@jbrowse/plugin-alignments 2.4.0 → 2.4.1

package/esm/PileupRenderer/PileupRenderer.js

@@ -88,14 +88,16 @@ export default class PileupRenderer extends BoxRendererType {
                 }
             }
         }
-        const [leftPx, rightPx] = bpSpanPx(feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, region, bpPerPx);
+        const s = feature.get('start') - expansionBefore;
+        const e = feature.get('end') + expansionAfter;
+        const [leftPx, rightPx] = bpSpanPx(s, e, region, bpPerPx);
         if (displayMode === 'compact') {
             heightPx /= 3;
         }
         if (feature.get('refName') !== region.refName) {
             throw new Error(`feature ${feature.id()} is not on the current region's reference sequence ${region.refName}`);
         }
-        const topPx = layout.addRect(feature.id(), feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, heightPx, feature);
+        const topPx = layout.addRect(feature.id(), s, e, heightPx, feature);
         if (topPx === null) {
             return null;
         }
@@ -261,10 +263,9 @@ export default class PileupRenderer extends BoxRendererType {
         const modifications = getModificationPositions(mm, seq, strand);
         // probIndex applies across multiple modifications e.g.
         let probIndex = 0;
-        for (let i = 0; i < modifications.length; i++) {
-            const { type, positions } = modifications[i];
+        for (const { type, positions } of modifications) {
             const col = modificationTagMap[type] || 'black';
-            // @ts-ignore
+            // @ts-expect-error
             const base = Color(col);
             for (const readPos of getNextRefPos(cigarOps, positions)) {
                 const r = start + readPos;
@@ -371,7 +372,7 @@ export default class PileupRenderer extends BoxRendererType {
             ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx);
         }
     }
-    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }) {
+    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, theme, canvasWidth, }) {
         const { config, bpPerPx, regions, colorBy, colorTagMap = {} } = renderArgs;
         const { tag = '', type: colorType = '' } = colorBy || {};
         const { feature } = feat;
@@ -426,30 +427,23 @@ export default class PileupRenderer extends BoxRendererType {
                 }
                 break;
             }
-            case 'insertSizeAndPairOrientation':
+            case 'insertSizeAndPairOrientation': {
                 break;
+            }
             case 'modifications':
-            case 'methylation':
+            case 'methylation': {
                 // this coloring is similar to igv.js, and is helpful to color negative
                 // strand reads differently because their c-g will be flipped (e.g. g-c
                 // read right to left)
-                if (feature.get('flags') & 16) {
-                    ctx.fillStyle = '#c8dcc8';
-                }
-                else {
-                    ctx.fillStyle = '#c8c8c8';
-                }
+                ctx.fillStyle = feature.get('flags') & 16 ? '#c8dcc8' : '#c8c8c8';
                 break;
-            case 'normal':
-            default:
-                if (defaultColor) {
-                    // avoid a readConfObject call here
-                    ctx.fillStyle = '#c8c8c8';
-                }
-                else {
-                    ctx.fillStyle = readConfObject(config, 'color', { feature });
-                }
+            }
+            default: {
+                ctx.fillStyle = defaultColor
+                    ? 'lightgrey'
+                    : readConfObject(config, 'color', { feature });
                 break;
+            }
         }
         this.drawRect(ctx, feat, renderArgs);
         // second pass for color types that render per-base things that go over the
@@ -499,7 +493,7 @@ export default class PileupRenderer extends BoxRendererType {
                 break;
         }
     }
-    drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
+    drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels = true, theme, }) {
         const { Color, bpPerPx, regions } = renderArgs;
         const { heightPx, topPx, feature } = feat;
         const [region] = regions;
@@ -528,30 +522,30 @@ export default class PileupRenderer extends BoxRendererType {
             if (mismatch.type === 'mismatch') {
                 if (!drawSNPsMuted) {
                     const baseColor = colorForBase[mismatch.base] || '#888';
-                    fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth, !mismatchAlpha
-                        ? baseColor
-                        : mismatch.qual !== undefined
-                            ? // @ts-ignore
+                    fillRect(ctx, Math.round(leftPx), topPx, widthPx, heightPx, canvasWidth, mismatchAlpha
+                        ? mismatch.qual === undefined
+                            ? baseColor
+                            : // @ts-expect-error
                                 Color(baseColor)
                                     .alpha(Math.min(1, mismatch.qual / 50))
                                     .hsl()
                                     .string()
-                            : baseColor);
+                        : baseColor);
                 }
                 if (widthPx >= charWidth && heightPx >= heightLim) {
                     // normal SNP coloring
                     const contrastColor = drawSNPsMuted
                         ? 'black'
                         : contrastForBase[mismatch.base] || 'black';
-                    ctx.fillStyle = !mismatchAlpha
-                        ? contrastColor
-                        : mismatch.qual !== undefined
-                            ? // @ts-ignore
+                    ctx.fillStyle = mismatchAlpha
+                        ? mismatch.qual === undefined
+                            ? contrastColor
+                            : // @ts-expect-error
                                 Color(contrastColor)
                                     .alpha(Math.min(1, mismatch.qual / 50))
                                     .hsl()
                                     .string()
-                            : contrastColor;
+                        : contrastColor;
                     ctx.fillText(mbase, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
                 }
             }
@@ -708,6 +702,7 @@ export default class PileupRenderer extends BoxRendererType {
                 charWidth,
                 charHeight,
                 canvasWidth,
+                theme,
             });
             this.drawMismatches({
                 ctx,
@@ -723,6 +718,7 @@ export default class PileupRenderer extends BoxRendererType {
                 colorForBase,
                 contrastForBase,
                 canvasWidth,
+                theme,
             });
             if (showSoftClip) {
                 this.drawSoftClipping({

