@jbrowse/bandage-core 11.4.0 → 11.6.1
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/alleleProjection/projectAlleles.js +1 -1
- package/dist/bubbles/bubbleHalos.js +9 -6
- package/dist/bubbles/classifyBubble.js +8 -5
- package/dist/bubbles/popBubble.js +3 -3
- package/dist/bubbles/superbubbles.js +11 -11
- package/dist/chunks/{chunk-FFHJGWDK.js → chunk-2C5SATRZ.js} +5 -5
- package/dist/chunks/{chunk-4XWZNPQ2.js → chunk-2JL2JVZ2.js} +1 -1
- package/dist/chunks/{chunk-BZFOFC4D.js → chunk-2VMKQKVO.js} +17 -7
- package/dist/chunks/{chunk-GM7M25NW.js → chunk-2XEAITWM.js} +15 -5
- package/dist/chunks/{chunk-7BTO7MZS.js → chunk-376YFQOY.js} +2 -2
- package/dist/chunks/{chunk-EFD753MS.js → chunk-3FWNQNF7.js} +1 -1
- package/dist/chunks/{chunk-B5X2RLJG.js → chunk-3YBP46PB.js} +27 -2
- package/dist/chunks/{chunk-EJRJAAN7.js → chunk-4DMSPNYV.js} +47 -27
- package/dist/chunks/{chunk-I4BYUNJN.js → chunk-4WXFQOYV.js} +5 -5
- package/dist/chunks/{chunk-OMUPUB4J.js → chunk-56L6R6D2.js} +2 -2
- package/dist/chunks/{chunk-C44YRP5F.js → chunk-5OJZV6YT.js} +3 -2
- package/dist/chunks/{chunk-234NFZS4.js → chunk-5ORP7EFJ.js} +1 -1
- package/dist/chunks/{chunk-TUQKGAK3.js → chunk-5WB7O7IT.js} +4 -4
- package/dist/chunks/{chunk-3VCKBSML.js → chunk-6YRSOL4K.js} +2 -2
- package/dist/chunks/{chunk-REOWLPH4.js → chunk-7OTWJQGA.js} +13 -13
- package/dist/chunks/{chunk-77EGQQJU.js → chunk-BFUS3ENH.js} +2 -2
- package/dist/chunks/{chunk-TGUFT6KK.js → chunk-BLUEFYIR.js} +4 -1
- package/dist/chunks/{chunk-JQ52XYD2.js → chunk-BVWMVWLJ.js} +12 -12
- package/dist/chunks/{chunk-3GP3KT5L.js → chunk-BW2NMXRV.js} +5 -5
- package/dist/chunks/{chunk-2Q22S52W.js → chunk-C6E6HXP5.js} +8 -8
- package/dist/chunks/{chunk-5I3K4R2G.js → chunk-CFXXFHRK.js} +2 -1
- package/dist/chunks/{chunk-JMABOQWL.js → chunk-CO6RGQAD.js} +1 -6
- package/dist/chunks/{chunk-M75QPZNJ.js → chunk-D3E7AXBB.js} +68 -26
- package/dist/chunks/{chunk-CGMSKIEO.js → chunk-DV5B5UU7.js} +55 -8
- package/dist/chunks/{chunk-G6UIYQZR.js → chunk-EQDQ7P4Y.js} +3 -2
- package/dist/chunks/{chunk-FRTYQQDI.js → chunk-EVXXFMZ7.js} +9 -9
- package/dist/chunks/{chunk-BXLLMWC3.js → chunk-F3KQQDKP.js} +1 -1
- package/dist/chunks/{chunk-6EOB6ANX.js → chunk-GZ36HNPJ.js} +1 -1
- package/dist/chunks/{chunk-3HGYGISG.js → chunk-HV35LDYH.js} +3 -3
- package/dist/chunks/{chunk-XSF4RQRP.js → chunk-JGHZ3N34.js} +22 -15
- package/dist/chunks/{chunk-D4ZFRBB4.js → chunk-JGQQAUVL.js} +3 -3
- package/dist/chunks/{chunk-PSCSZSVK.js → chunk-KA4F3N55.js} +4 -4
- package/dist/chunks/{chunk-SOMZGDVS.js → chunk-KJDERUQF.js} +1 -1
- package/dist/chunks/{chunk-E4ZM4OOJ.js → chunk-KZMSSPS6.js} +2 -2
- package/dist/chunks/{chunk-JDZ5GTZT.js → chunk-MEVTV4FI.js} +1 -1
- package/dist/chunks/{chunk-PNMJFFNB.js → chunk-MHZTTLBU.js} +1 -1
- package/dist/chunks/{chunk-VIQL7GZ4.js → chunk-MXLYBDOX.js} +14 -13
- package/dist/chunks/{chunk-3LZ334X4.js → chunk-NXBW6KY6.js} +6 -7
- package/dist/chunks/{chunk-7O7EGTYG.js → chunk-OUM54ZSQ.js} +2 -2
- package/dist/chunks/{chunk-WA5WNP6V.js → chunk-OYCQVJYY.js} +1 -1
- package/dist/chunks/{chunk-TZLEHZVC.js → chunk-P5PBJONQ.js} +1 -1
- package/dist/chunks/chunk-PQIFYQVI.js +21 -0
- package/dist/chunks/{chunk-6VVGFQ7S.js → chunk-QCOVHLJO.js} +1 -1
- package/dist/chunks/{chunk-TEXAKEJX.js → chunk-QD35GH4C.js} +3 -3
- package/dist/chunks/{chunk-CE6ZIKJX.js → chunk-RLCYVZ4B.js} +1 -1
- package/dist/chunks/{chunk-6YJESZND.js → chunk-ROLACYCO.js} +20 -20
- package/dist/chunks/{chunk-A7H753BA.js → chunk-SDI6BVG7.js} +5 -6
- package/dist/chunks/{chunk-A4JDEUAI.js → chunk-SNF2MIEF.js} +1 -1
- package/dist/chunks/{chunk-NMWQUFPF.js → chunk-SVVFWTG4.js} +2 -2
- package/dist/chunks/{chunk-PFRQBCGC.js → chunk-T3H5ELLA.js} +4 -4
