@jbrowse/bandage-core 9.10.0 → 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/dist/bubbles/popBubble.js +3 -2
- package/dist/bubbles/superbubbles.js +4 -3
- package/dist/chunks/{chunk-Q6UIUY6X.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-5GZEPPEW.js → chunk-BEWLQADP.js} +1 -1
- package/dist/chunks/{chunk-2VTM3DHG.js → chunk-CDPYXHVR.js} +1 -1
- package/dist/chunks/{chunk-K5NYTPLC.js → chunk-DCJC32QW.js} +1 -1
- package/dist/chunks/{chunk-IZI7KIVX.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-LZWSZRUY.js → chunk-FG762CCP.js} +3 -8
- package/dist/chunks/{chunk-73RSLGZT.js → chunk-FLFBYSJO.js} +1 -1
- package/dist/chunks/{chunk-FUUJ76KD.js → chunk-ICXMWYOA.js} +5 -5
- package/dist/chunks/{chunk-CXKZYLYS.js → chunk-IM4SJUPO.js} +12 -22
- package/dist/chunks/{chunk-6PYZYBBF.js → chunk-KAN2WTG5.js} +1 -1
- package/dist/chunks/{chunk-BDWQQK33.js → chunk-KJYSOHVN.js} +1 -1
- package/dist/chunks/{chunk-4IYP43W6.js → chunk-NP356MC2.js} +1 -1
- package/dist/chunks/{chunk-TFAFIRZB.js → chunk-OEPCRURR.js} +1 -1
- package/dist/chunks/{chunk-PT37VS5B.js → chunk-OOLNLCIO.js} +1 -1
- package/dist/chunks/{chunk-OA7RIMZ2.js → chunk-PSMKPSO4.js} +89 -22
- package/dist/chunks/{chunk-NGODVSCA.js → chunk-Q6IOQP4J.js} +8 -8
- package/dist/chunks/{chunk-LTUWJKHD.js → chunk-Q7LYHGGQ.js} +114 -6
- package/dist/chunks/{chunk-MVMP6AGI.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-XZ2BLAA6.js → chunk-REE4GUDM.js} +1 -1
- package/dist/chunks/{chunk-2FLBFVMO.js → chunk-RJXPPYA7.js} +13 -13
- package/dist/chunks/{chunk-KYY5363X.js → chunk-VOWI544A.js} +1 -1
- package/dist/chunks/{chunk-FJZ2TB46.js → chunk-VZNKA3K2.js} +2 -2
- package/dist/chunks/{chunk-HRAU4VTB.js → chunk-W4GZCVUK.js} +6 -6
- package/dist/chunks/{chunk-DMH4NL2M.js → chunk-WI7ZHJ27.js} +2 -2
- package/dist/cli/figure.js +24 -23
- package/dist/cli/fold.js +6 -5
- package/dist/figure.js +19 -18
- package/dist/figureData.js +20 -19
- package/dist/figureSettings.js +7 -6
- 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 +57 -47
- package/dist/layout/forceCache.js +7 -6
- package/dist/layout/trimToWindow.js +17 -23
- package/dist/layout/tubeMapLayout.js +4 -3
- package/dist/layout/walkRowDraw.js +6 -5
- package/dist/layout/walkRowLayout.js +4 -3
- package/dist/layout/walkRows.js +3 -2
- package/dist/layout/walkStrip.js +7 -6
- package/dist/layoutModes.js +8 -7
- package/dist/pathAnchoring.js +2 -1
- package/dist/pathColors.js +3 -2
- package/dist/pathVisits.js +8 -0
- package/dist/pipeline.js +6 -5
- package/dist/referenceRampCss.js +5 -4
- package/dist/referenceStrip.js +5 -4
- package/dist/renderer/GeometryBuilder.js +4 -3
- package/dist/tubeMap/bundle.js +5 -4
- package/dist/tubeMap/coarsen.js +15 -13
- package/dist/tubeMap/draw.js +4 -3
- package/dist/tubeMap/nodeColors.js +5 -4
- package/dist/types/gbzWindow.d.ts +15 -1
- package/dist/types/gfa/gfaConverter.d.ts +1 -1
- package/dist/types/index.d.ts +2 -1
- package/dist/types/layout/deletionRoutes.d.ts +1 -1
- 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 +7 -6
- package/dist/walkEncoding.js +5 -4
- package/dist/walkHighlight.js +6 -5
- package/package.json +1 -1
package/dist/cli/fold.js
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package/dist/figureData.js
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} from "./chunks/chunk-
|
|
14
|
+
} from "./chunks/chunk-Q7LYHGGQ.js";
|
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15
|
import "./chunks/chunk-WSIFAZU7.js";
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16
|
import "./chunks/chunk-RAKOB6IV.js";
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import "./chunks/chunk-G45YY72K.js";
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18
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import "./chunks/chunk-BPLIXMH7.js";
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19
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import "./chunks/chunk-FYQWPEEY.js";
|
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17
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|
export {
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GBZ_CUT_DEFAULTS,
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NoReferenceSampleError,
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23
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NodeLimitError,
|
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24
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compactTables,
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25
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cutWindowGFA,
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cutWindowTables,
|
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27
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haplotypePrefix,
|
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28
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haplotypeWanted,
|
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29
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nodeLimitError,
|
package/dist/gfa/gfaConverter.js
CHANGED
|
@@ -1,9 +1,10 @@
|
|
|
1
1
|
import {
|
|
2
2
|
convertGFAToGraph
|
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3
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} from "../chunks/chunk-
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} from "../chunks/chunk-QXAB2FLJ.js";
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import "../chunks/chunk-QYBZZI5H.js";
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5
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import "../chunks/chunk-CDLPYR5O.js";
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-
import "../chunks/chunk-
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import "../chunks/chunk-EMUUNWRU.js";
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import "../chunks/chunk-RAEABQNW.js";
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9
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|
|
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|
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|
package/dist/gfa/graphTables.js
CHANGED
package/dist/index.js
CHANGED
|
@@ -1,17 +1,27 @@
|
|
|
1
1
|
import {
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|
wheelZoomFactor
|
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3
|
} 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-
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+
