@jbrowse/plugin-gccontent 2.13.1 → 2.15.0

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Files changed (11) hide show
  1. package/dist/GCContentAdapter/GCContentAdapter.js +5 -7
  2. package/dist/LinearGCContentDisplay/components/EditGCContentParams.js +9 -3
  3. package/dist/LinearGCContentDisplay/shared.d.ts +1 -1
  4. package/dist/LinearGCContentDisplay/stateModel1.d.ts +1 -1
  5. package/dist/LinearGCContentDisplay/stateModel2.d.ts +1 -1
  6. package/esm/GCContentAdapter/GCContentAdapter.js +5 -7
  7. package/esm/LinearGCContentDisplay/components/EditGCContentParams.js +9 -3
  8. package/esm/LinearGCContentDisplay/shared.d.ts +1 -1
  9. package/esm/LinearGCContentDisplay/stateModel1.d.ts +1 -1
  10. package/esm/LinearGCContentDisplay/stateModel2.d.ts +1 -1
  11. package/package.json +3 -3
package/dist/GCContentAdapter/GCContentAdapter.js CHANGED
@@ -61,13 +61,11 @@ class GCContentAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  }
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  }
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  const pos = queryStart;
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- let score;
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- if (this.gcMode === 'content') {
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- score = (ng + nc) / (len || 1);
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- }
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- else if (this.gcMode === 'skew') {
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- score = (ng - nc) / (ng + nc || 1);
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- }
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+ const score = this.gcMode === 'content'
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+ ? (ng + nc) / (len || 1)
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+ : this.gcMode === 'skew'
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+ ? (ng - nc) / (ng + nc || 1)
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+ : 0;
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  observer.next(new util_1.SimpleFeature({
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  uniqueId: `${this.id}_${pos + i}`,
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  refName: query.refName,
package/dist/LinearGCContentDisplay/components/EditGCContentParams.js CHANGED
@@ -34,8 +34,12 @@ const EditGCContentParamsDialog = (0, mobx_react_1.observer)(function ({ model,
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  react_1.default.createElement(material_1.DialogContent, null,
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  react_1.default.createElement(material_1.Typography, null, "GC content is calculated in a particular sliding window of size N, and then the sliding window moves (steps) some number of bases M forward. Note that small step sizes can result in high CPU over large areas, and it is not recommended to make the step size larger than the window size as then the sliding window will miss contents."),
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  windowDelta > windowSize ? (react_1.default.createElement(ui_1.ErrorMessage, { error: "It is not recommended to make the step size larger than the window size" })) : null,
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- react_1.default.createElement(material_1.TextField, { label: "Size of sliding window (bp)", value: `${windowSize}`, onChange: event => setWindowSize(event.target.value) }),
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- react_1.default.createElement(material_1.TextField, { label: "Step size of sliding window (bp)", value: `${windowDelta}`, onChange: event => setWindowDelta(event.target.value) }),
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+ react_1.default.createElement(material_1.TextField, { label: "Size of sliding window (bp)", value: windowSize, onChange: event => {
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+ setWindowSize(event.target.value);
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+ } }),
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+ react_1.default.createElement(material_1.TextField, { label: "Step size of sliding window (bp)", value: windowDelta, onChange: event => {
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+ setWindowDelta(event.target.value);
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+ } }),
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  react_1.default.createElement(material_1.DialogActions, null,
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  react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
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  model.setGCContentParams({
@@ -44,6 +48,8 @@ const EditGCContentParamsDialog = (0, mobx_react_1.observer)(function ({ model,
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  });
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  handleClose();
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  } }, "Submit"),
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- react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
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+ react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
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+ handleClose();
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+ } }, "Cancel")))));
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  });
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  exports.default = EditGCContentParamsDialog;
package/dist/LinearGCContentDisplay/shared.d.ts CHANGED
@@ -151,7 +151,7 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
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  error: unknown;
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  message: string | undefined;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- onHorizontalScroll?: Function;
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+ onHorizontalScroll?: () => void;
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  blockState?: Record<string, any>;
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  }>;
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  readonly DisplayBlurb: import("react").FC<{
package/dist/LinearGCContentDisplay/stateModel1.d.ts CHANGED
@@ -144,7 +144,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
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  error: unknown;
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  message: string | undefined;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- onHorizontalScroll?: Function;
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+ onHorizontalScroll?: () => void;
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  blockState?: Record<string, any>;
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  }>;
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  readonly DisplayBlurb: import("react").FC<{
package/dist/LinearGCContentDisplay/stateModel2.d.ts CHANGED
@@ -149,7 +149,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
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  error: unknown;
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  message: string | undefined;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- onHorizontalScroll?: Function;
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+ onHorizontalScroll?: () => void;
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  blockState?: Record<string, any>;
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  }>;
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  readonly DisplayBlurb: import("react").FC<{
package/esm/GCContentAdapter/GCContentAdapter.js CHANGED
@@ -59,13 +59,11 @@ class GCContentAdapter extends BaseFeatureDataAdapter {
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  }
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  }
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  const pos = queryStart;