- package/dist/chunks/{chunk-QM7KEWWT.js → chunk-TXTSE44S.js} +1 -1
- package/dist/chunks/{chunk-UBQSRCWR.js → chunk-VACK24HF.js} +43 -3
- package/dist/chunks/{chunk-HSVFCA2J.js → chunk-VO6FKNZE.js} +1 -1
- package/dist/chunks/{chunk-B5ARSBOH.js → chunk-W2YAW36J.js} +8 -7
- package/dist/chunks/{chunk-TJOOHTJ6.js → chunk-WI6SUU5B.js} +2 -2
- package/dist/chunks/{chunk-GJU6BJJA.js → chunk-XR2HMGAS.js} +1 -1
- package/dist/chunks/{chunk-N7G5ROIV.js → chunk-XXOBCANT.js} +26 -12
- package/dist/chunks/{chunk-G3I4TCEZ.js → chunk-YEYQFNFQ.js} +1 -1
- package/dist/chunks/{chunk-UFUSPK2A.js → chunk-YYIU7P73.js} +4 -1
- package/dist/chunks/{chunk-CRCD3ODN.js → chunk-ZANALBSX.js} +11 -3
- package/dist/cli/figure.js +52 -47
- package/dist/cli/fold.js +12 -12
- package/dist/deletionEdges.js +5 -2
- package/dist/facetGrid.js +2 -2
- package/dist/figure.js +36 -36
- package/dist/figureData.js +38 -38
- package/dist/figureScene.js +26 -26
- package/dist/figureSettings.js +12 -12
- package/dist/foldVariants.js +2 -2
- package/dist/gaf/parseGaf.js +1 -1
- package/dist/gbzCut.js +4 -4
- package/dist/gbzWindow.js +3 -3
- package/dist/genes/backboneGenes.js +4 -4
- package/dist/genes/geneFiles.js +1 -1
- package/dist/genes/genePins.js +3 -3
- package/dist/gfa/gfaConverter.js +4 -4
- package/dist/gfa/graphTables.js +2 -2
- package/dist/gfa-core/gfaParser.js +1 -1
- package/dist/gfa-core/index.js +1 -1
- package/dist/graphLabels.js +7 -4
- package/dist/index.js +96 -90
- package/dist/labelLayout.js +11 -8
- package/dist/layout/anchoredLayout.js +1 -1
- package/dist/layout/forceCache.js +12 -12
- package/dist/layout/mergeRuns.js +2 -2
- package/dist/layout/placeOffReference.js +1 -1
- package/dist/layout/sampleRowLayout.js +2 -2
- package/dist/layout/trimToWindow.js +2 -2
- package/dist/layout/tubeMapLayout.js +14 -14
- package/dist/layout/walkRowDraw.js +12 -12
- package/dist/layout/walkRowLayout.js +7 -7
- package/dist/layout/walkRowLinks.js +1 -1
- package/dist/layout/walkRowRuns.js +4 -4
- package/dist/layout/walkRows.js +5 -5
- package/dist/layout/walkStrip.js +17 -17
- package/dist/layoutEngines.js +1 -1
- package/dist/layoutModes.js +17 -17
- package/dist/locus.js +8 -0
- package/dist/nodeWidths.js +5 -3
- package/dist/pansn.js +1 -1
- package/dist/pathAnchoring.js +4 -2
- package/dist/pathColors.js +8 -8
- package/dist/pipeline.js +11 -11
- package/dist/reference.js +2 -2
- package/dist/referenceStrip.js +12 -12
- package/dist/renderer/Canvas2DRenderer.js +1 -1
- package/dist/renderer/GeometryBuilder.js +15 -13
- package/dist/tubeMap/axis.js +8 -5
- package/dist/tubeMap/bundle.js +15 -15
- package/dist/tubeMap/coarsen.js +15 -15
- package/dist/tubeMap/deviations.js +18 -18
- package/dist/tubeMap/draw.js +10 -8
- package/dist/tubeMap/genes.js +9 -6
- package/dist/tubeMap/nodeColors.js +12 -12
- package/dist/tubeMap/reads.js +4 -4
- package/dist/types/figureData.d.ts +12 -0
- package/dist/types/gaf/parseGaf.d.ts +1 -1
- package/dist/types/gfa/graphTables.d.ts +3 -2
- package/dist/types/index.d.ts +1 -0
- package/dist/types/locus.d.ts +10 -0
- package/dist/types/nodeWidths.d.ts +2 -1
- package/dist/types/pathAnchoring.d.ts +2 -0
- package/dist/types/renderer/Canvas2DRenderer.d.ts +2 -0
- package/dist/types/renderer/GeometryBuilder.d.ts +1 -0
- package/dist/types/tubeMap/reads.d.ts +0 -1
- package/dist/types/util/geometry.d.ts +7 -1
- package/dist/types/version.d.ts +1 -1
- package/dist/util/SpatialIndex.js +7 -4
- package/dist/util/edgeCurves.js +6 -3
- package/dist/util/geometry.js +1 -1
- package/dist/util/hitDetection.js +8 -5
- package/dist/version.js +1 -1
- package/dist/viewport.js +12 -12
- package/dist/walkEncoding.js +12 -12
