jbrowse-plugin-mafviewer 1.2.3 → 1.2.4

package/dist/LinearMafDisplay/util.js

@@ -0,0 +1,16 @@
+import { max } from 'd3-array';
+// basically same as maxLength from https://observablehq.com/@d3/tree-of-life
+export function maxLength(d) {
+    return ((d.data.length || 0) + (d.children ? max(d.children, maxLength) || 0 : 0));
+}
+// basically same as setRadius from https://observablehq.com/@d3/tree-of-life
+export function setBrLength(d, y0, k) {
+    // @ts-expect-error
+    d.len = (y0 += Math.max(d.data.length || 0, 0)) * k;
+    if (d.children) {
+        d.children.forEach(d => {
+            setBrLength(d, y0, k);
+        });
+    }
+}
+//# sourceMappingURL=util.js.map

package/dist/LinearMafDisplay/util.js.map

@@ -0,0 +1 @@
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package/dist/LinearMafRenderer/LinearMafRenderer.d.ts

@@ -26,7 +26,7 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        canvasRecordedData: any;
+        canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -34,15 +34,15 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        reactElement: import("react/jsx-runtime").JSX.Element;
+        imageData: any;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<any, any>;
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
+        reactElement: React.ReactElement;
         html?: string;
     }>;
 }

package/dist/LinearMafRenderer/LinearMafRenderer.js

@@ -18,18 +18,16 @@ export default class LinearMafRenderer extends FeatureRendererType {
         const height = samples.length * rowHeight + 100;
         const width = (region.end - region.start) / bpPerPx;
         const features = await this.getFeatures(renderProps);
-        const res = await renderToAbstractCanvas(width, height, renderProps, async (ctx) => {
-            await updateStatus('Rendering alignment', statusCallback, () => {
-                makeImageData({
-                    ctx,
-                    renderArgs: {
-                        ...renderProps,
-                        features,
-                    },
-                });
+        const res = await updateStatus('Rendering alignment', statusCallback, () => renderToAbstractCanvas(width, height, renderProps, ctx => {
+            makeImageData({
+                ctx,
+                renderArgs: {
+                    ...renderProps,
+                    features,
+                },
             });
             return undefined;
-        });
+        }));
         const results = await super.render({
             ...renderProps,
             ...res,

package/dist/LinearMafRenderer/LinearMafRenderer.js.map

@@ -1 +1 @@
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+{"version":3,"file":"LinearMafRenderer.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/LinearMafRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAA;AAEzE,OAAO,EAEL,sBAAsB,EACtB,YAAY,GACb,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAe/C,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,mBAAmB;IAChE,iBAAiB,CAAC,MAAc;QAC9B,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QAC7B,MAAM,WAAW,GAAG,CAAC,CAAA;QAErB,OAAO;YACL,sEAAsE;YACtE,GAAI,MAAsC;YAC1C,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,WAAW,EAAE,CAAC,CAAC,CAAC;YACnD,GAAG,EAAE,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC;SAClC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,MAAM,CAAC,WAAuB;QAClC,MAAM,EACJ,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EACzB,OAAO,EACP,OAAO,EACP,OAAO,EACP,SAAS,GACV,GAAG,WAAW,CAAA;QACf,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,SAAS,GAAG,GAAG,CAAA;QAC/C,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QACnD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,WAAW,CAAC,CAAA;QACpD,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,qBAAqB,EAAE,cAAc,EAAE,GAAG,EAAE,CACzE,sBAAsB,CAAC,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,CAAC,EAAE;YACvD,aAAa,CAAC;gBACZ,GAAG;gBACH,UAAU,EAAE;oBACV,GAAG,WAAW;oBACd,QAAQ;iBACT;aACF,CAAC,CAAA;YACF,OAAO,SAAS,CAAA;QAClB,CAAC,CAAC,CACH,CAAA;QACD,MAAM,OAAO,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC;YACjC,GAAG,WAAW;YACd,GAAG,GAAG;YACN,KAAK;YACL,MAAM;SACP,CAAC,CAAA;QACF,OAAO;YACL,GAAG,OAAO;YACV,GAAG,GAAG;YACN,QAAQ,EAAE,IAAI,GAAG,EAAE;YACnB,KAAK;YACL,MAAM;YACN,uBAAuB,EAAE,IAAI;SAC9B,CAAA;IACH,CAAC;CACF"}