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- let score;
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- if (this.gcMode === 'content') {
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- score = (ng + nc) / (len || 1);
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- }
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- else if (this.gcMode === 'skew') {
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- score = (ng - nc) / (ng + nc || 1);
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- }
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+ const score = this.gcMode === 'content'
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+ ? (ng + nc) / (len || 1)
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+ : this.gcMode === 'skew'
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+ ? (ng - nc) / (ng + nc || 1)
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+ : 0;
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  observer.next(new SimpleFeature({
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  uniqueId: `${this.id}_${pos + i}`,
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  refName: query.refName,
package/esm/LinearGCContentDisplay/components/EditGCContentParams.js CHANGED
@@ -9,8 +9,12 @@ const EditGCContentParamsDialog = observer(function ({ model, handleClose, }) {
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  React.createElement(DialogContent, null,
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  React.createElement(Typography, null, "GC content is calculated in a particular sliding window of size N, and then the sliding window moves (steps) some number of bases M forward. Note that small step sizes can result in high CPU over large areas, and it is not recommended to make the step size larger than the window size as then the sliding window will miss contents."),
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  windowDelta > windowSize ? (React.createElement(ErrorMessage, { error: "It is not recommended to make the step size larger than the window size" })) : null,
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- React.createElement(TextField, { label: "Size of sliding window (bp)", value: `${windowSize}`, onChange: event => setWindowSize(event.target.value) }),
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- React.createElement(TextField, { label: "Step size of sliding window (bp)", value: `${windowDelta}`, onChange: event => setWindowDelta(event.target.value) }),
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+ React.createElement(TextField, { label: "Size of sliding window (bp)", value: windowSize, onChange: event => {
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+ setWindowSize(event.target.value);
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+ } }),
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+ React.createElement(TextField, { label: "Step size of sliding window (bp)", value: windowDelta, onChange: event => {
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+ setWindowDelta(event.target.value);
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+ } }),
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  React.createElement(DialogActions, null,
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  React.createElement(Button, { variant: "contained", onClick: () => {
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  model.setGCContentParams({
@@ -19,6 +23,8 @@ const EditGCContentParamsDialog = observer(function ({ model, handleClose, }) {
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  });
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  handleClose();
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  } }, "Submit"),
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- React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
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+ React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
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+ handleClose();
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+ } }, "Cancel")))));
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  });
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  export default EditGCContentParamsDialog;
package/esm/LinearGCContentDisplay/shared.d.ts CHANGED
@@ -151,7 +151,7 @@ export default function SharedModelF(pluginManager: PluginManager, configSchema:
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  error: unknown;
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  message: string | undefined;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- onHorizontalScroll?: Function;
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+ onHorizontalScroll?: () => void;
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  blockState?: Record<string, any>;
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  }>;
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  readonly DisplayBlurb: import("react").FC<{
package/esm/LinearGCContentDisplay/stateModel1.d.ts CHANGED
@@ -144,7 +144,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
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  error: unknown;
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  message: string | undefined;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- onHorizontalScroll?: Function;
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+ onHorizontalScroll?: () => void;
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  blockState?: Record<string, any>;
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  }>;
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  readonly DisplayBlurb: import("react").FC<{
package/esm/LinearGCContentDisplay/stateModel2.d.ts CHANGED
@@ -149,7 +149,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
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  error: unknown;
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  message: string | undefined;
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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- onHorizontalScroll?: Function;
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+ onHorizontalScroll?: () => void;
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  blockState?: Record<string, any>;
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  }>;
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  readonly DisplayBlurb: import("react").FC<{
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-gccontent",
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- "version": "2.13.1",
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+ "version": "2.15.0",
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  "description": "JBrowse 2 gccontent concepts",
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  "keywords": [
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  "jbrowse",
@@ -40,7 +40,7 @@
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  "@jbrowse/plugin-linear-genome-view": "^2.0.0",
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  "@jbrowse/plugin-sequence": "^2.0.0",
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  "@jbrowse/plugin-wiggle": "^2.0.0",
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- "@mui/material": "^5.0.0",
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+ "@mui/material": "^6.0.0",
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  "mobx": "^6.0.0",
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  "mobx-react": "^9.0.0",
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  "mobx-state-tree": "^5.0.0",
@@ -53,5 +53,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
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- "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
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+ "gitHead": "87eeb1fbf8311dbf88d5e75b5a265f03beffdda8"
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  }