@jbrowse/bandage-core 6.2.0 → 7.1.0
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/chunks/{chunk-GOY6REMT.js → chunk-2LQ5BWT7.js} +1 -1
- package/dist/chunks/{chunk-5HF753RL.js → chunk-2WA4EY25.js} +27 -23
- package/dist/chunks/{chunk-EZPBJPK6.js → chunk-3JANT2SW.js} +6 -3
- package/dist/chunks/{chunk-N62KBLFC.js → chunk-3ZZSX5HN.js} +1 -1
- package/dist/chunks/{chunk-R6ZUK4Y3.js → chunk-4FQTTG5F.js} +1 -1
- package/dist/chunks/{chunk-YFRTTBCZ.js → chunk-6UFS3EWI.js} +3 -3
- package/dist/chunks/{chunk-M6SAUIYR.js → chunk-AWCMVPVP.js} +1 -1
- package/dist/chunks/{chunk-P2KU2TXS.js → chunk-CNQSHEBS.js} +1 -1
- package/dist/chunks/{chunk-CS3E4ETM.js → chunk-DRA7733Q.js} +1 -1
- package/dist/chunks/{chunk-X5L37W4J.js → chunk-E7FWQQHP.js} +1 -1
- package/dist/chunks/{chunk-3GMVZMKD.js → chunk-EXSXBIMH.js} +1 -1
- package/dist/chunks/{chunk-YMSSF2RK.js → chunk-FP4H7SFT.js} +1 -1
- package/dist/chunks/{chunk-DKOB2OPC.js → chunk-GJMC3PGM.js} +3 -3
- package/dist/chunks/{chunk-T43W7NKK.js → chunk-JKXE6CIP.js} +2 -2
- package/dist/chunks/{chunk-7R2UGY4I.js → chunk-KREASK3Z.js} +7 -13
- package/dist/chunks/{chunk-HE3NRWH7.js → chunk-MAPRJ2H2.js} +1 -1
- package/dist/chunks/{chunk-A7VOULBP.js → chunk-MH5IA57M.js} +1 -1
- package/dist/chunks/{chunk-MREQ7GIA.js → chunk-MLSWIMZO.js} +1 -1
- package/dist/chunks/{chunk-4EMPBO7S.js → chunk-N6FECAXP.js} +51 -1
- package/dist/chunks/{chunk-CTSBC2O6.js → chunk-OWFPAIJI.js} +1 -1
- package/dist/chunks/{chunk-6CO564AN.js → chunk-TQ7VCGJR.js} +1 -1
- package/dist/chunks/{chunk-YQZWW2V6.js → chunk-UGD6ZMOF.js} +31 -6
- package/dist/chunks/{chunk-GD7FYNGS.js → chunk-VECR253P.js} +1 -1
- package/dist/chunks/{chunk-VUBLSA6P.js → chunk-VST5SR4C.js} +2 -2
- package/dist/chunks/{chunk-Y3IOTZJA.js → chunk-WFB5TXRA.js} +1 -1
- package/dist/chunks/{chunk-STNG3Y5X.js → chunk-YZ5CCEDH.js} +0 -30
- package/dist/cli/figure.js +23 -23
- package/dist/deletionEdges.js +5 -1
- package/dist/figure.js +20 -20
- package/dist/graphLabels.js +2 -2
- package/dist/index.js +37 -27
- package/dist/labelLayout.js +6 -6
- package/dist/layout/deletionRoutes.js +1 -3
- package/dist/layout/tubeMapLayout.js +4 -4
- package/dist/layout/walkRowDraw.js +17 -7
- package/dist/layout/walkRowLayout.js +1 -1
- package/dist/layout/walkStrip.js +10 -9
- package/dist/layoutModes.js +6 -6
- package/dist/pathColors.js +3 -3
- package/dist/pipeline.js +3 -3
- package/dist/referenceRampCss.js +6 -6
- package/dist/referenceStrip.js +6 -6
- package/dist/renderer/GeometryBuilder.js +5 -5
- package/dist/tubeMap/axis.js +3 -3
- package/dist/tubeMap/coarsen.js +4 -4
- package/dist/tubeMap/genes.js +4 -4
- package/dist/tubeMap/nodeColors.js +6 -6
- package/dist/types/deletionEdges.d.ts +7 -0
- package/dist/types/figure.d.ts +2 -1
- package/dist/types/index.d.ts +4 -4
- package/dist/types/labelLayout.d.ts +0 -1
- package/dist/types/layout/deletionRoutes.d.ts +0 -1
- package/dist/types/layout/walkRowDraw.d.ts +11 -0
- package/dist/types/layout/walkRowLayout.d.ts +2 -1
- package/dist/types/layout/walkStrip.d.ts +1 -1
- package/dist/types/version.d.ts +1 -1
- package/dist/util/SpatialIndex.js +3 -3
- package/dist/util/edgeCurves.js +2 -2
- package/dist/util/hitDetection.js +4 -4
- package/dist/version.js +1 -1
- package/dist/viewport.js +4 -4
- package/dist/walkEncoding.js +6 -6
- package/dist/walkHighlight.js +7 -7
- package/dist/walkKey.js +3 -3
- package/package.json +1 -1
package/dist/pipeline.js
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forceLayout,
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layoutExtent,
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loadGraph
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package/dist/referenceRampCss.js
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package/dist/referenceStrip.js
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package/dist/tubeMap/axis.js
