jbrowse-plugin-mafviewer 1.3.2 → 1.4.0

package/dist/LinearMafRenderer/rendering/spatialIndex.d.ts

@@ -1,60 +1,9 @@
 import type { RenderedBase, RenderingContext } from './types';
-/**
- * Creates a RenderedBase object for spatial indexing
- * @param xPos - X coordinate of the base
- * @param rowTop - Y coordinate of the row top
- * @param context - Rendering context with dimensions
- * @param pos - Genomic coordinate
- * @param chr - Chromosome/sequence name
- * @param sampleId - Sample identifier
- * @param base - The base character
- * @param isMatch - Whether this base matches the reference
- * @param isMismatch - Whether this base is a mismatch
- * @param isGap - Whether this is a gap
- * @param isInsertion - Whether this is an insertion
- * @param featureId - Feature identifier
- */
-export declare function createRenderedBase(xPos: number, rowTop: number, context: RenderingContext, pos: number, chr: string, sampleId: string, base: string, isMatch: boolean, isMismatch: boolean, isGap: boolean, isInsertion: boolean, featureId: string): RenderedBase;
-/**
- * Creates a RenderedBase object for insertions with custom width
- * Uses the actual rendered width instead of the standard scale-based width
- * This ensures accurate spatial queries for different insertion rendering types:
- * - Small insertions: INSERTION_LINE_WIDTH (1px) or INSERTION_BORDER_HEIGHT (5px) with borders
- * - Large insertions (text): measured text width + padding
- * - Large insertions (line): INSERTION_BORDER_WIDTH (2px)
- *
- * @param xPos - X coordinate of the insertion
- * @param rowTop - Y coordinate of the row top
- * @param width - Actual rendered width of the insertion
- * @param context - Rendering context with dimensions
- * @param pos - Genomic coordinate
- * @param chr - Chromosome/sequence name
- * @param sampleId - Sample identifier
- * @param insertionSequence - The insertion sequence
- * @param featureId - Feature identifier
- */
-export declare function createRenderedInsertion(xPos: number, rowTop: number, width: number, context: RenderingContext, pos: number, chr: string, sampleId: string, insertionSequence: string, featureId: string): RenderedBase;
-/**
- * Checks if an item should be added to the spatial index based on distance filtering
- * Only returns true if the X position is >0.5px away from the last inserted item
- * This reduces spatial index density while maintaining useful spatial queries
- *
- * @param xPos - X position to check
- * @param context - Rendering context with lastInsertedX tracking
- * @param bypassDistanceFilter - If true, always return true (e.g., for insertions)
- * @returns Whether the item should be added to spatial index
- *
- * @example
- * // Items at X positions: 100.0, 100.3, 100.8, 101.5
- * // Only items at 100.0, 100.8, 101.5 would return true (>0.5px apart)
- * // Unless bypassDistanceFilter=true, then all would return true
- */
+export declare function createRenderedBaseCoords(xPos: number, rowTop: number, context: RenderingContext): {
+    minX: number;
+    minY: number;
+    maxX: number;
+    maxY: number;
+};
 export declare function shouldAddToSpatialIndex(xPos: number, context: RenderingContext, bypassDistanceFilter?: boolean): boolean;
-/**
- * Adds a rendered base directly to the RBush spatial index
- * Updates the lastInsertedX tracking for distance filtering
- *
- * @param context - Rendering context with spatial index
- * @param renderedBase - The base to add to the spatial index
- */
-export declare function addToSpatialIndex(context: RenderingContext, renderedBase: RenderedBase): void;
+export declare function addToSpatialIndex(context: RenderingContext, minX: number, minY: number, maxX: number, maxY: number, renderedBase: RenderedBase): void;