package/dist/LinearMafRenderer/makeImageData.js

@@ -31,10 +31,11 @@ export function makeImageData({ ctx, renderArgs, }) {
                 continue;
             }
             const t = rowHeight * row;
+            const t2 = offset + t;
             // gaps
             ctx.beginPath();
             ctx.fillStyle = 'black';
-            for (let i = 0, o = 0; i < alignment.length; i++) {
+            for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
                 if (seq[i] !== '-') {
                     if (alignment[i] === '-') {
                         const l = leftPx + scale * o;
@@ -48,31 +49,31 @@ export function makeImageData({ ctx, renderArgs, }) {
             if (!showAllLetters) {
                 // matches
                 ctx.fillStyle = 'lightgrey';
-                for (let i = 0, o = 0; i < alignment.length; i++) {
+                for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
                     if (seq[i] !== '-') {
                         const c = alignment[i];
                         const l = leftPx + scale * o;
                         if (seq[i] === c && c !== '-' && c !== ' ') {
-                            fillRect(ctx, l, offset + t, scale + f, h, canvasWidth);
+                            fillRect(ctx, l, t2, scale + f, h, canvasWidth);
                         }
                         o++;
                     }
                 }
             }
             // mismatches
-            for (let i = 0, o = 0; i < alignment.length; i++) {
+            for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
                 const c = alignment[i];
                 if (seq[i] !== '-') {
                     if (c !== '-') {
                         const l = leftPx + scale * o;
                         if (seq[i] !== c && c !== ' ') {
-                            fillRect(ctx, l, offset + t, scale + f, h, canvasWidth, mismatchRendering
+                            fillRect(ctx, l, t2, scale + f, h, canvasWidth, mismatchRendering
                                 ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                                     (colorForBase[c] ?? 'black')
                                 : 'orange');
                         }
                         else if (showAllLetters) {
-                            fillRect(ctx, l, offset + t, scale + f, h, canvasWidth, mismatchRendering
+                            fillRect(ctx, l, t2, scale + f, h, canvasWidth, mismatchRendering
                                 ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                                     (colorForBase[c] ?? 'black')
                                 : 'lightblue');
@@ -84,7 +85,7 @@ export function makeImageData({ ctx, renderArgs, }) {
             // font
             const charSizeW = 10;
             if (scale >= charSizeW) {
-                for (let i = 0, o = 0; i < alignment.length; i++) {
+                for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
                     if (seq[i] !== '-') {
                         const l = leftPx + scale * o;
                         const offset = (scale - charSizeW) / 2 + 1;
@@ -117,7 +118,8 @@ export function makeImageData({ ctx, renderArgs, }) {
                 continue;
             }
             const t = rowHeight * row;
-            for (let i = 0, o = 0; i < alignment.length; i++) {
+            const t2 = offset + t;
+            for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
                 let ins = '';
                 while (seq[i] === '-') {
                     if (alignment[i] !== '-' && alignment[i] !== ' ') {
@@ -130,25 +132,25 @@ export function makeImageData({ ctx, renderArgs, }) {
                     if (ins.length > 10) {
                         const txt = `${ins.length}`;
                         if (bpPerPx > 10) {
-                            fillRect(ctx, l - 1, t, 2, h, canvasWidth, 'purple');
+                            fillRect(ctx, l - 1, t2, 2, h, canvasWidth, 'purple');
                         }
                         else if (h > charHeight) {
-                            const rwidth = measureText(txt);
-                            const padding = 5;
-                            fillRect(ctx, l - rwidth / 2 - padding, t, rwidth + 2 * padding, h, canvasWidth, 'purple');
+                            const rwidth = measureText(txt, 10);
+                            const padding = 2;
+                            fillRect(ctx, l - rwidth / 2 - padding, t2, rwidth + 2 * padding, h, canvasWidth, 'purple');
                             ctx.fillStyle = 'white';
                             ctx.fillText(txt, l - rwidth / 2, t + h);
                         }
                         else {
                             const padding = 2;
-                            fillRect(ctx, l - padding, t, 2 * padding, h, canvasWidth, 'purple');
+                            fillRect(ctx, l - padding, t2, 2 * padding, h, canvasWidth, 'purple');
                         }
                     }
                     else {
-                        fillRect(ctx, l, offset + t, 1, h, canvasWidth, 'purple');
+                        fillRect(ctx, l, t2, 1, h, canvasWidth, 'purple');
                         if (bpPerPx < 0.2 && rowHeight > 5) {
-                            fillRect(ctx, l - 2, offset + t, 5, 1, canvasWidth);
-                            fillRect(ctx, l - 2, offset + t + h - 1, 5, 1, canvasWidth);
+                            fillRect(ctx, l - 2, t2, 5, 1, canvasWidth);
+                            fillRect(ctx, l - 2, t2 + h - 1, 5, 1, canvasWidth);
                         }
                     }
                 }

package/dist/LinearMafRenderer/makeImageData.js.map

@@ -1 +1 @@
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package/dist/MafAddTrackWorkflow/index.js

