@jbrowse/bandage-core 10.0.0 → 10.1.0

package/dist/chunks/{chunk-Q6IOQP4J.js → chunk-VIERZJO2.js}

@@ -1,9 +1,9 @@
 import {
   layoutEngine
-} from "./chunk-VK6XMP6B.js";
+} from "./chunk-FLUQODT2.js";
 import {
   layoutModeByValue
-} from "./chunk-ICXMWYOA.js";
+} from "./chunk-4R6QNG23.js";
 import {
   parseRegion
 } from "./chunk-FLFBYSJO.js";
@@ -12,21 +12,21 @@ import {
 } from "./chunk-LOCJN3BZ.js";
 import {
   version
-} from "./chunk-CDPYXHVR.js";
+} from "./chunk-MZIOBJZB.js";
 import {
   axisScaleOf
-} from "./chunk-OOLNLCIO.js";
+} from "./chunk-L5WF4ZPS.js";
 import {
   facetLifts,
   walkLift
-} from "./chunk-QIVPRZ4H.js";
+} from "./chunk-R456ME6J.js";
 import {
   walkKey
 } from "./chunk-2LQ5BWT7.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-NP356MC2.js";
+} from "./chunk-SBMJNRTV.js";
 import {
   abgrAlpha,
   abgrBlue,
@@ -36,14 +36,14 @@ import {
 import {
   pathLegend,
   walkLabelsOf
-} from "./chunk-REE4GUDM.js";
+} from "./chunk-TWRLC3KK.js";
 import {
   drawingBounds,
   engineSettingsOf,
   fitTransform,
   forceLayout,
   loadGraph
-} from "./chunk-W4GZCVUK.js";
+} from "./chunk-XTCNEKO5.js";
 import {
   referenceLabel
 } from "./chunk-RAKOB6IV.js";

package/dist/chunks/{chunk-JVLURPFW.js → chunk-VPE4AYP7.js}

@@ -1,5 +1,5 @@
 // src/layout/deletionRoutes.ts
-var ROUTE_ID = "\0deletion:";
+import { ROUTE_ID } from "@jbrowse/graph-stress-layout";
 var ROUTE_FRACTION = 0.5;
 function withDeletionRoutes(graph, deletions, dropped = /* @__PURE__ */ new Set()) {
   const routes = new Map(
@@ -73,7 +73,6 @@ function takeRoutes(positions, routes) {
 }
 
 export {
-  ROUTE_ID,
   withDeletionRoutes,
   routeNodes,
   takeRoutes

package/dist/chunks/{chunk-W4GZCVUK.js → chunk-XTCNEKO5.js}

@@ -4,26 +4,26 @@ import {
 import {
   smoothChain
 } from "./chunk-OPPVSPEF.js";
+import {
+  routeNodes,
+  takeRoutes,
+  withDeletionRoutes
+} from "./chunk-VPE4AYP7.js";
 import {
   orientToReference
 } from "./chunk-PUG7LXDF.js";
 import {
   convertGFAToGraph
-} from "./chunk-QXAB2FLJ.js";
+} from "./chunk-IW6CYVX2.js";
 import {
   graphFromTables
 } from "./chunk-PSMKPSO4.js";
 import {
   parseGFA
 } from "./chunk-CDLPYR5O.js";
-import {
-  routeNodes,
-  takeRoutes,
-  withDeletionRoutes
-} from "./chunk-JVLURPFW.js";
 import {
   anchorGraph
-} from "./chunk-EMUUNWRU.js";
+} from "./chunk-M6LK4GII.js";
 import {
   gfaTables
 } from "./chunk-G45YY72K.js";