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package/dist/tubeMap/coarsen.js
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package/dist/tubeMap/genes.js
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export type { WalkAxis, WalkRow, WalkRows, WalkRun } from './layout/walkRows.js';
|
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|
-
export { BAR_PX as WALK_BAR_PX, DISAGREES as WALK_DISAGREES, GAP_PX as WALK_GAP_PX, GENE_INK as WALK_GENE_INK, OFF_REFERENCE as WALK_OFF_REFERENCE, ON_REFERENCE as WALK_ON_REFERENCE, OUTSIDE_CUT as WALK_OUTSIDE_CUT, alongRow, coalesceRuns, genesOnRow, placeRowGenes, readoutPlacement, rowGeneBoxes, rowSpan, runPaint, unitTicks, walkRowReadout, walkRowsKey, walkRowsKeyTree, walkRowsTree, } from './layout/walkRowDraw.js';
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-
export type { GeneBox, GeneGaps, KeyEntry, KeySwatch, ReadoutCall, RowGene, WalkRowsFrame, WalkRowsWithCalls, } from './layout/walkRowDraw.js';
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|
+
export { BAR_PX as WALK_BAR_PX, CALL_TICK as WALK_CALL_TICK, DISAGREES as WALK_DISAGREES, GAP_PX as WALK_GAP_PX, GENE_INK as WALK_GENE_INK, OFF_REFERENCE as WALK_OFF_REFERENCE, ON_REFERENCE as WALK_ON_REFERENCE, OUTSIDE_CUT as WALK_OUTSIDE_CUT, UNBACKED_TICK as WALK_UNBACKED_TICK, alongRow, callTickInk, coalesceRuns, genesOnRow, placeRowGenes, readoutPlacement, rowGeneBoxes, rowPitch, rowSpan, runPaint, unitTicks, walkRowReadout, walkRowsKey, walkRowsKeyTree, walkRowsTree, } from './layout/walkRowDraw.js';
|
|
63
|
+
export type { GeneBox, GeneGaps, KeyEntry, KeySwatch, ReadoutCall, RowGene, RowPitch, WalkRowsFrame, WalkRowsWithCalls, } from './layout/walkRowDraw.js';
|
|
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64
|
export { LABELLED_ROW_PX, WALK_STRIP_CEILING_PX, segmentAt, stripGeneGaps, stripMarks, stripRowAt, walkMarksTree, walkStripFrame, walkStripLabelsTree, } from './layout/walkStrip.js';
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65
|
export type { StripFrame, StripMark } from './layout/walkStrip.js';
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66
|
export { el, serializeEl } from './el.js';
|
|
@@ -32,7 +32,6 @@ export interface LabelLayoutSource {
|
|
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32
32
|
nodePositions?: Record<string, NodeSegment[]>;
|
|
33
33
|
labelsNodeSizes: boolean;
|
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34
|
nodeLengths: Map<string, number>;
|
|
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|
-
showDeletionEdges: boolean;
|
|
36
35
|
deletions: DeletionEdge[];
|
|
37
36
|
deletionRoutes?: DeletionRoutes;
|
|
38
37
|
stranded?: boolean;
|
|
@@ -22,7 +22,6 @@ export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge
|
|
|
22
22
|
routes: Map<number, string>;
|
|
23
23
|
ids: Set<string>;
|
|
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24
|
};
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|
-
export declare function closableDeletions(graph: Graph, deletions: DeletionEdge[]): Set<number>;
|
|
26
25
|
export declare function routeNodes(graph: Graph, deletions: DeletionEdge[], routes: Map<number, string>, drawnOf: (bp: number) => number, opts: BandageScaleOpts): GraphNode[];
|
|
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26
|
export declare function takeRoutes(positions: Record<string, NodeSegment[]>, routes: Map<number, string>): {
|
|
28
27
|
nodePositions: {
|
|
@@ -7,6 +7,7 @@ export declare const OUTSIDE_CUT = "#bdbdbd";
|
|
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7
7
|
export declare const GENE_INK = "#1c1c22";
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8
8
|
export declare const BAR_PX = 12;
|
|
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9
|
export declare const GAP_PX = 4;