package/esm/PileupRenderer/PileupRenderer.js.map

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package/esm/PileupRenderer/components/PileupRendering.js

@@ -113,10 +113,10 @@ function PileupRendering(props) {
         }
     }
     function callMouseHandler(handlerName, event) {
-        // @ts-ignore
+        // @ts-expect-error
         // eslint-disable-next-line react/destructuring-assignment
         const featureHandler = props[`onFeature${handlerName}`];
-        // @ts-ignore
+        // @ts-expect-error
         // eslint-disable-next-line react/destructuring-assignment
         const canvasHandler = props[`on${handlerName}`];
         if (featureHandler && featureIdUnderMouse) {

package/esm/PileupRenderer/components/PileupRendering.js.map

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package/esm/PileupRenderer/configSchema.js

@@ -43,7 +43,7 @@ const PileupRenderer = ConfigurationSchema('PileupRenderer', {
     minSubfeatureWidth: {
         type: 'number',
         description: 'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
-        defaultValue: 0.7,
+        defaultValue: 1,
     },
     /**
      * #slot

package/esm/PileupRenderer/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,cAAc,GAAG,mBAAmB,CACxC,gBAAgB,EAChB;IACE;;;OAGG;IACH,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,iDAAiD;QAC9D,YAAY,EAAE,MAAM;QACpB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IAED;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,iBAAiB,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;QAC/D,YAAY,EAAE,IAAI;QAClB,WAAW,EACT,oIAAoI;KACvI;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,aAAa,EAAE;YACtC,QAAQ;YACR,SAAS;YACT,UAAU;SACX,CAAC;QACF,WAAW,EAAE,2BAA2B;QACxC,YAAY,EAAE,QAAQ;KACvB;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,0IAA0I;QAC5I,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,qDAAqD;QAClE,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,oDAAoD;QACjE,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,kDAAkD;QAC/D,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,iCAAiC;QAC9C,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,4BAA4B,EAAE;QAC5B,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,kEAAkE;QACpE,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,KAAK;QACnB,WAAW,EAAE,6BAA6B;KAC3C;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,cAAc,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,cAAc,GAAG,mBAAmB,CACxC,gBAAgB,EAChB;IACE;;;OAGG;IACH,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,iDAAiD;QAC9D,YAAY,EAAE,MAAM;QACpB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IAED;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,iBAAiB,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;QAC/D,YAAY,EAAE,IAAI;QAClB,WAAW,EACT,oIAAoI;KACvI;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,aAAa,EAAE;YACtC,QAAQ;YACR,SAAS;YACT,UAAU;SACX,CAAC;QACF,WAAW,EAAE,2BAA2B;QACxC,YAAY,EAAE,QAAQ;KACvB;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,0IAA0I;QAC5I,YAAY,EAAE,CAAC;KAChB;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,qDAAqD;QAClE,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,oDAAoD;QACjE,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,kDAAkD;QAC/D,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,iCAAiC;QAC9C,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,4BAA4B,EAAE;QAC5B,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,kEAAkE;QACpE,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,KAAK;QACnB,WAAW,EAAE,6BAA6B;KAC3C;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,cAAc,CAAA"}