- package/dist/walkHighlight.js +13 -13
- package/dist/walkKey.js +8 -5
- package/package.json +1 -1
package/dist/tubeMap/draw.js
CHANGED
|
@@ -8,21 +8,23 @@ import {
|
|
|
8
8
|
tubeMapMismatchAt,
|
|
9
9
|
tubeMapPicture,
|
|
10
10
|
tubeMapTrackAt
|
|
11
|
-
} from "../chunks/chunk-
|
|
11
|
+
} from "../chunks/chunk-HV35LDYH.js";
|
|
12
12
|
import "../chunks/chunk-BX4AUMZE.js";
|
|
13
13
|
import "../chunks/chunk-MYDHU2UV.js";
|
|
14
|
-
import "../chunks/chunk-
|
|
15
|
-
import "../chunks/chunk-
|
|
16
|
-
import "../chunks/chunk-
|
|
17
|
-
import "../chunks/chunk-
|
|
18
|
-
import "../chunks/chunk-
|
|
19
|
-
import "../chunks/chunk-B5X2RLJG.js";
|
|
14
|
+
import "../chunks/chunk-SDI6BVG7.js";
|
|
15
|
+
import "../chunks/chunk-5OJZV6YT.js";
|
|
16
|
+
import "../chunks/chunk-MEVTV4FI.js";
|
|
17
|
+
import "../chunks/chunk-D3E7AXBB.js";
|
|
18
|
+
import "../chunks/chunk-W2YAW36J.js";
|
|
20
19
|
import "../chunks/chunk-EIY2SKD3.js";
|
|
20
|
+
import "../chunks/chunk-3YBP46PB.js";
|
|
21
|
+
import "../chunks/chunk-VACK24HF.js";
|
|
22
|
+
import "../chunks/chunk-CPMHA4W5.js";
|
|
21
23
|
import "../chunks/chunk-ZPZ7GNBT.js";
|
|
22
24
|
import "../chunks/chunk-BSOZW3FC.js";
|
|
23
25
|
import "../chunks/chunk-RJWPJCIB.js";
|
|
24
26
|
import "../chunks/chunk-HOAIOEI7.js";
|
|
25
|
-
import "../chunks/chunk-
|
|
27
|
+
import "../chunks/chunk-2JL2JVZ2.js";
|
|
26
28
|
export {
|
|
27
29
|
drawTubeMap,
|
|
28
30
|
drawTubeMapHighlight,
|
package/dist/tubeMap/genes.js
CHANGED
|
@@ -3,18 +3,21 @@ import {
|
|
|
3
3
|
drawTubeMapGenes,
|
|
4
4
|
tubeMapGeneRows,
|
|
5
5
|
tubeMapGenes
|
|
6
|
-
} from "../chunks/chunk-
|
|
7
|
-
import "../chunks/chunk-
|
|
8
|
-
import "../chunks/chunk-
|
|
6
|
+
} from "../chunks/chunk-GZ36HNPJ.js";
|
|
7
|
+
import "../chunks/chunk-VO6FKNZE.js";
|
|
8
|
+
import "../chunks/chunk-T3H5ELLA.js";
|
|
9
9
|
import "../chunks/chunk-HMXCN6PG.js";
|
|
10
10
|
import "../chunks/chunk-AB35TJST.js";
|
|
11
|
-
import "../chunks/chunk-
|
|
12
|
-
import "../chunks/chunk-
|
|
13
|
-
import "../chunks/chunk-
|
|
11
|
+
import "../chunks/chunk-2VMKQKVO.js";
|
|
12
|
+
import "../chunks/chunk-DV5B5UU7.js";
|
|
13
|
+
import "../chunks/chunk-3YBP46PB.js";
|
|
14
|
+
import "../chunks/chunk-VACK24HF.js";
|
|
14
15
|
import "../chunks/chunk-CPMHA4W5.js";
|
|
16
|
+
import "../chunks/chunk-ZPZ7GNBT.js";
|
|
15
17
|
import "../chunks/chunk-BSOZW3FC.js";
|
|
16
18
|
import "../chunks/chunk-RJWPJCIB.js";
|
|
17
19
|
import "../chunks/chunk-HOAIOEI7.js";
|
|
20
|
+
import "../chunks/chunk-2JL2JVZ2.js";
|
|
18
21
|
export {
|
|
19
22
|
GENE_ROW_PX,
|
|
20
23
|
drawTubeMapGenes,
|
|
@@ -1,26 +1,26 @@
|
|
|
1
1
|
import {
|
|
2
2
|
tubeMapNodeColors
|
|
3
|
-
} from "../chunks/chunk-
|
|
4
|
-
import "../chunks/chunk-
|
|
3
|
+
} from "../chunks/chunk-YEYQFNFQ.js";
|
|
4
|
+
import "../chunks/chunk-JGHZ3N34.js";
|
|
5
5
|
import "../chunks/chunk-G2FD7S3C.js";
|
|
6
6
|
import "../chunks/chunk-GQZVR5DW.js";
|
|
7
|
-
import "../chunks/chunk-
|
|
8
|
-
import "../chunks/chunk-
|
|
9
|
-
import "../chunks/chunk-
|
|
10
|
-
import "../chunks/chunk-B5X2RLJG.js";
|
|
7
|
+
import "../chunks/chunk-OYCQVJYY.js";
|
|
8
|
+
import "../chunks/chunk-BW2NMXRV.js";
|
|
9
|
+
import "../chunks/chunk-ZANALBSX.js";
|
|
11
10
|
import "../chunks/chunk-VX656OAZ.js";
|
|
12
|
-
import "../chunks/chunk-
|
|
13
|
-
import "../chunks/chunk-PFRQBCGC.js";
|
|
11
|
+
import "../chunks/chunk-T3H5ELLA.js";
|
|
14
12
|
import "../chunks/chunk-HMXCN6PG.js";
|
|
15
13
|
import "../chunks/chunk-AB35TJST.js";
|
|
16
|
-
import "../chunks/chunk-
|
|
17
|
-
import "../chunks/chunk-
|
|
18
|
-
import "../chunks/chunk-
|