|
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|
+
export declare const LABELLED_ROW_PX = 12;
|
|
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11
|
export declare function kb(bp: number): string;
|
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12
|
export interface ReadoutCall {
|
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13
|
bp: number;
|
|
@@ -109,11 +110,21 @@ export type WalkRowsWithCalls = Omit<WalkRows, 'reference' | 'rows'> & {
|
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|
109
110
|
call?: ReadoutCall;
|
|
110
111
|
})[];
|
|
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112
|
};
|
|
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|
+
export declare const CALL_TICK = "#111";
|
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|
+
export declare const UNBACKED_TICK = "#9e9e9e";
|
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115
|
export declare const DISAGREES = "#c62828";
|
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|
+
export declare function callTickInk(call: ReadoutCall): "#111" | "#9e9e9e" | "#c62828";
|
|
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117
|
export declare function walkRowsKeyTree(entries: KeyEntry[], x: number, y: number, idPrefix?: string): {
|
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118
|
width: number;
|
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|
tree: El;
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|
};
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|
+
export interface RowPitch {
|
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|
+
rowPx: number;
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|
+
barPx: number;
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|
+
labelled: boolean;
|
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|
+
readouts: boolean;
|
|
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|
+
}
|
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|
+
export declare function rowPitch(count: number, room: number, minRowPx?: number): RowPitch;
|
|
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128
|
export interface WalkRowsFrame {
|
|
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129
|
scaleX: number;
|
|
119
130
|
scaleY: number;
|
|
@@ -1,6 +1,7 @@
|
|
|
1
|
+
import type { RowPitch } from './walkRowDraw.js';
|
|
1
2
|
import type { WalkRows } from './walkRows.js';
|
|
2
3
|
import type { Graph, LayoutResult } from '../types.js';
|
|
3
|
-
export declare function walkRowsExtent(walks: WalkRows): {
|
|
4
|
+
export declare function walkRowsExtent(walks: WalkRows, pitch?: Pick<RowPitch, 'rowPx' | 'readouts'>): {
|
|
4
5
|
maxX: number;
|
|
5
6
|
maxY: number;
|
|
6
7
|
};
|
|
@@ -1,8 +1,8 @@
|
|
|
1
1
|
import type { GeneGaps, RowGene, WalkRowsFrame } from './walkRowDraw.js';
|
|
2
2
|
import type { WalkRow, WalkRows } from './walkRows.js';
|
|
3
3
|
import type { Graph, GraphNode } from '../types.js';
|
|
4
|
+
export { LABELLED_ROW_PX } from './walkRowDraw.js';
|
|
4
5
|
export declare const WALK_STRIP_CEILING_PX = 260;
|
|
5
|
-
export declare const LABELLED_ROW_PX = 12;
|
|
6
6
|
export interface StripMark {
|
|
7
7
|
row: string;
|
|
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8
|
start: number;
|
package/dist/types/version.d.ts
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
export declare const version = "
|
|
1
|
+
export declare const version = "7.1.0";
|
|
@@ -1,9 +1,9 @@
|
|
|
1
1
|
import {
|
|
2
2
|
EdgeSpatialIndex,
|
|
3
3
|
SpatialIndex
|
|
4
|
-
} from "../chunks/chunk-
|
|
5
|
-
import "../chunks/chunk-
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|
6
|
-
import "../chunks/chunk-
|
|
4
|
+
} from "../chunks/chunk-MLSWIMZO.js";
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5
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+