package/dist/LinearMafRenderer/rendering/spatialIndex.js

@@ -1,99 +1,19 @@
 import { GAP_STROKE_OFFSET, MIN_X_DISTANCE } from './types';
-/**
- * Creates a RenderedBase object for spatial indexing
- * @param xPos - X coordinate of the base
- * @param rowTop - Y coordinate of the row top
- * @param context - Rendering context with dimensions
- * @param pos - Genomic coordinate
- * @param chr - Chromosome/sequence name
- * @param sampleId - Sample identifier
- * @param base - The base character
- * @param isMatch - Whether this base matches the reference
- * @param isMismatch - Whether this base is a mismatch
- * @param isGap - Whether this is a gap
- * @param isInsertion - Whether this is an insertion
- * @param featureId - Feature identifier
- */
-export function createRenderedBase(xPos, rowTop, context, pos, chr, sampleId, base, isMatch, isMismatch, isGap, isInsertion, featureId) {
+export function createRenderedBaseCoords(xPos, rowTop, context) {
     return {
         minX: xPos,
         minY: rowTop,
         maxX: xPos + context.scale + GAP_STROKE_OFFSET,
         maxY: rowTop + context.h,
-        pos,
-        chr,
-        sampleId,
-        base,
-        isMatch,
-        isMismatch,
-        isGap,
-        isInsertion,
-        featureId,
     };
 }
-/**
- * Creates a RenderedBase object for insertions with custom width
- * Uses the actual rendered width instead of the standard scale-based width
- * This ensures accurate spatial queries for different insertion rendering types:
- * - Small insertions: INSERTION_LINE_WIDTH (1px) or INSERTION_BORDER_HEIGHT (5px) with borders
- * - Large insertions (text): measured text width + padding
- * - Large insertions (line): INSERTION_BORDER_WIDTH (2px)
- *
- * @param xPos - X coordinate of the insertion
- * @param rowTop - Y coordinate of the row top
- * @param width - Actual rendered width of the insertion
- * @param context - Rendering context with dimensions
- * @param pos - Genomic coordinate
- * @param chr - Chromosome/sequence name
- * @param sampleId - Sample identifier
- * @param insertionSequence - The insertion sequence
- * @param featureId - Feature identifier
- */
-export function createRenderedInsertion(xPos, rowTop, width, context, pos, chr, sampleId, insertionSequence, featureId) {
-    return {
-        minX: xPos,
-        minY: rowTop,
-        maxX: xPos + width,
-        maxY: rowTop + context.h,
-        pos,
-        chr,
-        sampleId,
-        base: insertionSequence,
-        isMatch: false,
-        isMismatch: false,
-        isGap: false,
-        isInsertion: true,
-        featureId,
-    };
-}
-/**
- * Checks if an item should be added to the spatial index based on distance filtering
- * Only returns true if the X position is >0.5px away from the last inserted item
- * This reduces spatial index density while maintaining useful spatial queries
- *
- * @param xPos - X position to check
- * @param context - Rendering context with lastInsertedX tracking
- * @param bypassDistanceFilter - If true, always return true (e.g., for insertions)
- * @returns Whether the item should be added to spatial index
- *
- * @example
- * // Items at X positions: 100.0, 100.3, 100.8, 101.5
- * // Only items at 100.0, 100.8, 101.5 would return true (>0.5px apart)
- * // Unless bypassDistanceFilter=true, then all would return true
- */
 export function shouldAddToSpatialIndex(xPos, context, bypassDistanceFilter = false) {
     return (bypassDistanceFilter ||
         Math.abs(xPos - context.lastInsertedX) > MIN_X_DISTANCE);
 }
-/**
- * Adds a rendered base directly to the RBush spatial index
- * Updates the lastInsertedX tracking for distance filtering
- *
- * @param context - Rendering context with spatial index
- * @param renderedBase - The base to add to the spatial index
- */
-export function addToSpatialIndex(context, renderedBase) {
-    context.spatialIndex.insert(renderedBase);
-    context.lastInsertedX = renderedBase.minX;
+export function addToSpatialIndex(context, minX, minY, maxX, maxY, renderedBase) {
+    context.spatialIndex.push(renderedBase);
+    context.spatialIndexCoords.push(minX, minY, maxX, maxY);
+    context.lastInsertedX = minX;
 }
 //# sourceMappingURL=spatialIndex.js.map

package/dist/LinearMafRenderer/rendering/spatialIndex.js.map

@@ -1 +1 @@
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package/dist/LinearMafRenderer/rendering/types.d.ts