@@ -1,6 +1,5 @@
 import { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes';
 import { types } from 'mobx-state-tree';
-// locals
 import MultiMAFWidget from './AddTrackWorkflow';
 export default function MafAddTrackWorkflowF(pluginManager) {
     pluginManager.addAddTrackWorkflowType(() => new AddTrackWorkflowType({

package/dist/MafAddTrackWorkflow/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafAddTrackWorkflow/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,oBAAoB,EAAE,MAAM,qCAAqC,CAAA;AAC1E,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,SAAS;AACT,OAAO,cAAc,MAAM,oBAAoB,CAAA;AAE/C,MAAM,CAAC,OAAO,UAAU,oBAAoB,CAAC,aAA4B;IACvE,aAAa,CAAC,uBAAuB,CACnC,GAAG,EAAE,CACH,IAAI,oBAAoB,CAAC;QACvB,IAAI,EAAE,WAAW;QACjB,cAAc,EAAE,cAAc;QAC9B,UAAU,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;KAC5B,CAAC,CACL,CAAA;AACH,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafAddTrackWorkflow/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,oBAAoB,EAAE,MAAM,qCAAqC,CAAA;AAC1E,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,OAAO,cAAc,MAAM,oBAAoB,CAAA;AAE/C,MAAM,CAAC,OAAO,UAAU,oBAAoB,CAAC,aAA4B;IACvE,aAAa,CAAC,uBAAuB,CACnC,GAAG,EAAE,CACH,IAAI,oBAAoB,CAAC;QACvB,IAAI,EAAE,WAAW;QACjB,cAAc,EAAE,cAAc;QAC9B,UAAU,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;KAC5B,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/MafTabixAdapter/MafTabixAdapter.d.ts

@@ -19,7 +19,7 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
     getSamples(_query: Region): Promise<{
         samples: {
             id: string;
-            label: string;
+            label?: string;
             color?: string;
         }[];
         tree: Record<string, any> | undefined;

package/dist/MafTabixAdapter/MafTabixAdapter.js

@@ -9,16 +9,14 @@ import { normalize } from '../util';
 export default class MafTabixAdapter extends BaseFeatureDataAdapter {
     setupP;
     async setupPre() {
-        const config = this.config;
         if (!this.getSubAdapter) {
             throw new Error('no getSubAdapter available');
         }
-        const adapter = await this.getSubAdapter({
-            ...getSnapshot(config),
-            type: 'BedTabixAdapter',
-        });
         return {
-            adapter: adapter.dataAdapter,
+            adapter: (await this.getSubAdapter({
+                ...getSnapshot(this.config),
+                type: 'BedTabixAdapter',
+            })).dataAdapter,
         };
     }
     async setupPre2() {
@@ -54,7 +52,8 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
                     const data = feature.get('field5').split(',');
                     const alignments = {};
                     // eslint-disable-next-line @typescript-eslint/prefer-for-of
-                    for (let j = 0; j < data.length; j++) {
+                    const len = data.length;
+                    for (let j = 0; j < len; j++) {
                         const elt = data[j];
                         const seq = elt.split(':')[5];
                         const ad = elt.split(':');