|
14
|
+
import "../chunks/chunk-2VMKQKVO.js";
|
|
15
|
+
import "../chunks/chunk-DV5B5UU7.js";
|
|
16
|
+
import "../chunks/chunk-3YBP46PB.js";
|
|
17
|
+
import "../chunks/chunk-VACK24HF.js";
|
|
19
18
|
import "../chunks/chunk-CPMHA4W5.js";
|
|
19
|
+
import "../chunks/chunk-ZPZ7GNBT.js";
|
|
20
20
|
import "../chunks/chunk-BSOZW3FC.js";
|
|
21
21
|
import "../chunks/chunk-RJWPJCIB.js";
|
|
22
22
|
import "../chunks/chunk-HOAIOEI7.js";
|
|
23
|
-
import "../chunks/chunk-
|
|
23
|
+
import "../chunks/chunk-2JL2JVZ2.js";
|
|
24
24
|
export {
|
|
25
25
|
tubeMapNodeColors
|
|
26
26
|
};
|
package/dist/tubeMap/reads.js
CHANGED
|
@@ -1,16 +1,16 @@
|
|
|
1
1
|
import {
|
|
2
2
|
FORWARD_READ_COLORS,
|
|
3
3
|
REVERSE_READ_COLORS,
|
|
4
|
-
canonicalStrand,
|
|
5
4
|
readColor,
|
|
6
5
|
stepName,
|
|
7
6
|
tubeMapReads
|
|
8
|
-
} from "../chunks/chunk-
|
|
9
|
-
import "../chunks/chunk-
|
|
7
|
+
} from "../chunks/chunk-SDI6BVG7.js";
|
|
8
|
+
import "../chunks/chunk-5OJZV6YT.js";
|
|
9
|
+
import "../chunks/chunk-VACK24HF.js";
|
|
10
|
+
import "../chunks/chunk-CPMHA4W5.js";
|
|
10
11
|
export {
|
|
11
12
|
FORWARD_READ_COLORS,
|
|
12
13
|
REVERSE_READ_COLORS,
|
|
13
|
-
canonicalStrand,
|
|
14
14
|
readColor,
|
|
15
15
|
stepName,
|
|
16
16
|
tubeMapReads
|
|
@@ -77,6 +77,11 @@ export declare function figureData(graph: Graph, layout: LayoutResult, o?: Figur
|
|
|
77
77
|
referenceAxis: boolean;
|
|
78
78
|
colorScheme: import("./colorSchemes.js").ResolvedColorScheme;
|
|
79
79
|
referenceName: string | null;
|
|
80
|
+
referenceRamp: {
|
|
81
|
+
start: number;
|
|
82
|
+
end: number;
|
|
83
|
+
} | null;
|
|
84
|
+
deletions: number;
|
|
80
85
|
};
|
|
81
86
|
panels: {
|
|
82
87
|
panel: string[];
|
|
@@ -96,6 +101,7 @@ export declare function figureData(graph: Graph, layout: LayoutResult, o?: Figur
|
|
|
96
101
|
length: number[];
|
|
97
102
|
depth: number[];
|
|
98
103
|
backbone: boolean[];
|
|
104
|
+
referenceVisits: number[];
|
|
99
105
|
};
|
|
100
106
|
rowLabels: {
|
|
101
107
|
label: string[];
|
|
@@ -128,6 +134,11 @@ export declare function gfaFigureData(text: string, name: string, spec?: GfaFigu
|
|
|
128
134
|
referenceAxis: boolean;
|
|
129
135
|
colorScheme: import("./colorSchemes.js").ResolvedColorScheme;
|
|
130
136
|
referenceName: string | null;
|
|
137
|
+
referenceRamp: {
|
|
138
|
+
start: number;
|
|
139
|
+
end: number;
|
|
140
|
+
} | null;
|
|
141
|
+
deletions: number;
|
|
131
142
|
};
|
|
132
143
|
panels: {
|
|
133
144
|
panel: string[];
|
|
@@ -147,6 +158,7 @@ export declare function gfaFigureData(text: string, name: string, spec?: GfaFigu
|
|
|
147
158
|
length: number[];
|
|
148
159
|
depth: number[];
|
|
149
160
|
backbone: boolean[];
|
|
161
|
+
referenceVisits: number[];
|
|
150
162
|
};
|
|
151
163
|
rowLabels: {
|
|
152
164
|
label: string[];
|
|
@@ -19,7 +19,7 @@ export interface GafRecord {
|
|
|
19
19
|
cs?: string;
|
|
20
20
|
}
|
|
21
21
|
export declare function parseGafPath(column: string): GafStep[] | undefined;
|
|
22
|
-
export declare function parseGafLine(
|
|
22
|
+
export declare function parseGafLine(text: string): GafRecord | undefined;
|
|
23
23
|
export declare function parseGaf(text: string): GafRecord[];
|
|
24
24
|
export type CsOp = {
|
|
25
25
|
op: 'match';
|
|
@@ -38,9 +38,10 @@ export declare function tablePath(w: GraphTables['walks'], p: number): Omit<Grap
|
|
|
38
38
|
};
|
|
39
39
|
/**
|
|
40
40
|
* Each segment's Graph node id: its name and its one drawn orientation, first
|
|
41
|
-
* claimed by a link and else by a walk
|
|
41
|
+
* claimed by a link and else by a walk. Counts each segment's walk steps into
|
|
42
|
+
* `traversals` when given one.