package/esm/PileupRenderer/sortUtil.js

@@ -59,7 +59,7 @@ export const sortFeature = (features, sortedBy) => {
                 const acode = bMismatch && bMismatch.base.toUpperCase();
                 const bcode = aMismatch && aMismatch.base.toUpperCase();
                 if (acode === bcode && acode === '*') {
-                    // @ts-ignore
+                    // @ts-expect-error
                     return aMismatch.length - bMismatch.length;
                 }
                 return ((acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0));
@@ -72,9 +72,10 @@ export const sortFeature = (features, sortedBy) => {
             break;
         }
     }
-    const sortedMap = new Map(featuresInCenterLine
-        .concat(featuresOutsideCenter)
-        .map(feature => [feature.id(), feature]));
+    const sortedMap = new Map([...featuresInCenterLine, ...featuresOutsideCenter].map(feature => [
+        feature.id(),
+        feature,
+    ]));
     return sortedMap;
 };
 //# sourceMappingURL=sortUtil.js.map

package/esm/PileupRenderer/sortUtil.js.map

@@ -1 +1 @@
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package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -2,6 +2,7 @@ import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { featureSpanPx, bpSpanPx } from '@jbrowse/core/util';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { getOrigin, getScale, WiggleBaseRenderer, YSCALEBAR_LABEL_OFFSET, } from '@jbrowse/plugin-wiggle';
+const fudgeFactor = 0.6;
 export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     // note: the snps are drawn on linear scale even if the data is drawn in log
     // scape hence the two different scales being used
@@ -28,6 +29,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
             scaleType: 'linear',
         });
         const originY = getOrigin(scaleOpts.scaleType);
+        const originLinear = getOrigin('linear');
         const indicatorThreshold = readConfObject(cfg, 'indicatorThreshold');
         const drawInterbaseCounts = readConfObject(cfg, 'drawInterbaseCounts');
         const drawArcs = readConfObject(cfg, 'drawArcs');
@@ -35,8 +37,9 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
         // get the y coordinate that we are plotting at, this can be log scale
         const toY = (n) => height - (viewScale(n) || 0) + offset;
         const toHeight = (n) => toY(originY) - toY(n);
-        const indicatorToY = (n) => height - (indicatorViewScale(n) || 0) + offset;
-        const indicatorToHeight = (n) => indicatorToY(getOrigin('linear')) - indicatorToY(n);
+        // used specifically for indicator
+        const toY2 = (n) => height - (indicatorViewScale(n) || 0) + offset;
+        const toHeight2 = (n) => toY2(originLinear) - toY2(n);
         const { bases } = theme.palette;
         const colorForBase = {
             A: bases.A.main,
@@ -49,7 +52,6 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
             hardclip: 'red',
             meth: 'red',
             unmeth: 'blue',
-            ref: 'lightgrey',
         };
         const feats = [...features.values()];
         const coverage = feats.filter(f => f.get('type') !== 'skip');
@@ -60,7 +62,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
         for (let i = 0; i < coverage.length; i++) {
             const feature = coverage[i];
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-            const w = rightPx - leftPx + 0.3;
+            const w = rightPx - leftPx + fudgeFactor;
             const score = feature.get('score');
             ctx.fillRect(leftPx, toY(score), w, toHeight(score));
         }
@@ -81,7 +83,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
             const score = feature.get('score');
             const snpinfo = feature.get('snpinfo');
-            const w = Math.max(rightPx - leftPx + 0.3, 1);
+            const w = Math.max(rightPx - leftPx + fudgeFactor, 1);
             const totalScore = snpinfo.total;
             const keys = Object.keys(snpinfo.cov).sort();
             let curr = 0;
@@ -94,7 +96,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
                         '#888';
                 const height = toHeight(score);
                 const bottom = toY(score) + height;
-                ctx.fillRect(leftPx, bottom - ((total + curr) / score) * height, w, (total / score) * height);
+                ctx.fillRect(Math.round(leftPx), bottom - ((total + curr) / score) * height, w, (total / score) * height);
                 curr += total;
             }
             const interbaseEvents = Object.keys(snpinfo.noncov);
@@ -104,8 +106,9 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
                 for (let i = 0; i < interbaseEvents.length; i++) {
                     const base = interbaseEvents[i];
                     const { total } = snpinfo.noncov[base];
+                    const r = 0.6;
                     ctx.fillStyle = colorForBase[base];
-                    ctx.fillRect(leftPx - 0.6 + extraHorizontallyFlippedOffset, indicatorHeight + indicatorToHeight(curr), 1.2, indicatorToHeight(total));
+                    ctx.fillRect(leftPx - r + extraHorizontallyFlippedOffset, indicatorHeight + toHeight2(curr), r * 2, toHeight2(total));
                     curr += total;
                 }
             }