@@ -1,4 +1,3 @@
-import RBush from 'rbush';
 export declare const FONT_CONFIG = "bold 10px Courier New,monospace";
 export declare const CHAR_SIZE_WIDTH = 10;
 export declare const GAP_STROKE_OFFSET = 0.4;
@@ -21,24 +20,12 @@ export interface GenomicRegion {
     end: number;
     refName: string;
 }
-/**
- * Represents a rendered letter/base with its spatial and genomic coordinates
- * This structure is designed for insertion into an RBush spatial index
- */
 export interface RenderedBase {
-    minX: number;
-    minY: number;
-    maxX: number;
-    maxY: number;
     pos: number;
     chr: string;
-    sampleId: string;
     base: string;
-    isMatch: boolean;
-    isMismatch: boolean;
-    isGap: boolean;
-    isInsertion: boolean;
-    featureId: string;
+    sampleId: number;
+    isInsertion?: boolean;
 }
 /**
  * Shared rendering context containing all necessary parameters for rendering operations
@@ -56,7 +43,8 @@ export interface RenderingContext {
     showAllLetters: boolean;
     mismatchRendering: boolean;
     showAsUpperCase: boolean;
-    spatialIndex: RBush<RenderedBase>;
+    spatialIndex: RenderedBase[];
+    spatialIndexCoords: number[];
     lastInsertedX: number;
 }
 export interface AlignmentRecord {

package/dist/LinearMafRenderer/rendering/types.js.map

@@ -1 +1 @@
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package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js

@@ -39,24 +39,25 @@ export default function MultiMAFWidget({ model }) {
                     } }, ['BigMafAdapter', 'MafTabixAdapter'].map(r => (React.createElement(FormControlLabel, { key: r, value: r, control: React.createElement(Radio, null), checked: fileTypeChoice === r, label: r }))))),
             fileTypeChoice === 'BigMafAdapter' ? (React.createElement(FileSelector, { location: loc, name: "Path to bigMaf", rootModel: rootModel, setLocation: arg => {
                     setLoc(arg);
-                } })) : fileTypeChoice === 'MafTabixAdapter' ? (React.createElement(React.Fragment, null,
-                React.createElement(FormControl, null,
-                    React.createElement(FormLabel, null, "Index type"),
-                    React.createElement(RadioGroup, { value: fileTypeChoice, onChange: event => {
-                            setIndexTypeChoice(event.target.value);
-                        } }, ['TBI', 'CSI'].map(r => (React.createElement(FormControlLabel, { key: r, value: r, control: React.createElement(Radio, null), checked: indexTypeChoice === r, label: r }))))),
-                React.createElement(FileSelector, { location: loc, name: "Path to MAF tabix", rootModel: rootModel, setLocation: arg => {
-                        setLoc(arg);
-                    } }),
-                React.createElement(FileSelector, { location: indexLoc, name: "Path to MAF tabix index", rootModel: rootModel, setLocation: arg => {
-                        setIndexLoc(arg);
-                    } }))) : (React.createElement(React.Fragment, null,
-                React.createElement(FileSelector, { location: loc, name: "Path to TAF.gz (Bgzipped TAF)", rootModel: rootModel, setLocation: arg => {
-                        setLoc(arg);
-                    } }),
-                React.createElement(FileSelector, { location: indexLoc, name: "Path to TAF.gz.tai (TAF index)", rootModel: rootModel, setLocation: arg => {
-                        setIndexLoc(arg);
-                    } })))),
+                } })) : // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                fileTypeChoice === 'MafTabixAdapter' ? (React.createElement(React.Fragment, null,
+                    React.createElement(FormControl, null,
+                        React.createElement(FormLabel, null, "Index type"),
+                        React.createElement(RadioGroup, { value: fileTypeChoice, onChange: event => {
+                                setIndexTypeChoice(event.target.value);
+                            } }, ['TBI', 'CSI'].map(r => (React.createElement(FormControlLabel, { key: r, value: r, control: React.createElement(Radio, null), checked: indexTypeChoice === r, label: r }))))),
+                    React.createElement(FileSelector, { location: loc, name: "Path to MAF tabix", rootModel: rootModel, setLocation: arg => {
+                            setLoc(arg);
+                        } }),
+                    React.createElement(FileSelector, { location: indexLoc, name: "Path to MAF tabix index", rootModel: rootModel, setLocation: arg => {
+                            setIndexLoc(arg);
+                        } }))) : (React.createElement(React.Fragment, null,
+                    React.createElement(FileSelector, { location: loc, name: "Path to TAF.gz (Bgzipped TAF)", rootModel: rootModel, setLocation: arg => {
+                            setLoc(arg);
+                        } }),
+                    React.createElement(FileSelector, { location: indexLoc, name: "Path to TAF.gz.tai (TAF index)", rootModel: rootModel, setLocation: arg => {
+                            setIndexLoc(arg);
+                        } })))),
         React.createElement("div", null,
             React.createElement(FileSelector, { location: nhLoc, name: "Path to newick tree (.nh)", rootModel: rootModel, setLocation: arg => {
                     setNhLoc(arg);
@@ -94,24 +95,25 @@ export default function MultiMAFWidget({ model }) {
                                     samples: sampleNames,
                                     nhLocation: nhLoc,
                                 }
-                                : fileTypeChoice === 'MafTabixAdapter'
-                                    ? {
-                                        type: fileTypeChoice,
-                                        bedGzLocation: loc,
-                                        nhLocation: nhLoc,
-                                        index: {
-                                            indexType: indexTypeChoice,
-                                            location: indexLoc,
+                                : // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                                    fileTypeChoice === 'MafTabixAdapter'
+                                        ? {
+                                            type: fileTypeChoice,
+                                            bedGzLocation: loc,
+                                            nhLocation: nhLoc,
+                                            index: {
+                                                indexType: indexTypeChoice,
+                                                location: indexLoc,
+                                            },
+                                            samples: sampleNames,
+                                        }
+                                        : {
+                                            type: fileTypeChoice,
+                                            tafGzLocation: loc,
+                                            taiLocation: indexLoc,
+                                            nhLocation: nhLoc,
+                                            samples: sampleNames,
                                         },
-                                        samples: sampleNames,
-                                    }
-                                    : {
-                                        type: fileTypeChoice,
-                                        tafGzLocation: loc,
-                                        taiLocation: indexLoc,
-                                        nhLocation: nhLoc,
-                                        samples: sampleNames,
-                                    },
                         });
                         model.view?.showTrack(trackId);
                     }

