@jbrowse/bandage-core 9.1.0 → 9.2.0

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.
Files changed (46) hide show
  1. package/dist/bubbles/superbubbles.js +2 -2
  2. package/dist/chunks/{chunk-FFFQNQUI.js → chunk-A4MYLGKG.js} +1 -1
  3. package/dist/chunks/chunk-B4645SM2.js +358 -0
  4. package/dist/chunks/chunk-B4YH42OP.js +24 -0
  5. package/dist/chunks/{chunk-XLCTQHBE.js → chunk-BLRJ6IGK.js} +1 -1
  6. package/dist/chunks/{chunk-RRZMMYBG.js → chunk-BV64PQ2C.js} +1 -1
  7. package/dist/chunks/{chunk-W253V6RR.js → chunk-CVYDR2OP.js} +1 -1
  8. package/dist/chunks/{chunk-UID3QBWH.js → chunk-FM6XRXPX.js} +1 -1
  9. package/dist/chunks/{chunk-MIW3HYPE.js → chunk-GFRPX6M2.js} +2 -2
  10. package/dist/chunks/{chunk-3TGUKQWQ.js → chunk-HOOVOF2Y.js} +21 -21
  11. package/dist/chunks/{chunk-MBB7ATM6.js → chunk-LFKMASER.js} +1 -1
  12. package/dist/chunks/{chunk-6ZNQJ5ZD.js → chunk-OXTR3BVF.js} +1 -1
  13. package/dist/chunks/{chunk-WDTXW7T2.js → chunk-UD5FOCI2.js} +1 -1
  14. package/dist/chunks/{chunk-MXDQGA7A.js → chunk-XKM5OHQQ.js} +1 -1
  15. package/dist/chunks/{chunk-DPV2CUIE.js → chunk-XPT66H6H.js} +1 -1
  16. package/dist/cli/figure.js +26 -26
  17. package/dist/cli/fold.js +72 -0
  18. package/dist/figure.js +16 -16
  19. package/dist/figureSettings.js +4 -4
  20. package/dist/foldVariants.js +9 -0
  21. package/dist/gfa/writeRgfa.js +6 -0
  22. package/dist/index.js +61 -61
  23. package/dist/layout/forceCache.js +4 -4
  24. package/dist/layout/trimToWindow.js +13 -0
  25. package/dist/layout/walkRowDraw.js +4 -4
  26. package/dist/layout/walkStrip.js +5 -5
  27. package/dist/layoutModes.js +2 -2
  28. package/dist/pipeline.js +3 -3
  29. package/dist/referenceRampCss.js +3 -3
  30. package/dist/referenceStrip.js +3 -3
  31. package/dist/renderer/GeometryBuilder.js +2 -2
  32. package/dist/tubeMap/nodeColors.js +3 -3
  33. package/dist/types/cli/fold.d.ts +1 -0
  34. package/dist/types/foldVariants.d.ts +2 -0
  35. package/dist/types/gfa/writeRgfa.d.ts +2 -0
  36. package/dist/types/layout/trimToWindow.d.ts +4 -0
  37. package/dist/types/version.d.ts +1 -1
  38. package/dist/version.js +1 -1
  39. package/dist/viewport.js +4 -4
  40. package/dist/walkEncoding.js +3 -3
  41. package/dist/walkHighlight.js +4 -4
  42. package/package.json +3 -2
  43. package/dist/chunks/{chunk-HBEKUQO4.js → chunk-BR25DGIJ.js} +4 -4
  44. package/dist/chunks/{chunk-WNUZP3WQ.js → chunk-M7SRZJ32.js} +3 -3
  45. package/dist/chunks/{chunk-FUVI4WQP.js → chunk-ZDJDM77V.js} +3 -3
  46. package/dist/chunks/{chunk-OOXIMURX.js → chunk-ZGRYFUXE.js} +8 -8
package/dist/pipeline.js CHANGED
@@ -11,18 +11,18 @@ import {
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  forceLayout,
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  layoutExtent,
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  loadGraph
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- } from "./chunks/chunk-OOXIMURX.js";
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+ } from "./chunks/chunk-ZGRYFUXE.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-OA7RIMZ2.js";
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  import "./chunks/chunk-OCMBULGN.js";
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+ import "./chunks/chunk-OA7RIMZ2.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-JVLURPFW.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-BPLIXMH7.js";
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  import "./chunks/chunk-TAMCZHLW.js";
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- import "./chunks/chunk-JVLURPFW.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-N6FECAXP.js";
package/dist/referenceRampCss.js CHANGED
@@ -4,11 +4,11 @@ import {
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  rampHue,
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  rampHueCss,
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  rampStops
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- } from "./chunks/chunk-6ZNQJ5ZD.js";
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- import "./chunks/chunk-HBEKUQO4.js";
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+ } from "./chunks/chunk-OXTR3BVF.js";
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+ import "./chunks/chunk-BR25DGIJ.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-PBENCR5L.js";
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  import "./chunks/chunk-7GBL7SJY.js";
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+ import "./chunks/chunk-PBENCR5L.js";
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  import "./chunks/chunk-WFB5TXRA.js";
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  import "./chunks/chunk-3ZZSX5HN.js";
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  import "./chunks/chunk-AB35TJST.js";
package/dist/referenceStrip.js CHANGED
@@ -7,11 +7,11 @@ import {
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  stripBlockAt,
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  stripOverhang,
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  stripPixels
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- } from "./chunks/chunk-W253V6RR.js";
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- import "./chunks/chunk-HBEKUQO4.js";
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+ } from "./chunks/chunk-CVYDR2OP.js";
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+ import "./chunks/chunk-BR25DGIJ.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-PBENCR5L.js";
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  import "./chunks/chunk-7GBL7SJY.js";
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+ import "./chunks/chunk-PBENCR5L.js";
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  import "./chunks/chunk-WFB5TXRA.js";
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  import "./chunks/chunk-3ZZSX5HN.js";
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  import "./chunks/chunk-AB35TJST.js";
package/dist/renderer/GeometryBuilder.js CHANGED
@@ -11,10 +11,10 @@ import {
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  endTangent,
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  getNodeColor,
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  hslToRgb
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- } from "../chunks/chunk-HBEKUQO4.js";
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+ } from "../chunks/chunk-BR25DGIJ.js";
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  import "../chunks/chunk-G2FD7S3C.js";
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- import "../chunks/chunk-PBENCR5L.js";
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  import "../chunks/chunk-7GBL7SJY.js";
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+ import "../chunks/chunk-PBENCR5L.js";
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  import "../chunks/chunk-WFB5TXRA.js";
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  import "../chunks/chunk-3ZZSX5HN.js";
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  import "../chunks/chunk-AB35TJST.js";
package/dist/tubeMap/nodeColors.js CHANGED
@@ -1,10 +1,10 @@
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  import {
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  tubeMapNodeColors