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map

@@ -1 +1 @@
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package/esm/index.d.ts

@@ -1,11 +1,9 @@
 import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory } from './LinearPileupDisplay';
-import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
-import * as MismatchParser from './MismatchParser';
 export default class AlignmentsPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;
 }
-export { linearPileupDisplayConfigSchemaFactory, linearPileupDisplayStateModelFactory, MismatchParser, };
-export type { LinearPileupDisplayModel };
+export { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, } from './LinearPileupDisplay';
+export { type LinearPileupDisplayModel } from './LinearPileupDisplay/model';
+export * as MismatchParser from './MismatchParser';

package/esm/index.js

@@ -13,8 +13,7 @@ import AlignmentsTrackF from './AlignmentsTrack';
 import AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail';
 import PileupRPCMethodsF from './PileupRPC';
 import GuessAlignmentsTypesF from './GuessAlignmentsTypes';
-import LinearPileupDisplayF, { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, } from './LinearPileupDisplay';
-import * as MismatchParser from './MismatchParser';
+import LinearPileupDisplayF from './LinearPileupDisplay';
 export default class AlignmentsPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -41,5 +40,6 @@ export default class AlignmentsPlugin extends Plugin {
         ].map(f => f(pluginManager));
     }
 }
-export { linearPileupDisplayConfigSchemaFactory, linearPileupDisplayStateModelFactory, MismatchParser, };
+export { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, } from './LinearPileupDisplay';
+export * as MismatchParser from './MismatchParser';
 //# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,WAAW,MAAM,eAAe,CAAA;AACvC,OAAO,YAAY,MAAM,cAAc,CAAA;AACvC,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,mBAAmB,MAAM,sBAAsB,CAAA;AACtD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAC9C,OAAO,wBAAwB,MAAM,2BAA2B,CAAA;AAChE,OAAO,yBAAyB,MAAM,4BAA4B,CAAA;AAClE,OAAO,sBAAsB,MAAM,yBAAyB,CAAA;AAC5D,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,wBAAwB,MAAM,2BAA2B,CAAA;AAChE,OAAO,iBAAiB,MAAM,aAAa,CAAA;AAC3C,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AAExD,MAAM,CAAC,OAAO,OAAO,gBAAiB,SAAQ,MAAM;IAApD;;QACE,SAAI,GAAG,kBAAkB,CAAA;IAqB3B,CAAC;IAnBC,OAAO,CAAC,aAA4B;QAClC,CAAC;QAAA;YACC,YAAY;YACZ,WAAW;YACX,oBAAoB;YACpB,yBAAyB;YACzB,gBAAgB;YAChB,mBAAmB;YACnB,iBAAiB;YACjB,eAAe;YACf,iBAAiB;YACjB,oBAAoB;YACpB,sBAAsB;YACtB,uBAAuB;YACvB,wBAAwB;YACxB,wBAAwB;YACxB,qBAAqB;SACtB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAA;IAC9B,CAAC;CACF;AAED,OAAO,EACL,oCAAoC,EACpC,sCAAsC,GACvC,MAAM,uBAAuB,CAAA;AAE9B,OAAO,KAAK,cAAc,MAAM,kBAAkB,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.4.0",
+  "version": "2.4.1",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -65,5 +65,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "78707a2bc3ba8489f26a590ef83f62ede945d048"
+  "gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
 }

package/src/AlignmentsFeatureDetail/index.test.tsx

@@ -18,7 +18,7 @@ test('open up a widget', () => {
   })
   const session = Session.create(
     {
-      // @ts-ignore
+      // @ts-expect-error
       widget: { type: 'AlignmentsFeatureWidget' },
     },
     { pluginManager },

package/src/BamAdapter/BamAdapter.ts

@@ -151,7 +151,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart)
         const trimLength = trimEnd - trimStart
         const chunkSeq = chunk.get('seq') || chunk.get('residues')
-        sequence += chunkSeq.substr(trimStart, trimLength)
+        sequence += chunkSeq.slice(trimStart, trimStart + trimLength)
       })
 
     if (sequence.length !== end - start) {
@@ -230,7 +230,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
   async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {
     const { bam } = await this.configure()
     // this is a method to avoid calling on htsget adapters
-    // @ts-ignore
+    // @ts-expect-error
     if (bam.index.filehandle !== '?') {
       const bytes = await bytesForRegions(regions, bam)
       const fetchSizeLimit = this.getConf('fetchSizeLimit')