@jbrowse/bandage-core 9.9.2 → 10.0.0
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/README.md +3 -0
- package/dist/bubbles/popBubble.js +3 -2
- package/dist/bubbles/superbubbles.js +5 -4
- package/dist/chunks/{chunk-YAN2ZPNV.js → chunk-33T67FPZ.js} +1 -1
- package/dist/chunks/{chunk-TOVOJNT7.js → chunk-3APK25GI.js} +1 -1
- package/dist/chunks/{chunk-A6PSWTLX.js → chunk-4QTNXTGW.js} +1 -1
- package/dist/chunks/{chunk-ROQGMTFB.js → chunk-BEWLQADP.js} +6 -6
- package/dist/chunks/{chunk-BQ33OOLC.js → chunk-CDPYXHVR.js} +1 -1
- package/dist/chunks/{chunk-YS7VA5SI.js → chunk-DCJC32QW.js} +1 -1
- package/dist/chunks/{chunk-YGN4KL7W.js → chunk-E5UEYZWK.js} +1 -1
- package/dist/chunks/{chunk-IGJCTPFB.js → chunk-EMUUNWRU.js} +52 -43
- package/dist/chunks/{chunk-PIN7ZMTZ.js → chunk-EU6FBTQF.js} +4 -4
- package/dist/chunks/{chunk-WVBYR6Y7.js → chunk-FG762CCP.js} +3 -8
- package/dist/chunks/{chunk-73RSLGZT.js → chunk-FLFBYSJO.js} +1 -1
- package/dist/chunks/{chunk-IJRNMO4D.js → chunk-ICXMWYOA.js} +5 -5
- package/dist/chunks/{chunk-HOZI3FBG.js → chunk-IM4SJUPO.js} +12 -22
- package/dist/chunks/{chunk-6PYZYBBF.js → chunk-KAN2WTG5.js} +1 -1
- package/dist/chunks/{chunk-RK3MF4FD.js → chunk-KJYSOHVN.js} +1 -1
- package/dist/chunks/{chunk-F4BKWWLS.js → chunk-NP356MC2.js} +4 -4
- package/dist/chunks/{chunk-KJEMKHVB.js → chunk-OEPCRURR.js} +1 -1
- package/dist/chunks/{chunk-ZBLKAWSD.js → chunk-OOLNLCIO.js} +1 -1
- package/dist/chunks/chunk-OPPVSPEF.js +57 -0
- package/dist/chunks/{chunk-OA7RIMZ2.js → chunk-PSMKPSO4.js} +89 -22
- package/dist/chunks/chunk-Q6IOQP4J.js +292 -0
- package/dist/chunks/{chunk-LTUWJKHD.js → chunk-Q7LYHGGQ.js} +114 -6
- package/dist/chunks/{chunk-EE37PVQY.js → chunk-QIVPRZ4H.js} +12 -7
- package/dist/chunks/{chunk-J7YKQ5YW.js → chunk-QXAB2FLJ.js} +1 -1
- package/dist/chunks/chunk-RAEABQNW.js +227 -0
- package/dist/chunks/{chunk-EDASNMLY.js → chunk-REE4GUDM.js} +4 -4
- package/dist/chunks/{chunk-IZ3W5IU2.js → chunk-RJXPPYA7.js} +36 -36
- package/dist/chunks/{chunk-F5BYHLIN.js → chunk-VOWI544A.js} +1 -1
- package/dist/chunks/{chunk-P6O4RSOQ.js → chunk-VZNKA3K2.js} +5 -5
- package/dist/chunks/{chunk-FPTI3WAV.js → chunk-W4GZCVUK.js} +18 -13
- package/dist/chunks/{chunk-MECWJY2R.js → chunk-WI7ZHJ27.js} +5 -5
- package/dist/cli/figure.js +50 -48
- package/dist/cli/fold.js +8 -6
- package/dist/figure.js +31 -29
- package/dist/figureData.js +63 -0
- package/dist/figureSettings.js +9 -7
- package/dist/gbzCut.js +3 -2
- package/dist/gbzWindow.js +6 -1
- package/dist/gfa/gfaConverter.js +3 -2
- package/dist/gfa/graphTables.js +2 -1
- package/dist/index.js +173 -156
- package/dist/layout/forceCache.js +9 -7
- package/dist/layout/smoothChains.js +6 -0
- package/dist/layout/trimToWindow.js +17 -23
- package/dist/layout/tubeMapLayout.js +5 -4
- package/dist/layout/walkRowDraw.js +10 -9
- package/dist/layout/walkRowLayout.js +4 -3
- package/dist/layout/walkRows.js +3 -2
- package/dist/layout/walkStrip.js +11 -10
- package/dist/layoutModes.js +11 -10
- package/dist/pathAnchoring.js +2 -1
- package/dist/pathColors.js +4 -3
- package/dist/pathVisits.js +8 -0
- package/dist/pipeline.js +8 -6
- package/dist/referenceRampCss.js +8 -7
- package/dist/referenceStrip.js +8 -7
- package/dist/renderer/GeometryBuilder.js +7 -6
- package/dist/tubeMap/bundle.js +6 -5
- package/dist/tubeMap/coarsen.js +17 -15
- package/dist/tubeMap/draw.js +4 -3
- package/dist/tubeMap/nodeColors.js +8 -7
- package/dist/types/figureData.d.ts +146 -0
- package/dist/types/gbzWindow.d.ts +15 -1
- package/dist/types/gfa/gfaConverter.d.ts +1 -1
- package/dist/types/index.d.ts +4 -1
- package/dist/types/layout/deletionRoutes.d.ts +1 -1
- package/dist/types/layout/smoothChains.d.ts +2 -0
- package/dist/types/pathAnchoring.d.ts +3 -2
- package/dist/types/pathVisits.d.ts +64 -0
- package/dist/types/types.d.ts +2 -1
- package/dist/types/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/dist/viewport.js +9 -7
- package/dist/walkEncoding.js +8 -7
- package/dist/walkHighlight.js +9 -8
- package/package.json +1 -1
package/dist/index.js
CHANGED
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import {