|
|
42
43
|
*/
|
|
43
|
-
export declare function tableNodeIds({ nodes: n, links: l, walks: w }: GraphTables): string[];
|
|
44
|
+
export declare function tableNodeIds({ nodes: n, links: l, walks: w }: GraphTables, traversals?: Int32Array): string[];
|
|
44
45
|
/**
|
|
45
46
|
* The Graph `convertGFAToGraph` builds from `graphTablesGFA(tables)`, deep
|
|
46
47
|
* equal, built by index: a step costs a few array reads and its visit, where
|
package/dist/types/index.d.ts
CHANGED
|
@@ -56,6 +56,7 @@ export { genesFromBed, genesFromGff3Lines, genesFromText, mergeOverlappingByName
|
|
|
56
56
|
export { backboneGenes } from './genes/backboneGenes.js';
|
|
57
57
|
export type { BackboneGenes, GeneSource, IndexedGeneFile, } from './genes/backboneGenes.js';
|
|
58
58
|
export { HPRC_GBZ, cutGbzRegion, openGbz, parseRegion } from './gbzCut.js';
|
|
59
|
+
export { formatLocus, parseLocus } from './locus.js';
|
|
59
60
|
export type { GbzSource } from './gbzCut.js';
|
|
60
61
|
export { version } from './version.js';
|
|
61
62
|
export type { FigureOptions } from './figure.js';
|
|
@@ -13,4 +13,5 @@ export type NodeWidth = (typeof NODE_WIDTHS)[number]['value'];
|
|
|
13
13
|
export declare function meanDepth(graph: Graph): number;
|
|
14
14
|
export declare function nodeWidthPx(node: GraphNode, contigThickness: number, nodeWidth: NodeWidth, mean: number): number;
|
|
15
15
|
export declare function maxNodeWidthPx(contigThickness: number, nodeWidth: NodeWidth): number;
|
|
16
|
-
export declare function
|
|
16
|
+
export declare function walkLaneWidthPx(width: number, lanes: number): number;
|
|
17
|
+
export declare function nodeInk(graph: Graph | undefined, nodeById: ReadonlyMap<string, GraphNode> | undefined, contigThickness: number, nodeWidth: NodeWidth, lanes?: number): NodeInk;
|
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
import type { AnchoredNode } from './anchoredNodes.js';
|
|
1
2
|
import type { PathVisits } from './pathVisits.js';
|
|
2
3
|
import type { Graph, PathOrigin } from './types.js';
|
|
3
4
|
export declare function pathOrigin(pathName: string): {
|
|
@@ -23,3 +24,4 @@ export declare function trimOrigins(graph: Graph, kept: Map<string, {
|
|
|
23
24
|
first: number;
|
|
24
25
|
nodeIds: string[];
|
|
25
26
|
}>): PathOrigin[] | undefined;
|
|
27
|
+
export declare function referenceVisitStarts(graph: Graph): (node: AnchoredNode) => number[];
|
|
@@ -8,6 +8,7 @@ export declare class Canvas2DRenderer implements Renderer {
|
|
|
8
8
|
private highlightedEdge;
|
|
9
9
|
private highlightFactor;
|
|
10
10
|
private fit;
|
|
11
|
+
private painted;
|
|
11
12
|
constructor(canvas: HTMLCanvasElement);
|
|
12
13
|
setErrorHandler(_handler: (error: Error) => void): void;
|
|
13
14
|
releaseOffscreenTargets(): void;
|
|
@@ -18,6 +19,7 @@ export declare class Canvas2DRenderer implements Renderer {
|
|
|
18
19
|
updateTransform(transform: TransformUniform): void;
|
|
19
20
|
private fitted;
|
|
20
21
|
render(clearColor: [number, number, number, number]): void;
|
|
22
|
+
private paintedGroups;
|
|
21
23
|
renderHighlights(): void;
|
|
22
24
|
private edgeRun;
|
|
23
25
|
private liftedStrokes;
|
|
@@ -42,6 +42,7 @@ export interface ReferenceRamp {
|
|
|
42
42
|
span: number;
|
|
43
43
|
midpoints: Map<string, number>;
|
|
44
44
|
}
|
|
45
|
+
export declare function rampFraction(node: GraphNode, ramp: ReferenceRamp): number | undefined;
|
|
45
46
|
export interface ColorSchemeRange {
|
|
46
47
|
minDepth: number;
|
|
47
48
|
maxDepth: number;
|
|
@@ -1,7 +1,6 @@
|
|
|
1
1
|
import type { GafRecord } from '../gaf/parseGaf.js';
|
|
2
2
|
import type { Graph, GraphNode } from '../types.js';
|
|
3
3
|
import type { InputTrack } from '@jbrowse/tubemap-core';
|
|
4
|
-
export declare function canonicalStrand(node: GraphNode): "+" | "-";
|
|
5
4
|
export declare function stepName(node: GraphNode, strand: '+' | '-'): string;
|
|
6
5
|
export declare function tubeMapReads(graph: Graph, records: readonly GafRecord[], firstId: number): InputTrack[];
|
|
7
6
|
export declare const FORWARD_READ_COLORS: string[];
|
|
@@ -25,7 +25,13 @@ export declare function curveBounds(curves: BezierCurve[]): {
|
|
|
25
25
|
maxX: number;
|
|
26
26
|
maxY: number;
|
|
27
27
|
};
|
|
28
|
-
export
|
|
28
|
+
export interface Bounds {
|
|
29
|
+
minX: number;
|
|
30
|
+
minY: number;
|
|
31
|
+
maxX: number;
|
|
32
|
+
maxY: number;
|
|
33
|
+
}
|
|
34
|
+
export declare function dashCurves(curves: BezierCurve[], dashWorld: number, yToX?: number, bounds?: Bounds): BezierCurve[][];
|
|
29
35
|
export declare function translateCurves(curves: BezierCurve[], dx: number, dy: number): BezierCurve[];
|
|
30
36
|
type Side = 'start' | 'end';
|
|
31
37
|
export interface EdgeSides {
|
package/dist/types/version.d.ts
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
export declare const version = "11.