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- } from "../chunks/chunk-FFFQNQUI.js";
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- import "../chunks/chunk-HBEKUQO4.js";
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+ } from "../chunks/chunk-A4MYLGKG.js";
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+ import "../chunks/chunk-BR25DGIJ.js";
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  import "../chunks/chunk-G2FD7S3C.js";
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- import "../chunks/chunk-PBENCR5L.js";
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  import "../chunks/chunk-7GBL7SJY.js";
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+ import "../chunks/chunk-PBENCR5L.js";
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  import "../chunks/chunk-WFB5TXRA.js";
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  import "../chunks/chunk-3ZZSX5HN.js";
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  import "../chunks/chunk-AB35TJST.js";
package/dist/types/cli/fold.d.ts ADDED
@@ -0,0 +1 @@
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+ export {};
package/dist/types/foldVariants.d.ts ADDED
@@ -0,0 +1,2 @@
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+ import type { Graph } from './types.js';
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+ export declare function foldVariants(graph: Graph, belowBp: number): Graph;
package/dist/types/gfa/writeRgfa.d.ts ADDED
@@ -0,0 +1,2 @@
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+ import type { Graph } from '../types.js';
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+ export declare function writeRgfa(graph: Graph): string;
package/dist/types/layout/trimToWindow.d.ts CHANGED
@@ -3,3 +3,7 @@ export declare function trimToWindow(graph: Graph, window: {
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  start: number;
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  end: number;
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  }): Graph;
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+ export declare function clipToWindow(graph: Graph, window: {
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+ start: number;
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+ end: number;
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+ }, reachBp: number): Graph;
package/dist/types/version.d.ts CHANGED
@@ -1 +1 @@
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- export declare const version = "9.1.0";
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+ export declare const version = "9.2.0";
package/dist/version.js CHANGED
@@ -1,6 +1,6 @@
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  import {
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  version
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- } from "./chunks/chunk-UID3QBWH.js";
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+ } from "./chunks/chunk-FM6XRXPX.js";
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  export {
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  version
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  };
package/dist/viewport.js CHANGED
@@ -5,19 +5,19 @@ import {
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  screenToLayout,
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  viewportOf,
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  zoomAbout
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- } from "./chunks/chunk-MXDQGA7A.js";
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- import "./chunks/chunk-OOXIMURX.js";
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+ } from "./chunks/chunk-XKM5OHQQ.js";
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+ import "./chunks/chunk-ZGRYFUXE.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-OA7RIMZ2.js";
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  import "./chunks/chunk-OCMBULGN.js";
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+ import "./chunks/chunk-OA7RIMZ2.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-JVLURPFW.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-BPLIXMH7.js";
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  import "./chunks/chunk-TAMCZHLW.js";
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- import "./chunks/chunk-JVLURPFW.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-N6FECAXP.js";
package/dist/walkEncoding.js CHANGED
@@ -9,11 +9,11 @@ import {
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  schemeColor,
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  schemeCss,
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  schemeRgb
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- } from "./chunks/chunk-DPV2CUIE.js";
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- import "./chunks/chunk-HBEKUQO4.js";
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+ } from "./chunks/chunk-XPT66H6H.js";
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+ import "./chunks/chunk-BR25DGIJ.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-PBENCR5L.js";
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  import "./chunks/chunk-7GBL7SJY.js";
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+ import "./chunks/chunk-PBENCR5L.js";
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  import "./chunks/chunk-WFB5TXRA.js";
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  import "./chunks/chunk-3ZZSX5HN.js";
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  import "./chunks/chunk-AB35TJST.js";
package/dist/walkHighlight.js CHANGED
@@ -2,12 +2,12 @@ import {
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  facetLifts,
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  walkHighlight,
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  walkLift
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- } from "./chunks/chunk-MBB7ATM6.js";
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- import "./chunks/chunk-DPV2CUIE.js";
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- import "./chunks/chunk-HBEKUQO4.js";
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+ } from "./chunks/chunk-LFKMASER.js";
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+ import "./chunks/chunk-XPT66H6H.js";
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+ import "./chunks/chunk-BR25DGIJ.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-PBENCR5L.js";
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  import "./chunks/chunk-7GBL7SJY.js";
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+ import "./chunks/chunk-PBENCR5L.js";
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  import "./chunks/chunk-WFB5TXRA.js";
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  import "./chunks/chunk-3ZZSX5HN.js";
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  import "./chunks/chunk-AB35TJST.js";
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/bandage-core",
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- "version": "9.1.0",
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+ "version": "9.2.0",
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  "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",
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  "license": "GPL-3.0-or-later",
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  "repository": {