} from "./chunks/chunk-EU6FBTQF.js";
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import {
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tubeMapNodeAt
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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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26
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|
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|
|
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|
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|
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|
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|
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} from "./chunks/chunk-
|
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|
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import {
|
|
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|
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referenceKnots,
|
|
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|
-
warpX
|
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|
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} from "./chunks/chunk-HK5Y2YWV.js";
|
|
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|
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} from "./chunks/chunk-OEPCRURR.js";
|
|
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33
|
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|
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34
|
drawTubeMapRuler,
|
|
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35
|
referenceBoxes,
|
|
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|
|
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|
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|
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|
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|
bundleRoutes
|
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|
-
} from "./chunks/chunk-
|
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|
-
import {
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|
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connectorAt,
|
|
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|
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drawLitConnector,
|
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|
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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-FG762CCP.js";
|
|
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42
|
import {
|
|
43
43
|
createForceLayoutCache
|
|
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|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-33T67FPZ.js";
|
|
45
45
|
import {
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|
46
46
|
graphBubbles,
|
|
47
47
|
superbubblesFromGraph
|
|
48
|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-BEWLQADP.js";
|
|
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49
|
import {
|
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50
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|
bubblesFromGraph
|
|
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51
|
} from "./chunks/chunk-CLOP7UVD.js";
|
|
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|
import {
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53
53
|
bubbleSubgraph
|
|
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|
-
} from "./chunks/chunk-
|
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|
+
} from "./chunks/chunk-4QTNXTGW.js";
|
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|
import {
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|
genesFromBed,
|
|
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|
genesFromGff3Lines,
|
|
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|
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|
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74
|
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|
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stripBlockAt
|
|
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|
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} from "./chunks/chunk-
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|
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|
+
} from "./chunks/chunk-KJYSOHVN.js";
|
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|
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|
|
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78
|
LAYOUT_QUALITIES
|
|
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|
} from "./chunks/chunk-K5SIJGAE.js";
|
|
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|
import {
|
|
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|
FIGURE_DEFAULTS,
|
|
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|
figureSpecSettings
|
|
83
|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-E5UEYZWK.js";
|
|
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|
import {
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|
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|
edgeHoverText,
|
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|
regionLabel
|
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|
} from "./chunks/chunk-AZFVORTC.js";
|
|
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|
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|
|
89
89
|
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|
|
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|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-RJXPPYA7.js";
|
|
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|
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|
|
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92
|
svgCanvas
|
|
93
93
|
} from "./chunks/chunk-47DYCZOK.js";
|
|
@@ -102,7 +102,7 @@ import {
|
|
|
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102
|
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|
|
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103
|
walkStripFrame,
|
|
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104
|
walkStripLabelsTree
|
|
105
|
-
} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-WI7ZHJ27.js";
|
|
106
106
|
import {
|
|
107
107
|
BAR_PX,
|
|
108
108
|
CALL_TICK,
|
|
@@ -129,27 +129,27 @@ import {
|
|
|
129
129
|
walkRowsKey,
|
|
130
130
|
walkRowsKeyTree,
|
|
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|
walkRowsTree