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AddTrackWorkflow.js","sourceRoot":"","sources":["../../src/MafAddTrackWorkflow/AddTrackWorkflow.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC7D,OAAO,EAEL,UAAU,EACV,yBAAyB,EACzB,sBAAsB,GACvB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EACL,MAAM,EACN,WAAW,EACX,gBAAgB,EAChB,SAAS,EACT,KAAK,EACL,KAAK,EACL,UAAU,EACV,SAAS,GACV,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAI1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,KAAK,EAAE,MAAM;KACd;IACD,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,EAAE;QACvB,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE;KACzB;IACD,MAAM,EAAE;QACN,SAAS,EAAE,EAAE;QACb,YAAY,EAAE,GAAG;QACjB,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAC,CAAA;AAKH,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EAAE,KAAK,EAA4B;IACxE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAC9C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAClD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,WAAW,CAAC,CAAA;IACvD,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GACvC,QAAQ,CAAqB,eAAe,CAAC,CAAA;IAC/C,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GACzC,QAAQ,CAAmB,KAAK,CAAC,CAAA;IAEnC,MAAM,SAAS,GAAG,OAAO,CAAM,KAAK,CAAC,CAAA;IACrC,OAAO,CACL,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,oBAAC,KAAK;YACH,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,WAAW;gBACV,oBAAC,SAAS,oBAAsB;gBAChC,oBAAC,UAAU,IACT,KAAK,EAAE,cAAc,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,iBAAiB,CAAC,KAAK,CAAC,MAAM,CAAC,KAA2B,CAAC,CAAA;oBAC7D,CAAC,IAEA,CAAC,eAAe,EAAE,iBAAiB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAC7C,oBAAC,gBAAgB,IACf,GAAG,EAAE,CAAC,EACN,KAAK,EAAE,CAAC,EACR,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,OAAO,EAAE,cAAc,KAAK,CAAC,EAC7B,KAAK,EAAE,CAAC,GACR,CACH,CAAC,CACS,CACD;YACb,cAAc,KAAK,eAAe,CAAC,CAAC,CAAC,CACpC,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,gBAAgB,EACrB,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;oBACjB,MAAM,CAAC,GAAG,CAAC,CAAA;gBACb,CAAC,GACD,CACH,CAAC,CAAC,CAAC,uEAAuE;gBAC3E,cAAc,KAAK,iBAAiB,CAAC,CAAC,CAAC,CACrC;oBACE,oBAAC,WAAW;wBACV,oBAAC,SAAS,qBAAuB;wBACjC,oBAAC,UAAU,IACT,KAAK,EAAE,cAAc,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;gCAChB,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAyB,CAAC,CAAA;4BAC5D,CAAC,IAEA,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACvB,oBAAC,gBAAgB,IACf,GAAG,EAAE,CAAC,EACN,KAAK,EAAE,CAAC,EACR,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,OAAO,EAAE,eAAe,KAAK,CAAC,EAC9B,KAAK,EAAE,CAAC,GACR,CACH,CAAC,CACS,CACD;oBACd,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,mBAAmB,EACxB,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,MAAM,CAAC,GAAG,CAAC,CAAA;wBACb,CAAC,GACD;oBACF,oBAAC,YAAY,IACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAC,yBAAyB,EAC9B,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,WAAW,CAAC,GAAG,CAAC,CAAA;wBAClB,CAAC,GACD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;oBACE,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,+BAA+B,EACpC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,MAAM,CAAC,GAAG,CAAC,CAAA;wBACb,CAAC,GACD;oBACF,oBAAC,YAAY,IACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAC,gCAAgC,EACrC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,WAAW,CAAC,GAAG,CAAC,CAAA;wBAClB,CAAC,GACD,CACD,CACJ,CACK;QACR;YACE,oBAAC,YAAY,IACX,QAAQ,EAAE,KAAK,EACf,IAAI,EAAC,2BAA2B,EAChC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;oBACjB,QAAQ,CAAC,GAAG,CAAC,CAAA;gBACf,CAAC,GACD;YACF,oBAAC,SAAS,IACR,SAAS,QACT,IAAI,EAAE,EAAE,EACR,KAAK,EAAE,OAAO,EACd,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAChC,CAAC,EACD,UAAU,EAAC,0DAA0D,EACrE,WAAW,EACT,wFAAwF,EAE1F,OAAO,EAAC,UAAU,EAClB,SAAS,SACT,CACE;QAEN,oBAAC,SAAS,IACR,KAAK,EAAE,SAAS,EAChB,UAAU,EAAC,YAAY,EACvB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YAClC,CAAC,GACD;QACF,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,CAAC;oBACH,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI,WAAW,GAAG,EAAc,CAAA;oBAChC,IAAI,CAAC;wBACH,WAAW,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;oBACnC,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,WAAW,GAAG,OAAO,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;oBAC3C,CAAC;oBAED,MAAM,OAAO,GAAG;wBACd,GAAG,SAAS,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,IAAI,IAAI,CAAC,GAAG,EAAE,EAAE;wBAC/D,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,eAAe;qBACzC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;oBAEV,IAAI,sBAAsB,CAAC,OAAO,CAAC,EAAE,CAAC;wBACpC,OAAO,CAAC,YAAY,CAAC;4BACnB,OAAO;4BACP,IAAI,EAAE,UAAU;4BAChB,IAAI,EAAE,SAAS;4BACf,aAAa,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC;4BAC/B,OAAO,EACL,cAAc,KAAK,eAAe;gCAChC,CAAC,CAAC;oCACE,IAAI,EAAE,cAAc;oCACpB,cAAc,EAAE,GAAG;oCACnB,OAAO,EAAE,WAAW;oCACpB,UAAU,EAAE,KAAK;iCAClB;gCACH,CAAC,CAAC,uEAAuE;oCACvE,cAAc,KAAK,iBAAiB;wCACpC,CAAC,CAAC;4CACE,IAAI,EAAE,cAAc;4CACpB,aAAa,EAAE,GAAG;4CAClB,UAAU,EAAE,KAAK;4CACjB,KAAK,EAAE;gDACL,SAAS,EAAE,eAAe;gDAC1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package/dist/index.js

@@ -1,6 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { version } from '../package.json';
-import BgzipTaffyAdapterF from './BgzipTaffyAdapter';
 import BigMafAdapterF from './BigMafAdapter';
 import LinearMafDisplayF from './LinearMafDisplay';
 import LinearMafRendererF from './LinearMafRenderer';
@@ -18,7 +17,6 @@ export default class MafViewerPlugin extends Plugin {
         LinearMafDisplayF(pluginManager);
         LinearMafRendererF(pluginManager);
         MafTabixAdapterF(pluginManager);
-        BgzipTaffyAdapterF(pluginManager);
         MafAddTrackWorkflowF(pluginManager);
         MafGetSequencesF(pluginManager);
         MafGetSamplesF(pluginManager);

package/dist/index.js.map

@@ -1 +1 @@
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