@@ -28,7 +28,8 @@
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  "access": "public"
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  },
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  "bin": {
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- "bandage-figure": "dist/cli/figure.js"
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+ "bandage-figure": "dist/cli/figure.js",
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+ "bandage-fold": "dist/cli/fold.js"
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  },
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  "files": [
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  "dist"
package/dist/chunks/{chunk-HBEKUQO4.js → chunk-BR25DGIJ.js} RENAMED
@@ -3,16 +3,16 @@ import {
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  fadeAbgr,
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  packAbgr
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  } from "./chunk-G2FD7S3C.js";
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- import {
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- meanDepth,
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- nodeWidthPx
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- } from "./chunk-PBENCR5L.js";
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  import {
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  PATH_LIGHTNESS,
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  PATH_SATURATION,
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  nameHue,
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  pathHueAt
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  } from "./chunk-7GBL7SJY.js";
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+ import {
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+ meanDepth,
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+ nodeWidthPx
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+ } from "./chunk-PBENCR5L.js";
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  import {
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  baseEdgeCurves
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  } from "./chunk-WFB5TXRA.js";
package/dist/chunks/{chunk-WNUZP3WQ.js → chunk-M7SRZJ32.js} RENAMED
@@ -1,12 +1,12 @@
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+ import {
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+ sampleRowLayout
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+ } from "./chunk-LOEA5IHZ.js";
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  import {
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  hasTubeMapBackbone,
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  hasTubeMapPaths,
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  tubeMapLayout,
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  tubeMapReferenceLayout
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  } from "./chunk-INJ2UVOT.js";
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- import {
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- sampleRowLayout
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- } from "./chunk-LOEA5IHZ.js";
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  import {
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  anchoredLayout
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  } from "./chunk-L3O7AWLI.js";
package/dist/chunks/{chunk-FUVI4WQP.js → chunk-ZDJDM77V.js} RENAMED
@@ -4,14 +4,14 @@ import {
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  import {
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  coversGraph
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  } from "./chunk-2AWUWGAD.js";
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+ import {
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+ bubbleSegmentIds
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+ } from "./chunk-XKWD2RY3.js";
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  import {
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  bubblesFromGraph,
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  walkIndexOf,
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  walkRoutes
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  } from "./chunk-GOZYKNQ2.js";
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- import {
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- bubbleSegmentIds
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- } from "./chunk-XKWD2RY3.js";
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  import {
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  SATURATED_PATH_COUNT
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  } from "./chunk-FX4RDMDN.js";
package/dist/chunks/{chunk-OOXIMURX.js → chunk-ZGRYFUXE.js} RENAMED
@@ -4,15 +4,20 @@ import {
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  import {
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  seededNodes
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  } from "./chunk-IGVV37VI.js";
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- import {
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- graphFromTables
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- } from "./chunk-OA7RIMZ2.js";
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  import {
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  convertGFAToGraph
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  } from "./chunk-OCMBULGN.js";
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+ import {
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+ graphFromTables
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+ } from "./chunk-OA7RIMZ2.js";
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  import {
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  parseGFA
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  } from "./chunk-CDLPYR5O.js";
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+ import {
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+ routeNodes,
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+ takeRoutes,
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+ withDeletionRoutes
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+ } from "./chunk-JVLURPFW.js";
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  import {
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  anchorGraph
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  } from "./chunk-ST2IBUAN.js";
@@ -20,11 +25,6 @@ import {
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  mergeRuns,
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  splitRuns
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  } from "./chunk-TAMCZHLW.js";
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- import {
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- routeNodes,
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- takeRoutes,
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- withDeletionRoutes
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- } from "./chunk-JVLURPFW.js";
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  import {
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  spreadFor
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  } from "./chunk-UVBGRJQX.js";