|
|
1
|
+
export declare const version = "11.6.1";
|
|
@@ -1,15 +1,18 @@
|
|
|
1
1
|
import {
|
|
2
2
|
EdgeSpatialIndex,
|
|
3
3
|
SpatialIndex
|
|
4
|
-
} from "../chunks/chunk-
|
|
5
|
-
import "../chunks/chunk-
|
|
4
|
+
} from "../chunks/chunk-6YRSOL4K.js";
|
|
5
|
+
import "../chunks/chunk-OYCQVJYY.js";
|
|
6
6
|
import "../chunks/chunk-HMXCN6PG.js";
|
|
7
|
-
import "../chunks/chunk-
|
|
8
|
-
import "../chunks/chunk-
|
|
7
|
+
import "../chunks/chunk-DV5B5UU7.js";
|
|
8
|
+
import "../chunks/chunk-3YBP46PB.js";
|
|
9
|
+
import "../chunks/chunk-VACK24HF.js";
|
|
9
10
|
import "../chunks/chunk-CPMHA4W5.js";
|
|
11
|
+
import "../chunks/chunk-ZPZ7GNBT.js";
|
|
10
12
|
import "../chunks/chunk-BSOZW3FC.js";
|
|
11
13
|
import "../chunks/chunk-RJWPJCIB.js";
|
|
12
14
|
import "../chunks/chunk-HOAIOEI7.js";
|
|
15
|
+
import "../chunks/chunk-2JL2JVZ2.js";
|
|
13
16
|
export {
|
|
14
17
|
EdgeSpatialIndex,
|
|
15
18
|
SpatialIndex
|
package/dist/util/edgeCurves.js
CHANGED
|
@@ -1,13 +1,16 @@
|
|
|
1
1
|
import {
|
|
2
2
|
baseEdgeCurves
|
|
3
|
-
} from "../chunks/chunk-
|
|
3
|
+
} from "../chunks/chunk-OYCQVJYY.js";
|
|
4
4
|
import "../chunks/chunk-HMXCN6PG.js";
|
|
5
|
-
import "../chunks/chunk-
|
|
6
|
-
import "../chunks/chunk-
|
|
5
|
+
import "../chunks/chunk-DV5B5UU7.js";
|
|
6
|
+
import "../chunks/chunk-3YBP46PB.js";
|
|
7
|
+
import "../chunks/chunk-VACK24HF.js";
|
|
7
8
|
import "../chunks/chunk-CPMHA4W5.js";
|
|
9
|
+
import "../chunks/chunk-ZPZ7GNBT.js";
|
|
8
10
|
import "../chunks/chunk-BSOZW3FC.js";
|
|
9
11
|
import "../chunks/chunk-RJWPJCIB.js";
|
|
10
12
|
import "../chunks/chunk-HOAIOEI7.js";
|
|
13
|
+
import "../chunks/chunk-2JL2JVZ2.js";
|
|
11
14
|
export {
|
|
12
15
|
baseEdgeCurves
|
|
13
16
|
};
|
package/dist/util/geometry.js
CHANGED
|
@@ -4,16 +4,19 @@ import {
|
|
|
4
4
|
findHoveredEdge,
|
|
5
5
|
findHoveredNode,
|
|
6
6
|
nodesUnderBox
|
|
7
|
-
} from "../chunks/chunk-
|
|
8
|
-
import "../chunks/chunk-
|
|
9
|
-
import "../chunks/chunk-
|
|
7
|
+
} from "../chunks/chunk-56L6R6D2.js";
|
|
8
|
+
import "../chunks/chunk-6YRSOL4K.js";
|
|
9
|
+
import "../chunks/chunk-OYCQVJYY.js";
|
|
10
10
|
import "../chunks/chunk-HMXCN6PG.js";
|
|
11
|
-
import "../chunks/chunk-
|
|
12
|
-
import "../chunks/chunk-
|
|
11
|
+
import "../chunks/chunk-DV5B5UU7.js";
|
|
12
|
+
import "../chunks/chunk-3YBP46PB.js";
|
|
13
|
+
import "../chunks/chunk-VACK24HF.js";
|
|
13
14
|
import "../chunks/chunk-CPMHA4W5.js";
|
|
15
|
+
import "../chunks/chunk-ZPZ7GNBT.js";
|
|
14
16
|
import "../chunks/chunk-BSOZW3FC.js";
|
|
15
17
|
import "../chunks/chunk-RJWPJCIB.js";
|
|
16
18
|
import "../chunks/chunk-HOAIOEI7.js";
|
|
19
|
+
import "../chunks/chunk-2JL2JVZ2.js";
|
|
17
20
|
export {
|
|
18
21
|
distanceToCubicBezier,
|
|
19
22
|
distanceToSegment,
|
package/dist/version.js
CHANGED
package/dist/viewport.js
CHANGED
|
@@ -5,31 +5,31 @@ import {
|
|
|
5
5
|
screenToLayout,
|
|
6
6
|
viewportOf,
|
|
7
7
|
zoomAbout
|
|
8
|
-
} from "./chunks/chunk-
|
|
9
|
-
import "./chunks/chunk-
|
|
8
|
+
} from "./chunks/chunk-RLCYVZ4B.js";
|
|
9
|
+