package/dist/MafTabixAdapter/MafTabixAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MafTabixAdapter.js","sourceRoot":"","sources":["../../src/MafTabixAdapter/MafTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAGL,aAAa,EACb,YAAY,GACb,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAWnC,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,sBAAsB;IAC1D,MAAM,CAA+C;IAE5D,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,OAAO;YACL,OAAO,EAAE,CACP,MAAM,IAAI,CAAC,aAAa,CAAC;gBACvB,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC3B,IAAI,EAAE,iBAAiB;aACxB,CAAC,CACH,CAAC,WAAqC;SACxC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,SAAS;QACb,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACjD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,IAAkB;QAC5B,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,OAAO,YAAY,CAAC,mBAAmB,EAAE,cAAc,EAAE,GAAG,EAAE,CAC5D,IAAI,CAAC,SAAS,EAAE,CACjB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1C,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1C,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa,EAAE,IAAkB;QAC3C,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC1C,MAAM,QAAQ,GAAG,MAAM,YAAY,CACjC,wBAAwB,EACxB,cAAc,EACd,GAAG,EAAE,CAAC,cAAc,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CACjE,CAAA;YAED,MAAM,YAAY,CAAC,uBAAuB,EAAE,cAAc,EAAE,GAAG,EAAE;gBAC/D,IAAI,sBAAsB,GAAG,EAAE,CAAA;gBAC/B,MAAM,eAAe,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;gBACvD,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;oBAC/B,MAAM,IAAI,GAAI,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAY,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBACzD,MAAM,UAAU,GAAG,EAAoC,CAAA;oBAEvD,4DAA4D;oBAC5D,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAA;oBACvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;wBAC7B,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAE,CAAA;wBACpB,MAAM,GAAG,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;wBAC9B,MAAM,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;wBACzB,MAAM,EAAE,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;wBAC5B,MAAM,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,CAAC,GAAG,EAAE,CAAA;wBACjC,IAAI,YAAY,CAAA;wBAChB,IAAI,IAAI,GAAG,EAAE,CAAA;wBACb,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;4BACpB,YAAY,GAAG,EAAE,CAAA;4BACjB,IAAI,GAAG,EAAG,CAAA;wBACZ,CAAC;6BAAM,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC;4BAC9B,YAAY,GAAG,GAAG,EAAE,IAAI,EAAE,EAAE,CAAA;4BAC5B,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;wBACvB,CAAC;6BAAM,CAAC;4BACN,YAAY,GAAG,EAAE,CAAA;4BACjB,IAAI,GAAG,CAAC,EAAE,EAAE,GAAG,IAAI,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;wBAChC,CAAC;wBACD,IAAI,YAAY,EAAE,CAAC;4BACjB,sBAAsB,GAAG,sBAAsB,IAAI,YAAY,CAAA;4BAE/D,UAAU,CAAC,YAAY,CAAC,GAAG;gCACzB,GAAG,EAAE,IAAI;gCACT,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;gCACd,OAAO,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;gCAChB,MAAM,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gCAC9B,OAAO,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;gCAChB,IAAI,EAAE,GAAG;6BACV,CAAA;wBACH,CAAC;oBACH,CAAC;oBAED,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;wBAChB,EAAE,EAAE,OAAO,CAAC,EAAE,EAAE;wBAChB,IAAI,EAAE;4BACJ,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;4BAC3B,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC;4BACvB,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC;4BAC/B,IAAI,EAAE,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC;4BACzB,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;4BAC3B,UAAU;4BACV,GAAG,EACD,UAAU,CAAC,eAAe,IAAI,KAAK,CAAC,YAAY,CAAC,EAAE,IAAI;gCACvD,UAAU,CAAC,sBAAsB,CAAC,EAAE,IAAI;yBAC3C;qBACF,CAAC,CACH,CAAA;gBACH,CAAC;YACH,CAAC,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,MAAc;QAC7B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACxC,MAAM,EAAE,GACN,KAAK,CAAC,GAAG,KAAK,gBAAgB;YAC5B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,MAAM,YAAY,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QAEhD,2EAA2E;QAC3E,OAAO;QACP,OAAO;YACL,OAAO,EAAE,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YAC3C,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;SACvC,CAAA;IACH,CAAC;IAED,aAAa,KAAU,CAAC;CACzB"}

package/dist/MafTabixAdapter/configSchema.js

@@ -58,6 +58,34 @@ const configSchema = ConfigurationSchema('MafTabixAdapter', {
             locationType: 'UriLocation',
         },
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        // populate from just snap.uri
+        return snap.uri
+            ? {
+                ...snap,
+                ...(snap.nhUri
+                    ? {
+                        nhLocation: {
+                            uri: snap.nhUri,
+                            baseUri: snap.baseUri,
+                        },
+                    }
+                    : {}),
+                bedGzLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+                index: {
+                    location: {
+                        uri: `${snap.uri}.tbi`,
+                        baseUri: snap.baseUri,
+                    },
+                },
+            }
+            : snap;
+    },
+});
 export default configSchema;
 //# sourceMappingURL=configSchema.js.map

package/dist/MafTabixAdapter/configSchema.js.map

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