|
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-VZNKA3K2.js";
|
|
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133
|
import {
|
|
134
134
|
Canvas2DRenderer
|
|
135
135
|
} from "./chunks/chunk-WBCOREDZ.js";
|
|
136
136
|
import {
|
|
137
137
|
getDpr
|
|
138
138
|
} from "./chunks/chunk-4BYTEJGW.js";
|
|
139
|
-
import {
|
|
140
|
-
genePins
|
|
141
|
-
} from "./chunks/chunk-BUBZ32IC.js";
|
|
142
139
|
import {
|
|
143
140
|
EXON_COLOR,
|
|
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141
|
exonOutlineTree,
|
|
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142
|
exonStretches
|
|
146
143
|
} from "./chunks/chunk-3S3YVOJ7.js";
|
|
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|
+
import {
|
|
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|
+
genePins
|
|
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|
+
} from "./chunks/chunk-BUBZ32IC.js";
|
|
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|
import {
|
|
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148
|
RAMP_GRADIENT_CSS,
|
|
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149
|
rampHue,
|
|
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150
|
rampHueCss,
|
|
151
151
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rampStops
|
|
152
|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-DCJC32QW.js";
|
|
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|
import {
|
|
154
154
|
HALO_FACTOR,
|
|
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155
|
LEGEND_INSET_PX,
|
|
@@ -168,7 +168,7 @@ import {
|
|
|
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168
|
import {
|
|
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169
|
figureData,
|
|
170
170
|
gfaFigureData
|
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-Q6IOQP4J.js";
|
|
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172
|
import {
|
|
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173
|
LAYOUT_ENGINES,
|
|
174
174
|
layoutEngine
|
|
@@ -182,10 +182,10 @@ import {
|
|
|
182
182
|
LAYOUT_MODES,
|
|
183
183
|
layoutModeByValue,
|
|
184
184
|
modeUsesLayoutEngine
|
|
185
|
-
} from "./chunks/chunk-
|
|
186
|
-
import "./chunks/chunk-
|
|
187
|
-
import "./chunks/chunk-CXKZYLYS.js";
|
|
185
|
+
} from "./chunks/chunk-ICXMWYOA.js";
|
|
186
|
+
import "./chunks/chunk-IM4SJUPO.js";
|
|
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187
|
import "./chunks/chunk-CWFNEKST.js";
|
|
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|
+
import "./chunks/chunk-LOEA5IHZ.js";
|
|
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189
|
import "./chunks/chunk-L3O7AWLI.js";
|
|
190
190
|
import "./chunks/chunk-TZFWUT2C.js";
|
|
191
191
|
import "./chunks/chunk-HNQPEMYE.js";
|
|
@@ -199,21 +199,23 @@ import {
|
|
|
199
199
|
cutGbzRegion,
|
|
200
200
|
openGbz,
|
|
201
201
|
parseRegion
|
|
202
|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-FLFBYSJO.js";
|
|
203
203
|
import {
|
|
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|
+
compactTables,
|
|
204
205
|
cutWindowGFA,
|
|
206
|
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cutWindowTables,
|
|
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207
|
haplotypeWanted,
|
|
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|
referencePathQuery,
|
|
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209
|
referenceSamplesOf,
|
|
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210
|
resolveReferenceSample
|
|
209
|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-Q7LYHGGQ.js";
|
|
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212
|
import "./chunks/chunk-WSIFAZU7.js";
|
|
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213
|
import {
|
|
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|
layoutGeometryInputs
|
|
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215
|
} from "./chunks/chunk-LOCJN3BZ.js";
|
|
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|
import {
|
|
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217
|
version
|
|
216
|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-CDPYXHVR.js";
|
|
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|
import {
|
|
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220
|
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|
|
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221
|
contains,
|
|
@@ -221,12 +223,12 @@ import {
|
|
|
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223
|
screenToLayout,
|
|
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|
viewportOf,
|
|
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zoomAbout
|
|
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|
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} from "./chunks/chunk-
|
|
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|
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} from "./chunks/chunk-OOLNLCIO.js";
|
|
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|
import {
|
|
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|
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walkHighlight,
|
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walkLift
|
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|
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} from "./chunks/chunk-
|
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|
+
} from "./chunks/chunk-QIVPRZ4H.js";
|
|
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|
import {
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|
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|
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|
|
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|
WALK_SCHEMES,
|
|
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|
|
|
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|
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|
|
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237
|
resolveEncoding,
|
|
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|
schemeCss
|
|
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|
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} from "./chunks/chunk-
|
|
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|
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} from "./chunks/chunk-VOWI544A.js";
|
|
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|
import {
|
|
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241
|
rangeText,
|
|