import "./chunks/chunk-7OTWJQGA.js";
|
|
10
|
+
import "./chunks/chunk-OPPVSPEF.js";
|
|
10
11
|
import "./chunks/chunk-3PZSBNLI.js";
|
|
11
12
|
import "./chunks/chunk-CKUVEHSS.js";
|
|
12
|
-
import "./chunks/chunk-OPPVSPEF.js";
|
|
13
13
|
import "./chunks/chunk-VPE4AYP7.js";
|
|
14
|
-
import "./chunks/chunk-
|
|
14
|
+
import "./chunks/chunk-2C5SATRZ.js";
|
|
15
15
|
import "./chunks/chunk-QYBZZI5H.js";
|
|
16
|
-
import "./chunks/chunk-
|
|
17
|
-
import "./chunks/chunk-
|
|
18
|
-
import "./chunks/chunk-B5X2RLJG.js";
|
|
16
|
+
import "./chunks/chunk-CFXXFHRK.js";
|
|
17
|
+
import "./chunks/chunk-W2YAW36J.js";
|
|
19
18
|
import "./chunks/chunk-VX656OAZ.js";
|
|
20
19
|
import "./chunks/chunk-DZR37KXT.js";
|
|
21
20
|
import "./chunks/chunk-EIY2SKD3.js";
|
|
22
|
-
import "./chunks/chunk-
|
|
23
|
-
import "./chunks/chunk-BZFOFC4D.js";
|
|
21
|
+
import "./chunks/chunk-2VMKQKVO.js";
|
|
24
22
|
import "./chunks/chunk-HKYXWZQS.js";
|
|
25
23
|
import "./chunks/chunk-34BOZKIE.js";
|
|
26
|
-
import "./chunks/chunk-
|
|
27
|
-
import "./chunks/chunk-
|
|
24
|
+
import "./chunks/chunk-DV5B5UU7.js";
|
|
25
|
+
import "./chunks/chunk-3YBP46PB.js";
|
|
26
|
+
import "./chunks/chunk-VACK24HF.js";
|
|
28
27
|
import "./chunks/chunk-CPMHA4W5.js";
|
|
28
|
+
import "./chunks/chunk-ZPZ7GNBT.js";
|
|
29
29
|
import "./chunks/chunk-BSOZW3FC.js";
|
|
30
30
|
import "./chunks/chunk-RJWPJCIB.js";
|
|
31
31
|
import "./chunks/chunk-HOAIOEI7.js";
|
|
32
|
-
import "./chunks/chunk-
|
|
32
|
+
import "./chunks/chunk-2JL2JVZ2.js";
|
|
33
33
|
export {
|
|
34
34
|
axisScaleOf,
|
|
35
35
|
contains,
|
package/dist/walkEncoding.js
CHANGED
|
@@ -9,27 +9,27 @@ import {
|
|
|
9
9
|
schemeColor,
|
|
10
10
|
schemeCss,
|
|
11
11
|
schemeRgb
|
|
12
|
-
} from "./chunks/chunk-
|
|
13
|
-
import "./chunks/chunk-
|
|
12
|
+
} from "./chunks/chunk-2XEAITWM.js";
|
|
13
|
+
import "./chunks/chunk-JGHZ3N34.js";
|
|
14
14
|
import "./chunks/chunk-G2FD7S3C.js";
|
|
15
15
|
import "./chunks/chunk-GQZVR5DW.js";
|
|
16
|
-
import "./chunks/chunk-
|
|
17
|
-
import "./chunks/chunk-
|
|
18
|
-
import "./chunks/chunk-
|
|
19
|
-
import "./chunks/chunk-B5X2RLJG.js";
|
|
16
|
+
import "./chunks/chunk-OYCQVJYY.js";
|
|
17
|
+
import "./chunks/chunk-BW2NMXRV.js";
|
|
18
|
+
import "./chunks/chunk-ZANALBSX.js";
|
|
20
19
|
import "./chunks/chunk-VX656OAZ.js";
|
|
21
|
-
import "./chunks/chunk-
|
|
22
|
-
import "./chunks/chunk-PFRQBCGC.js";
|
|
20
|
+
import "./chunks/chunk-T3H5ELLA.js";
|
|
23
21
|
import "./chunks/chunk-HMXCN6PG.js";
|
|
24
22
|
import "./chunks/chunk-AB35TJST.js";
|
|
25
|
-
import "./chunks/chunk-
|
|
26
|
-
import "./chunks/chunk-
|
|
27
|
-
import "./chunks/chunk-
|
|
23
|
+
import "./chunks/chunk-2VMKQKVO.js";
|
|
24
|
+
import "./chunks/chunk-DV5B5UU7.js";
|
|
25
|
+
import "./chunks/chunk-3YBP46PB.js";
|
|
26
|
+
import "./chunks/chunk-VACK24HF.js";
|
|
28
27
|
import "./chunks/chunk-CPMHA4W5.js";
|
|
28
|
+
import "./chunks/chunk-ZPZ7GNBT.js";
|
|
29
29
|
import "./chunks/chunk-BSOZW3FC.js";
|
|
30
30
|
import "./chunks/chunk-RJWPJCIB.js";
|
|
31
31
|