import "../chunks/chunk-WFB5TXRA.js";
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import "../chunks/chunk-N6FECAXP.js";
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import "../chunks/chunk-2CVHXFK7.js";
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import "../chunks/chunk-CPMHA4W5.js";
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import "../chunks/chunk-FYQWPEEY.js";
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package/dist/util/edgeCurves.js
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import {
|
|
2
2
|
baseEdgeCurves
|
|
3
|
-
} from "../chunks/chunk-
|
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|
-
import "../chunks/chunk-
|
|
3
|
+
} from "../chunks/chunk-WFB5TXRA.js";
|
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4
|
+
import "../chunks/chunk-N6FECAXP.js";
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5
|
import "../chunks/chunk-2CVHXFK7.js";
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|
import "../chunks/chunk-CPMHA4W5.js";
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7
|
import "../chunks/chunk-FYQWPEEY.js";
|
|
@@ -4,10 +4,10 @@ import {
|
|
|
4
4
|
findHoveredEdge,
|
|
5
5
|
findHoveredNode,
|
|
6
6
|
nodesUnderBox
|
|
7
|
-
} from "../chunks/chunk-
|
|
8
|
-
import "../chunks/chunk-
|
|
9
|
-
import "../chunks/chunk-
|
|
10
|
-
import "../chunks/chunk-
|
|
7
|
+
} from "../chunks/chunk-FP4H7SFT.js";
|
|
8
|
+
import "../chunks/chunk-MLSWIMZO.js";
|
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9
|
+
import "../chunks/chunk-WFB5TXRA.js";
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+
import "../chunks/chunk-N6FECAXP.js";
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|
import "../chunks/chunk-2CVHXFK7.js";
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import "../chunks/chunk-CPMHA4W5.js";
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13
|
import "../chunks/chunk-FYQWPEEY.js";
|
package/dist/version.js
CHANGED
package/dist/viewport.js
CHANGED
|
@@ -5,20 +5,20 @@ import {
|
|
|
5
5
|
screenToLayout,
|
|
6
6
|
viewportOf,
|
|
7
7
|
zoomAbout
|
|
8
|
-
} from "./chunks/chunk-
|
|
9
|
-
import "./chunks/chunk-
|
|
8
|
+
} from "./chunks/chunk-AWCMVPVP.js";
|
|
9
|
+
import "./chunks/chunk-6UFS3EWI.js";
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|
import "./chunks/chunk-PUG7LXDF.js";
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import "./chunks/chunk-IGVV37VI.js";
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import "./chunks/chunk-72N5DJHZ.js";
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import "./chunks/chunk-QYBZZI5H.js";
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|
import "./chunks/chunk-CDLPYR5O.js";
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|
-
import "./chunks/chunk-
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|
+
import "./chunks/chunk-YZ5CCEDH.js";
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import "./chunks/chunk-ES2N6V56.js";
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import "./chunks/chunk-ST2IBUAN.js";
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import "./chunks/chunk-TAMCZHLW.js";
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import "./chunks/chunk-UVBGRJQX.js";
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|
import "./chunks/chunk-6JEWNXCQ.js";
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|
-
import "./chunks/chunk-
|
|
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|
+
import "./chunks/chunk-N6FECAXP.js";
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22
|
import "./chunks/chunk-2CVHXFK7.js";
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|
import "./chunks/chunk-CPMHA4W5.js";
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|
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24
|