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|
walkKey,
|
|
@@ -244,22 +246,22 @@ import {
|
|
|
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|
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|
|
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247
|
buildGeometry,
|
|
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|
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|
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-NP356MC2.js";
|
|
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|
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|
|
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|
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|
|
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|
import {
|
|
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|
walkRowLabels,
|
|
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|
walkRowsExtent
|
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-3APK25GI.js";
|
|
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256
|
import {
|
|
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257
|
filterSamples,
|
|
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|
walkRows
|
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-KAN2WTG5.js";
|
|
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|
import {
|
|
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|
pathColorsLegible,
|
|
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|
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|
|
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|
walkLabelsOf
|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-REE4GUDM.js";
|
|
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|
import {
|
|
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|
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|
|
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|
maxNodeWidthPx,
|
|
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|
|
|
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|
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|
|
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282
|
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|
|
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|
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|
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|
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} from "./chunks/chunk-
|
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|
+
} from "./chunks/chunk-W4GZCVUK.js";
|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
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import
|
|
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|
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gfaTables
|
|
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|
-
} from "./chunks/chunk-G45YY72K.js";
|
|
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|
+
import "./chunks/chunk-QXAB2FLJ.js";
|
|
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|
+
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|
|
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|
import {
|
|
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291
|
graphFromTables,
|
|
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292
|
graphTablesGFA
|
|
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|
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} from "./chunks/chunk-
|
|
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|
-
import "./chunks/chunk-QYBZZI5H.js";
|
|
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|
+
} from "./chunks/chunk-PSMKPSO4.js";
|
|
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|
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|
|
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|
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|
|
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import "./chunks/chunk-
|
|
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|
+
import "./chunks/chunk-EMUUNWRU.js";
|
|
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|
+
import {
|
|
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|
+
PathVisits,
|
|
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|
+
PathVisitsBuilder
|
|
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|
+
} from "./chunks/chunk-RAEABQNW.js";
|
|
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|
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|
|
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|
import {
|
|
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|
WELL_KNOWN_SAMPLES,
|
|
@@ -306,6 +309,9 @@ import {
|
|
|
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309
|
referenceLabel,
|
|
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310
|
wellKnownSample
|
|
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311
|
} from "./chunks/chunk-RAKOB6IV.js";
|
|
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|
+
import {
|
|
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|
+
gfaTables
|
|
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|
+
} from "./chunks/chunk-G45YY72K.js";
|
|
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|
import {
|
|
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316
|
panSNContig,
|
|
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317
|
panSNHaplotype,
|
|
@@ -372,6 +378,8 @@ export {
|
|
|
372
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|
LAYOUT_QUALITIES,
|
|
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379
|
LEGEND_INSET_PX,
|
|
374
380
|
NODE_WIDTHS,
|
|
381
|
+
PathVisits,
|
|
382
|
+
PathVisitsBuilder,
|
|
375
383
|
RAMP_GRADIENT_CSS,
|
|
376
384
|
REFERENCE_RAMP_MAX_HUE,
|
|
377
385
|
REFERENCE_STRIP_ZONE_PX,
|
|
@@ -403,12 +411,14 @@ export {
|
|
|
403
411
|
clampZoom,
|
|
404
412
|
classifyBubble,
|
|
405
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|
coalesceRuns,
|
|
414
|
+
compactTables,
|
|
406
415
|
computeReferenceRamp,
|
|
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416
|
connectorAt,
|
|
408
417
|
contains,
|
|
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418
|
createForceLayoutCache,
|
|
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419
|
cutGbzRegion,
|
|
411
420
|
cutWindowGFA,
|
|
421
|
+
cutWindowTables,
|
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return out;
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