import "./chunks/chunk-HOAIOEI7.js";
|
|
32
|
-
import "./chunks/chunk-
|
|
32
|
+
import "./chunks/chunk-2JL2JVZ2.js";
|
|
33
33
|
export {
|
|
34
34
|
NO_VALUE_COLOR,
|
|
35
35
|
WALK_FIELDS,
|
package/dist/walkHighlight.js
CHANGED
|
@@ -2,29 +2,29 @@ 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-EVXXFMZ7.js";
|
|
6
|
+
import "./chunks/chunk-2XEAITWM.js";
|
|
7
|
+
import "./chunks/chunk-JGHZ3N34.js";
|
|
8
8
|
import "./chunks/chunk-G2FD7S3C.js";
|
|
9
9
|
import "./chunks/chunk-GQZVR5DW.js";
|
|
10
|
-
import "./chunks/chunk-
|
|
11
|
-
import "./chunks/chunk-
|
|
12
|
-
import "./chunks/chunk-
|
|
13
|
-
import "./chunks/chunk-B5X2RLJG.js";
|
|
10
|
+
import "./chunks/chunk-OYCQVJYY.js";
|
|
11
|
+
import "./chunks/chunk-BW2NMXRV.js";
|
|
12
|
+
import "./chunks/chunk-ZANALBSX.js";
|
|
14
13
|
import "./chunks/chunk-VX656OAZ.js";
|
|
15
14
|
import "./chunks/chunk-EIY2SKD3.js";
|
|
16
|
-
import "./chunks/chunk-
|
|
17
|
-
import "./chunks/chunk-PFRQBCGC.js";
|
|
15
|
+
import "./chunks/chunk-T3H5ELLA.js";
|
|
18
16
|
import "./chunks/chunk-HMXCN6PG.js";
|
|
19
17
|
import "./chunks/chunk-AB35TJST.js";
|
|
20
|
-
import "./chunks/chunk-
|
|
21
|
-
import "./chunks/chunk-
|
|
22
|
-
import "./chunks/chunk-
|
|
18
|
+
import "./chunks/chunk-2VMKQKVO.js";
|
|
19
|
+
import "./chunks/chunk-DV5B5UU7.js";
|
|
20
|
+
import "./chunks/chunk-3YBP46PB.js";
|
|
21
|
+
import "./chunks/chunk-VACK24HF.js";
|
|
23
22
|
import "./chunks/chunk-CPMHA4W5.js";
|
|
23
|
+
import "./chunks/chunk-ZPZ7GNBT.js";
|
|
24
24
|
import "./chunks/chunk-BSOZW3FC.js";
|
|
25
25
|
import "./chunks/chunk-RJWPJCIB.js";
|
|
26
26
|
import "./chunks/chunk-HOAIOEI7.js";
|
|
27
|
-
import "./chunks/chunk-
|
|
27
|
+
import "./chunks/chunk-2JL2JVZ2.js";
|
|
28
28
|
export {
|
|
29
29
|
facetLifts,
|
|
30
30
|
walkHighlight,
|
package/dist/walkKey.js
CHANGED
|
@@ -2,18 +2,21 @@ import {
|
|
|
2
2
|
rangeText,
|
|
3
3
|
walkKey,
|
|
4
4
|
walkPosition
|
|
5
|
-
} from "./chunks/chunk-
|
|
5
|
+
} from "./chunks/chunk-JGQQAUVL.js";
|
|
6
6
|
import "./chunks/chunk-EIY2SKD3.js";
|
|
7
|
-
import "./chunks/chunk-
|
|
7
|
+
import "./chunks/chunk-T3H5ELLA.js";
|
|
8
8
|
import "./chunks/chunk-HMXCN6PG.js";
|
|
9
9
|
import "./chunks/chunk-AB35TJST.js";
|
|
10
|
-
import "./chunks/chunk-
|
|
11
|
-
import "./chunks/chunk-
|
|
12
|
-
import "./chunks/chunk-
|
|
10
|
+
import "./chunks/chunk-2VMKQKVO.js";
|
|
11
|
+
import "./chunks/chunk-DV5B5UU7.js";
|
|
12
|
+
import "./chunks/chunk-3YBP46PB.js";
|
|
13
|
+
import "./chunks/chunk-VACK24HF.js";
|
|
13
14
|
import "./chunks/chunk-CPMHA4W5.js";
|
|
15
|
+
import "./chunks/chunk-ZPZ7GNBT.js";
|
|
14
16
|
import "./chunks/chunk-BSOZW3FC.js";
|
|
15
17
|
import "./chunks/chunk-RJWPJCIB.js";
|
|
16
18
|
import "./chunks/chunk-HOAIOEI7.js";
|
|
19
|
+
import "./chunks/chunk-2JL2JVZ2.js";
|
|
17
20
|
export {
|
|
18
21
|
rangeText,
|
|
19
22
|
walkKey,
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/bandage-core",
|
|
3
|
-
"version": "11.
|
|
3
|
+
"version": "11.6.1",
|
|
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": {
|