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wheelZoomFactor
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} from "./chunks/chunk-TDQLINVI.js";
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import {
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connectorAt,
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drawLitConnector,
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drawTubeMapConnectors,
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tubeMapConnectors
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} from "./chunks/chunk-2ZT7ZF7A.js";
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import {
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drawTubeMap,
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drawTubeMapHighlight,
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tubeMapMismatchAt,
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tubeMapPicture,
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tubeMapTrackAt
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} from "./chunks/chunk-EU6FBTQF.js";
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import {
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tubeMapFrame,
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tubeMapNodeAt
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} from "./chunks/chunk-2CMYNW3E.js";
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import {
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referenceKnots,
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warpX
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} from "./chunks/chunk-HK5Y2YWV.js";
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import {
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drawTubeMapGenes,
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tubeMapGenes
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} from "./chunks/chunk-WEDZ76AK.js";
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import "./chunks/chunk-XXT2JCAC.js";
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import {
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tubeMapNodeColors
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} from "./chunks/chunk-
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import {
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bundleRoutes
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import {
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connectorAt,
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drawLitConnector,
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drawTubeMapConnectors,
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tubeMapConnectors
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} from "./chunks/chunk-2ZT7ZF7A.js";
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} from "./chunks/chunk-OEPCRURR.js";
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import {
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drawTubeMapRuler,
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referenceBoxes,
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tubeX
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tubeMapPicture,
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tubeMapTrackAt
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} from "./chunks/chunk-PIN7ZMTZ.js";
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import "./chunks/chunk-XXT2JCAC.js";
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import {
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referenceKnots,
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warpX
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} from "./chunks/chunk-HK5Y2YWV.js";
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bundleRoutes
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} from "./chunks/chunk-FG762CCP.js";
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createForceLayoutCache
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} from "./chunks/chunk-
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} from "./chunks/chunk-33T67FPZ.js";