import "./chunks/chunk-BPLIXMH7.js";
|
package/dist/walkEncoding.js
CHANGED
|
@@ -9,18 +9,18 @@ import {
|
|
|
9
9
|
schemeColor,
|
|
10
10
|
schemeCss,
|
|
11
11
|
schemeRgb
|
|
12
|
-
} from "./chunks/chunk-
|
|
13
|
-
import "./chunks/chunk-
|
|
12
|
+
} from "./chunks/chunk-TQ7VCGJR.js";
|
|
13
|
+
import "./chunks/chunk-VST5SR4C.js";
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14
|
import "./chunks/chunk-UMNCCYBN.js";
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15
|
import "./chunks/chunk-PBENCR5L.js";
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|
16
|
-
import "./chunks/chunk-
|
|
17
|
-
import "./chunks/chunk-
|
|
16
|
+
import "./chunks/chunk-WFB5TXRA.js";
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+
import "./chunks/chunk-E7FWQQHP.js";
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|
import "./chunks/chunk-ES2N6V56.js";
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|
import "./chunks/chunk-ST2IBUAN.js";
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|
-
import "./chunks/chunk-
|
|
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|
+
import "./chunks/chunk-3ZZSX5HN.js";
|
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21
|
import "./chunks/chunk-AB35TJST.js";
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22
|
import "./chunks/chunk-TAMCZHLW.js";
|
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23
|
-
import "./chunks/chunk-
|
|
23
|
+
import "./chunks/chunk-N6FECAXP.js";
|
|
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24
|
import "./chunks/chunk-2CVHXFK7.js";
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25
|
import "./chunks/chunk-CPMHA4W5.js";
|
|
26
26
|
import "./chunks/chunk-BPLIXMH7.js";
|
package/dist/walkHighlight.js
CHANGED
|
@@ -2,19 +2,19 @@ import {
|
|
|
2
2
|
facetLifts,
|
|
3
3
|
walkHighlight,
|
|
4
4
|
walkLift
|
|
5
|
-
} from "./chunks/chunk-
|
|
6
|
-
import "./chunks/chunk-
|
|
7
|
-
import "./chunks/chunk-
|
|
5
|
+
} from "./chunks/chunk-MH5IA57M.js";
|
|
6
|
+
import "./chunks/chunk-TQ7VCGJR.js";
|
|
7
|
+
import "./chunks/chunk-VST5SR4C.js";
|
|
8
8
|
import "./chunks/chunk-UMNCCYBN.js";
|
|
9
9
|
import "./chunks/chunk-PBENCR5L.js";
|
|
10
|
-
import "./chunks/chunk-
|
|
11
|
-
import "./chunks/chunk-
|
|
10
|
+
import "./chunks/chunk-WFB5TXRA.js";
|
|
11
|
+
import "./chunks/chunk-E7FWQQHP.js";
|
|
12
12
|
import "./chunks/chunk-ES2N6V56.js";
|
|
13
13
|
import "./chunks/chunk-ST2IBUAN.js";
|
|
14
|
-
import "./chunks/chunk-
|
|
14
|
+
import "./chunks/chunk-3ZZSX5HN.js";
|
|
15
15
|
import "./chunks/chunk-AB35TJST.js";
|
|
16
16
|
import "./chunks/chunk-TAMCZHLW.js";
|
|
17
|
-
import "./chunks/chunk-
|
|
17
|
+
import "./chunks/chunk-N6FECAXP.js";
|
|
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18
|
import "./chunks/chunk-2CVHXFK7.js";
|
|
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19
|
import "./chunks/chunk-CPMHA4W5.js";
|
|
20
20
|
import "./chunks/chunk-BPLIXMH7.js";
|
package/dist/walkKey.js
CHANGED
|
@@ -2,11 +2,11 @@ import {
|
|
|
2
2
|
rangeText,
|
|
3
3
|
walkKey,
|
|
4
4
|
walkPosition
|
|
5
|
-
} from "./chunks/chunk-
|
|
6
|
-
import "./chunks/chunk-
|
|
5
|
+
} from "./chunks/chunk-2LQ5BWT7.js";
|
|
6
|
+
import "./chunks/chunk-3ZZSX5HN.js";
|
|
7
7
|
import "./chunks/chunk-AB35TJST.js";
|
|
8
8
|
import "./chunks/chunk-TAMCZHLW.js";
|
|
9
|
-
import "./chunks/chunk-
|
|
9
|
+
import "./chunks/chunk-N6FECAXP.js";
|
|
10
10
|
import "./chunks/chunk-2CVHXFK7.js";
|
|
11
11
|
import "./chunks/chunk-CPMHA4W5.js";
|
|
12
12
|
import "./chunks/chunk-FYQWPEEY.js";
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/bandage-core",
|
|
3
|
-
"version": "
|
|
3
|
+
"version": "7.1.0",
|
|
4
4
|
"description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
|
|
5
5
|
"license": "GPL-3.0-or-later",
|
|
6
6
|
"repository": {
|