package/dist/chunks/{chunk-VZNKA3K2.js → chunk-XYP6WL2N.js}

@@ -3,13 +3,13 @@ import {
   RAMP_GRADIENT_STOPS,
   rampHueCss,
   rampStops
-} from "./chunk-DCJC32QW.js";
+} from "./chunk-ZIUKZUPJ.js";
 import {
   el
 } from "./chunk-NNODIW4U.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-NP356MC2.js";
+} from "./chunk-SBMJNRTV.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";
@@ -30,6 +30,10 @@ var MIN_TILE_PX = 3;
 function kb(bp) {
   return `${(bp / 1e3).toFixed(bp < 1e4 ? 1 : 0)} kb`;
 }
+function signedLength(delta) {
+  const size = Math.abs(delta);
+  return `${delta > 0 ? "+" : "\u2212"}${size < 1e3 ? `${size} bp` : kb(size)}`;
+}
 function units(bp, unit) {
   return unit ? ` \u2248 ${Math.round(bp / unit)} units` : "";
 }
@@ -42,7 +46,7 @@ function walkRowReadout(row, reference, unit, call) {
   const called = call ? ` \xB7 called ${kb(call.bp)}${call.spanningReads === 0 ? " \xB7 no spanning read" : ""}` : "";
   if (complete) {
     const delta = bp - reference.bp;
-    const against = delta === 0 ? "" : ` (${delta > 0 ? "+" : "\u2212"}${kb(Math.abs(delta))})`;
+    const against = delta === 0 ? "" : ` (${signedLength(delta)})`;
     return `${kb(bp)}${units(bp, unit)}${against}${outside}${called}`;
   }
   const region = unit ? "repeat" : "window";

package/dist/chunks/{chunk-B4645SM2.js → chunk-YPYWYPHX.js}

@@ -173,7 +173,7 @@ function nearestOutside(i, side, links, allele, dist, nodes) {
   let best;
   for (const link of links[i]) {
     const j = link.other;
-    if (link.side === side && allele[j] !== allele[i] && Number.isFinite(dist[j]) && (best === void 0 || dist[j] < dist[best] || dist[j] === dist[best] && nodes[j].id < nodes[best].id)) {
+    if (link.side === side && allele[j] !== allele[i] && Number.isFinite(dist[j]) && (best === void 0 || dist[j] < dist[best] || dist[j] === dist[best] && nodes[j].name < nodes[best].name)) {
       best = j;
     }
   }
@@ -183,7 +183,7 @@ function distancesFromBackbone(nodes, links) {
   const dist = new Float64Array(nodes.length).fill(Infinity);
   const pred = new Int32Array(nodes.length).fill(-1);
   const heap = new MinHeap(
-    ([da, a], [db, b]) => da - db || cmp(nodes[a].id, nodes[b].id)
+    ([da, a], [db, b]) => da - db || cmp(nodes[a].name, nodes[b].name)
   );
   nodes.forEach((node, i) => {
     if (isBackbone(node)) {
@@ -205,7 +205,7 @@ function distancesFromBackbone(nodes, links) {
         dist[other] = d;
         pred[other] = i;
         heap.push([d, other]);
-      } else if (d === dist[other] && cmp(nodes[i].id, nodes[pred[other]].id) < 0) {
+      } else if (d === dist[other] && cmp(nodes[i].name, nodes[pred[other]].name) < 0) {
         pred[other] = i;
       }
     }

package/dist/chunks/{chunk-DCJC32QW.js → chunk-ZIUKZUPJ.js}

@@ -1,6 +1,6 @@
 import {
   REFERENCE_RAMP_MAX_HUE
-} from "./chunk-NP356MC2.js";
+} from "./chunk-SBMJNRTV.js";
 