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import {
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graphBubbles,
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superbubblesFromGraph
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} from "./chunks/chunk-
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} from "./chunks/chunk-BEWLQADP.js";
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import {
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bubblesFromGraph
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bubbleSubgraph
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+
visits.reversed[at] === 1
|
|
85
|
+
);
|
|
92
86
|
}
|
|
93
87
|
});
|
|
94
88
|
});
|
|
95
|
-
return out;
|
|
89
|
+
return out.build();
|
|
96
90
|
}
|
|
97
91
|
function clipToWindow(graph, window, reachBp) {
|
|
98
92
|
const nodes = graph.nodes.map((node) => {
|
|
@@ -8,14 +8,15 @@ import {
|
|
|
8
8
|
tubeMapReferenceLayout,
|
|
9
9
|
tubeMapTracks,
|
|
10
10
|
tubeWidth
|
|
11
|
-
} from "../chunks/chunk-
|
|
11
|
+
} from "../chunks/chunk-IM4SJUPO.js";
|
|
12
12
|
import "../chunks/chunk-CWFNEKST.js";
|
|
13
13
|
import "../chunks/chunk-C44YRP5F.js";
|
|
14
|
-
import "../chunks/chunk-
|
|
14
|
+
import "../chunks/chunk-REE4GUDM.js";
|
|
15
|
+
import "../chunks/chunk-EMUUNWRU.js";
|
|
16
|
+
import "../chunks/chunk-RAEABQNW.js";
|
|
17
|
+
import "../chunks/chunk-BPLIXMH7.js";
|
|
15
18
|
import "../chunks/chunk-3ZZSX5HN.js";
|
|
16
19
|
import "../chunks/chunk-AB35TJST.js";
|
|
17
|
-
import "../chunks/chunk-IGJCTPFB.js";
|
|
18
|
-
import "../chunks/chunk-BPLIXMH7.js";
|
|
19
20
|
import "../chunks/chunk-TAMCZHLW.js";
|
|
20
21
|
import "../chunks/chunk-N6FECAXP.js";
|
|
21
22
|
import "../chunks/chunk-2CVHXFK7.js";
|
|
@@ -26,19 +26,20 @@ import {
|
|
|
26
26
|
walkRowsKey,
|
|
27
27
|
walkRowsKeyTree,
|
|
28
28
|
walkRowsTree
|
|
29
|
-
} from "../chunks/chunk-
|
|
30
|
-
import "../chunks/chunk-
|
|
31
|
-
import "../chunks/chunk-
|
|
29
|
+
} from "../chunks/chunk-VZNKA3K2.js";
|
|
30
|
+
import "../chunks/chunk-DCJC32QW.js";
|
|
31
|
+
import "../chunks/chunk-NNODIW4U.js";
|
|
32
|
+
import "../chunks/chunk-NP356MC2.js";
|
|
32
33
|
import "../chunks/chunk-G2FD7S3C.js";
|
|
33
|
-
import "../chunks/chunk-EDASNMLY.js";
|
|
34
|
-
import "../chunks/chunk-PBENCR5L.js";
|
|
35
34
|
import "../chunks/chunk-WFB5TXRA.js";
|
|
36
|
-
import "../chunks/chunk-
|
|
37
|
-
import "../chunks/chunk-
|
|
38
|
-
import "../chunks/chunk-
|
|
35
|
+
import "../chunks/chunk-REE4GUDM.js";
|
|
36
|
+
import "../chunks/chunk-PBENCR5L.js";
|
|
37
|
+
import "../chunks/chunk-EMUUNWRU.js";
|
|
38
|
+
import "../chunks/chunk-RAEABQNW.js";
|
|
39
39
|
import "../chunks/chunk-ES2N6V56.js";
|
|
40
|
-
import "../chunks/chunk-IGJCTPFB.js";
|
|
41
40
|
import "../chunks/chunk-BPLIXMH7.js";
|
|
41
|
+
import "../chunks/chunk-3ZZSX5HN.js";
|
|
42
|
+
import "../chunks/chunk-AB35TJST.js";
|
|
42
43
|
import "../chunks/chunk-TAMCZHLW.js";
|
|
43
44
|
import "../chunks/chunk-N6FECAXP.js";
|
|
44
45
|
import "../chunks/chunk-2CVHXFK7.js";
|
|
@@ -2,9 +2,10 @@ import {
|
|
|
2
2
|
walkRowLabels,
|
|
3
3
|
walkRowLayout,
|
|
4
4
|
walkRowsExtent
|
|
5
|
-
} from "../chunks/chunk-
|
|
6
|
-
import "../chunks/chunk-
|
|
7
|
-
import "../chunks/chunk-
|
|
5
|
+
} from "../chunks/chunk-3APK25GI.js";
|
|
6
|
+
import "../chunks/chunk-KAN2WTG5.js";
|
|
7
|
+
import "../chunks/chunk-EMUUNWRU.js";
|
|
8
|
+
import "../chunks/chunk-RAEABQNW.js";
|
|
8
9
|
import "../chunks/chunk-BPLIXMH7.js";
|
|
9
10
|
import "../chunks/chunk-CPMHA4W5.js";
|
|
10
11
|
import "../chunks/chunk-FYQWPEEY.js";
|
package/dist/layout/walkRows.js
CHANGED
|
@@ -1,8 +1,9 @@
|
|
|
1
1
|
import {
|
|
2
2
|
filterSamples,
|
|
3
3
|
walkRows
|
|
4
|
-
} from "../chunks/chunk-
|
|
5
|
-
import "../chunks/chunk-
|
|
4
|
+
} from "../chunks/chunk-KAN2WTG5.js";
|
|
5
|
+
import "../chunks/chunk-EMUUNWRU.js";
|
|
6
|
+
import "../chunks/chunk-RAEABQNW.js";
|
|
6
7
|
import "../chunks/chunk-BPLIXMH7.js";
|
|
7
8
|
import "../chunks/chunk-FYQWPEEY.js";
|
|
8
9
|
export {
|