
for (const
|
|
214
|
-
|
|
249
|
+
if (!i)
|
|
250
|
+
for (const o of c)
|
|
251
|
+
o.child_features.push(e);
|
|
215
252
|
} else {
|
|
216
|
-
let
|
|
217
|
-
|
|
253
|
+
let i = this._underConstructionOrphans[s];
|
|
254
|
+
i || (i = { Parent: [], Derives_from: [] }, this._underConstructionOrphans[s] = i), i.Parent.push(e);
|
|
218
255
|
}
|
|
219
256
|
}
|
|
220
257
|
for (const s of t.Derives_from) {
|
|
221
258
|
const c = this._underConstructionById[s];
|
|
222
259
|
if (c) {
|
|
223
|
-
let
|
|
224
|
-
for (const
|
|
225
|
-
const l = `Derives_from,${s}`, u = this._completedReferences[
|
|
226
|
-
u[l] && (
|
|
260
|
+
let i = !1;
|
|
261
|
+
for (const o of r) {
|
|
262
|
+
const l = `Derives_from,${s}`, u = this._completedReferences[o] || (this._completedReferences[o] = {});
|
|
263
|
+
u[l] && (i = !0), u[l] = !0;
|
|
227
264
|
}
|
|
228
|
-
if (!
|
|
229
|
-
for (const
|
|
230
|
-
|
|
265
|
+
if (!i)
|
|
266
|
+
for (const o of c)
|
|
267
|
+
o.derived_features.push(e);
|
|
231
268
|
} else {
|
|
232
|
-
let
|
|
233
|
-
|
|
269
|
+
let i = this._underConstructionOrphans[s];
|
|
270
|
+
i || (i = { Parent: [], Derives_from: [] }, this._underConstructionOrphans[s] = i), i.Derives_from.push(e);
|
|
234
271
|
}
|
|
235
272
|
}
|
|
236
273
|
}
|
|
237
274
|
}
|
|
238
|
-
function
|
|
239
|
-
const e = [], t = new
|
|
275
|
+
function $(n) {
|
|
276
|
+
const e = [], t = new m({
|
|
240
277
|
featureCallback: (r) => e.push(r),
|
|
241
278
|
disableDerivesFromReferences: !0,
|
|
242
279
|
errorCallback: (r) => {
|
|
@@ -247,8 +284,8 @@ function P(n) {
|
|
|
247
284
|
t.addLine(r);
|
|
248
285
|
return t.finish(), e;
|
|
249
286
|
}
|
|
250
|
-
function
|
|
251
|
-
const e = [], t = new
|
|
287
|
+
function B(n) {
|
|
288
|
+
const e = [], t = new m({
|
|
252
289
|
featureCallback: (r) => e.push(r),
|
|
253
290
|
disableDerivesFromReferences: !0,
|
|
254
291
|
errorCallback: (r) => {
|
|
@@ -259,8 +296,8 @@ function $(n) {
|
|
|
259
296
|
t.addLine(r);
|
|
260
297
|
return t.finish(), e;
|
|
261
298
|
}
|
|
262
|
-
function
|
|
263
|
-
const e = [], t = new
|
|
299
|
+
function T(n) {
|
|
300
|
+
const e = [], t = new m({
|
|
264
301
|
featureCallback: (r) => e.push(r),
|
|
265
302
|
disableDerivesFromReferences: !0,
|
|
266
303
|
errorCallback: (r) => {
|
|
@@ -268,13 +305,28 @@ function O(n) {
|
|
|
268
305
|
}
|
|
269
306
|
});
|
|
270
307
|
for (const r of n) {
|
|
271
|
-
const s =
|
|
308
|
+
const s = _(r.fields);
|
|
272
309
|
r.lineHash !== void 0 && (s.attributes || (s.attributes = {}), s.attributes._lineHash = [String(r.lineHash)]), t.addParsedFeatureLine(s);
|
|
273
310
|
}
|
|
274
311
|
return t.finish(), e;
|
|
275
312
|
}
|
|
313
|
+
function q(n, e) {
|
|
314
|
+
const t = [], r = new m({
|
|
315
|
+
featureCallback: (c) => t.push(c),
|
|
316
|
+
disableDerivesFromReferences: !0,
|
|
317
|
+
errorCallback: (c) => {
|
|
318
|
+
throw new Error(c);
|
|
319
|
+
}
|
|
320
|
+
}), s = e ? _ : D;
|
|
321
|
+
for (const c of n) {
|
|
322
|
+
const i = s(c.fields);
|
|
323
|
+
c.lineHash !== void 0 && (i.attributes || (i.attributes = {}), i.attributes._lineHash = [String(c.lineHash)]), r.addParsedFeatureLine(i);
|
|
324
|
+
}
|
|
325
|
+
return r.finish(), t;
|
|
326
|
+
}
|
|
276
327
|
export {
|
|
277
|
-
|
|
278
|
-
|
|
279
|
-
|
|
328
|
+
B as parseArraySync,
|
|
329
|
+
T as parseRecordsSync,
|
|
330
|
+
q as parseRecordsSyncFast,
|
|
331
|
+
$ as parseStringSync
|
|
280
332
|
};
|