 // src/referenceRampCss.ts
 function rampHueCss(hue) {

package/dist/cli/figure.js

@@ -6,18 +6,18 @@ import {
 } from "../chunks/chunk-BXEPA4KS.js";
 import {
   figureSvg
-} from "../chunks/chunk-RJXPPYA7.js";
+} from "../chunks/chunk-CFPER2S2.js";
 import "../chunks/chunk-47DYCZOK.js";
-import "../chunks/chunk-WI7ZHJ27.js";
+import "../chunks/chunk-RPDXZLCG.js";
+import "../chunks/chunk-WBCOREDZ.js";
+import "../chunks/chunk-4BYTEJGW.js";
 import {
   genesOnRow,
   placeRowGenes
-} from "../chunks/chunk-VZNKA3K2.js";
-import "../chunks/chunk-WBCOREDZ.js";
-import "../chunks/chunk-4BYTEJGW.js";
+} from "../chunks/chunk-XYP6WL2N.js";
 import "../chunks/chunk-3S3YVOJ7.js";
 import "../chunks/chunk-BUBZ32IC.js";
-import "../chunks/chunk-DCJC32QW.js";
+import "../chunks/chunk-ZIUKZUPJ.js";
 import "../chunks/chunk-DRG4236Y.js";
 import "../chunks/chunk-FP4H7SFT.js";
 import "../chunks/chunk-MLSWIMZO.js";
@@ -26,16 +26,14 @@ import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind,
   layoutEngine
-} from "../chunks/chunk-VK6XMP6B.js";
-import "../chunks/chunk-Q6FRNVDU.js";
-import "../chunks/chunk-LYJ4US66.js";
+} from "../chunks/chunk-FLUQODT2.js";
 import {
   LAYOUT_MODES,
   layoutModeByValue
-} from "../chunks/chunk-ICXMWYOA.js";
-import "../chunks/chunk-IM4SJUPO.js";
-import "../chunks/chunk-CWFNEKST.js";
+} from "../chunks/chunk-4R6QNG23.js";
 import "../chunks/chunk-LOEA5IHZ.js";
+import "../chunks/chunk-DK5P2YOL.js";
+import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-L3O7AWLI.js";
 import "../chunks/chunk-TZFWUT2C.js";
 import "../chunks/chunk-HNQPEMYE.js";
@@ -52,35 +50,35 @@ import {
 import "../chunks/chunk-Q7LYHGGQ.js";
 import "../chunks/chunk-WSIFAZU7.js";
 import "../chunks/chunk-LOCJN3BZ.js";
-import "../chunks/chunk-CDPYXHVR.js";
-import "../chunks/chunk-OOLNLCIO.js";
-import "../chunks/chunk-QIVPRZ4H.js";
-import "../chunks/chunk-VOWI544A.js";
+import "../chunks/chunk-MZIOBJZB.js";
+import "../chunks/chunk-L5WF4ZPS.js";
+import "../chunks/chunk-R456ME6J.js";
+import "../chunks/chunk-ALDGONEI.js";
 import "../chunks/chunk-2LQ5BWT7.js";
-import "../chunks/chunk-NP356MC2.js";
+import "../chunks/chunk-SBMJNRTV.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-3APK25GI.js";
+import "../chunks/chunk-C7MZJSPT.js";
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-KAN2WTG5.js";
-import "../chunks/chunk-REE4GUDM.js";
+} from "../chunks/chunk-RIPAA7OK.js";
+import "../chunks/chunk-TWRLC3KK.js";
 import "../chunks/chunk-PBENCR5L.js";
 import {
   engineSettingsOf,
   forceLayout,
   loadGraph
-} from "../chunks/chunk-W4GZCVUK.js";
+} from "../chunks/chunk-XTCNEKO5.js";
 import "../chunks/chunk-IGVV37VI.js";
 import "../chunks/chunk-OPPVSPEF.js";
+import "../chunks/chunk-VPE4AYP7.js";
 import "../chunks/chunk-PUG7LXDF.js";
-import "../chunks/chunk-QXAB2FLJ.js";
+import "../chunks/chunk-IW6CYVX2.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-PSMKPSO4.js";
 import "../chunks/chunk-CDLPYR5O.js";
-import "../chunks/chunk-JVLURPFW.js";
-import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-M6LK4GII.js";
 import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-ES2N6V56.js";
 import {

package/dist/cli/fold.js

@@ -4,19 +4,19 @@ import {
 } from "../chunks/chunk-B4YH42OP.js";
 import {
   foldVariants
-} from "../chunks/chunk-B4645SM2.js";
+} from "../chunks/chunk-YPYWYPHX.js";
 import {
   loadGraph
-} from "../chunks/chunk-W4GZCVUK.js";
+} from "../chunks/chunk-XTCNEKO5.js";
 import "../chunks/chunk-IGVV37VI.js";
 import "../chunks/chunk-OPPVSPEF.js";
+import "../chunks/chunk-VPE4AYP7.js";
 import "../chunks/chunk-PUG7LXDF.js";
-import "../chunks/chunk-QXAB2FLJ.js";
+import "../chunks/chunk-IW6CYVX2.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-PSMKPSO4.js";
 import "../chunks/chunk-CDLPYR5O.js";
-import "../chunks/chunk-JVLURPFW.js";
-import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-M6LK4GII.js";
 import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-G45YY72K.js";

package/dist/figure.js

@@ -1,41 +1,41 @@
 import {
   figureSvg
-} from "./chunks/chunk-RJXPPYA7.js";
+} from "./chunks/chunk-CFPER2S2.js";
 import "./chunks/chunk-47DYCZOK.js";
-import "./chunks/chunk-WI7ZHJ27.js";
-import "./chunks/chunk-VZNKA3K2.js";
+import "./chunks/chunk-RPDXZLCG.js";
 import "./chunks/chunk-WBCOREDZ.js";
 import "./chunks/chunk-4BYTEJGW.js";
+import "./chunks/chunk-XYP6WL2N.js";
 import "./chunks/chunk-3S3YVOJ7.js";
 import "./chunks/chunk-BUBZ32IC.js";
-import "./chunks/chunk-DCJC32QW.js";
+import "./chunks/chunk-ZIUKZUPJ.js";
 import "./chunks/chunk-DRG4236Y.js";
 import "./chunks/chunk-FP4H7SFT.js";
 import "./chunks/chunk-MLSWIMZO.js";
 import "./chunks/chunk-NNODIW4U.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-CDPYXHVR.js";
-import "./chunks/chunk-OOLNLCIO.js";
-import "./chunks/chunk-QIVPRZ4H.js";
-import "./chunks/chunk-VOWI544A.js";
+import "./chunks/chunk-MZIOBJZB.js";
+import "./chunks/chunk-L5WF4ZPS.js";
+import "./chunks/chunk-R456ME6J.js";
+import "./chunks/chunk-ALDGONEI.js";
 import "./chunks/chunk-2LQ5BWT7.js";
-import "./chunks/chunk-NP356MC2.js";
+import "./chunks/chunk-SBMJNRTV.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-3APK25GI.js";
-import "./chunks/chunk-KAN2WTG5.js";
-import "./chunks/chunk-REE4GUDM.js";
+import "./chunks/chunk-C7MZJSPT.js";
+import "./chunks/chunk-RIPAA7OK.js";
+import "./chunks/chunk-TWRLC3KK.js";
 import "./chunks/chunk-PBENCR5L.js";
-import "./chunks/chunk-W4GZCVUK.js";
+import "./chunks/chunk-XTCNEKO5.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OPPVSPEF.js";
+import "./chunks/chunk-VPE4AYP7.js";
 import "./chunks/chunk-PUG7LXDF.js";
-import "./chunks/chunk-QXAB2FLJ.js";
+import "./chunks/chunk-IW6CYVX2.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-PSMKPSO4.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-JVLURPFW.js";
-import "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-RAKOB6IV.js";

package/dist/figureData.js

@@ -1,14 +1,12 @@
 import {
   figureData,
   gfaFigureData
-} from "./chunks/chunk-Q6IOQP4J.js";
-import "./chunks/chunk-VK6XMP6B.js";
-import "./chunks/chunk-Q6FRNVDU.js";
-import "./chunks/chunk-LYJ4US66.js";
-import "./chunks/chunk-ICXMWYOA.js";
-import "./chunks/chunk-IM4SJUPO.js";
-import "./chunks/chunk-CWFNEKST.js";
+} from "./chunks/chunk-VIERZJO2.js";
+import "./chunks/chunk-FLUQODT2.js";
+import "./chunks/chunk-4R6QNG23.js";
 import "./chunks/chunk-LOEA5IHZ.js";
+import "./chunks/chunk-DK5P2YOL.js";
+import "./chunks/chunk-CWFNEKST.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";
 import "./chunks/chunk-HNQPEMYE.js";
@@ -19,28 +17,28 @@ import "./chunks/chunk-FLFBYSJO.js";
 import "./chunks/chunk-Q7LYHGGQ.js";
 import "./chunks/chunk-WSIFAZU7.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-CDPYXHVR.js";
-import "./chunks/chunk-OOLNLCIO.js";
-import "./chunks/chunk-QIVPRZ4H.js";
-import "./chunks/chunk-VOWI544A.js";
+import "./chunks/chunk-MZIOBJZB.js";
+import "./chunks/chunk-L5WF4ZPS.js";
+import "./chunks/chunk-R456ME6J.js";
+import "./chunks/chunk-ALDGONEI.js";
 import "./chunks/chunk-2LQ5BWT7.js";
-import "./chunks/chunk-NP356MC2.js";
+import "./chunks/chunk-SBMJNRTV.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-3APK25GI.js";
-import "./chunks/chunk-KAN2WTG5.js";
-import "./chunks/chunk-REE4GUDM.js";
+import "./chunks/chunk-C7MZJSPT.js";
+import "./chunks/chunk-RIPAA7OK.js";
+import "./chunks/chunk-TWRLC3KK.js";
 import "./chunks/chunk-PBENCR5L.js";
-import "./chunks/chunk-W4GZCVUK.js";
+import "./chunks/chunk-XTCNEKO5.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OPPVSPEF.js";
+import "./chunks/chunk-VPE4AYP7.js";
 import "./chunks/chunk-PUG7LXDF.js";
-import "./chunks/chunk-QXAB2FLJ.js";
+import "./chunks/chunk-IW6CYVX2.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-PSMKPSO4.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-JVLURPFW.js";
-import "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-RAKOB6IV.js";

package/dist/figureSettings.js

@@ -1,17 +1,17 @@
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-E5UEYZWK.js";
-import "./chunks/chunk-W4GZCVUK.js";
+} from "./chunks/chunk-MVFDSFV2.js";
+import "./chunks/chunk-XTCNEKO5.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OPPVSPEF.js";
+import "./chunks/chunk-VPE4AYP7.js";
 import "./chunks/chunk-PUG7LXDF.js";
-import "./chunks/chunk-QXAB2FLJ.js";
+import "./chunks/chunk-IW6CYVX2.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-PSMKPSO4.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-JVLURPFW.js";
-import "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-G45YY72K.js";

package/dist/foldVariants.js

@@ -1,6 +1,6 @@
 import {
   foldVariants
-} from "./chunks/chunk-B4645SM2.js";
+} from "./chunks/chunk-YPYWYPHX.js";
 import "./chunks/chunk-2CVHXFK7.js";
 import "./chunks/chunk-CPMHA4W5.js";
 import "./chunks/chunk-FYQWPEEY.js";

package/dist/gfa/gfaConverter.js

@@ -1,9 +1,9 @@
 import {
   convertGFAToGraph
-} from "../chunks/chunk-QXAB2FLJ.js";
+} from "../chunks/chunk-IW6CYVX2.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
-import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-M6LK4GII.js";
 import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-FYQWPEEY.js";