@jbrowse/plugin-alignments 2.3.4 → 2.4.1

package/dist/PileupRenderer/PileupRenderer.js

@@ -59,10 +59,8 @@ function getColorBaseMap(theme) {
     };
 }
 function getContrastBaseMap(theme) {
-    return Object.fromEntries(Object.entries(getColorBaseMap(theme)).map(([key, value]) => [
-        key,
-        theme.palette.getContrastText(value),
-    ]));
+    const map = getColorBaseMap(theme);
+    return Object.fromEntries(Object.entries(map).map(([k, v]) => [k, theme.palette.getContrastText(v)]));
 }
 const alignmentColoring = {
     color_fwd_strand_not_proper: '#ECC8C8',
@@ -118,14 +116,16 @@ class PileupRenderer extends BoxRendererType_1.default {
                 }
             }
         }
-        const [leftPx, rightPx] = (0, util_1.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] = (0, util_1.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;
         }
@@ -291,10 +291,9 @@ class PileupRenderer extends BoxRendererType_1.default {
         const modifications = (0, MismatchParser_1.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 (0, MismatchParser_1.getNextRefPos)(cigarOps, positions)) {
                 const r = start + readPos;
@@ -401,7 +400,7 @@ class PileupRenderer extends BoxRendererType_1.default {
             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;
@@ -456,30 +455,23 @@ class PileupRenderer extends BoxRendererType_1.default {
                 }
                 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 = (0, configuration_1.readConfObject)(config, 'color', { feature });
-                }
+            }
+            default: {
+                ctx.fillStyle = defaultColor
+                    ? 'lightgrey'
+                    : (0, configuration_1.readConfObject)(config, 'color', { feature });
                 break;
+            }
         }
         this.drawRect(ctx, feat, renderArgs);
         // second pass for color types that render per-base things that go over the
@@ -529,7 +521,7 @@ class PileupRenderer extends BoxRendererType_1.default {
                 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;
@@ -558,30 +550,30 @@ class PileupRenderer extends BoxRendererType_1.default {
             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);
                 }
             }
@@ -738,6 +730,7 @@ class PileupRenderer extends BoxRendererType_1.default {
                 charWidth,
                 charHeight,
                 canvasWidth,
+                theme,
             });
             this.drawMismatches({
                 ctx,
@@ -753,6 +746,7 @@ class PileupRenderer extends BoxRendererType_1.default {
                 colorForBase,
                 contrastForBase,
                 canvasWidth,
+                theme,
             });
             if (showSoftClip) {
                 this.drawSoftClipping({

package/dist/PileupRenderer/PileupRenderer.js.map

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package/dist/PileupRenderer/components/PileupRendering.js

@@ -138,10 +138,10 @@ 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/dist/PileupRenderer/components/PileupRendering.js.map

@@ -1 +1 @@
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package/dist/PileupRenderer/configSchema.js

@@ -45,7 +45,7 @@ const PileupRenderer = (0, configuration_1.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/dist/PileupRenderer/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,qDAAuC;AAEvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,cAAc,GAAG,IAAA,mCAAmB,EACxC,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,uBAAK,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,uBAAK,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,kBAAe,cAAc,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,qDAAuC;AAEvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,cAAc,GAAG,IAAA,mCAAmB,EACxC,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,uBAAK,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,uBAAK,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,kBAAe,cAAc,CAAA"}

package/dist/PileupRenderer/sortUtil.js

@@ -62,7 +62,7 @@ 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));
@@ -75,9 +75,10 @@ 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;
 };
 exports.sortFeature = sortFeature;

package/dist/PileupRenderer/sortUtil.js.map

@@ -1 +1 @@
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+{"version":3,"file":"sortUtil.js","sourceRoot":"","sources":["../../src/PileupRenderer/sortUtil.ts"],"names":[],"mappings":";;;AAAA,6CAA4D;AAQrD,MAAM,WAAW,GAAG,CACzB,QAA8B,EAC9B,QAAoB,EACpB,EAAE;IACF,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;IAClD,MAAM,oBAAoB,GAAc,EAAE,CAAA;IAC1C,MAAM,qBAAqB,GAAc,EAAE,CAAA;IAC3C,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,QAAQ,CAAA;IAE9B,mFAAmF;IACnF,YAAY,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE;QAChC,MAAM,OAAO,GAAG,UAAU,CAAA;QAC1B,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAClC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC9B,IAAI,IAAA,qBAAc,EAAC,GAAG,GAAG,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,CAAC,EAAE;YAC5C,oBAAoB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;SACtC;aAAM;YACL,qBAAqB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;SACvC;IACH,CAAC,CAAC,CAAA;IAEF,MAAM,MAAM,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;IACxE,QAAQ,IAAI,EAAE;QACZ,KAAK,gBAAgB,CAAC,CAAC;YACrB,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;YACpE,MAAK;SACN;QAED,KAAK,KAAK,CAAC,CAAC;YACV,MAAM,GAAG,GAAG,QAAQ,CAAC,GAAa,CAAA;YAClC,MAAM,MAAM,GAAG,CAAC,CAAU,EAAE,CAAS,EAAE,EAAE;gBACvC,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAC7C,CAAC,CAAA;YACD,MAAM,QAAQ,GACZ,oBAAoB,CAAC,CAAC,CAAC;gBACvB,OAAO,MAAM,CAAC,oBAAoB,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,QAAQ,CAAA;YAC1D,IAAI,QAAQ,EAAE;gBACZ,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACjC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAC7C,CAAA;aACF;iBAAM;gBACL,oBAAoB,CAAC,IAAI,CACvB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC,CACxD,CAAA;aACF;YACD,MAAK;SACN;QAED,iEAAiE;QACjE,KAAK,WAAW,CAAC,CAAC;YAChB,MAAM,aAAa,GAAyB,EAAE,CAAA;YAC9C,oBAAoB,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE;gBACrC,MAAM,UAAU,GAAe,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;gBACxD,UAAU,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE;oBAC5B,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;oBAClC,MAAM,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,KAAK,GAAG,CAAC,CAAA;oBACzC,MAAM,SAAS,GACb,QAAQ,CAAC,IAAI,KAAK,WAAW,IAAI,QAAQ,CAAC,IAAI,KAAK,UAAU,CAAA;oBAC/D,MAAM,GAAG,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAA;oBAC3C,IAAI,GAAG,IAAI,MAAM,IAAI,GAAG,GAAG,MAAM,GAAG,GAAG,EAAE;wBACvC,aAAa,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,QAAQ,CAAC,CAAC,CAAA;qBAC7C;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YAEF,MAAM,OAAO,GAAG,IAAI,GAAG,CAAC,aAAa,CAAC,CAAA;YACtC,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;gBACjC,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;gBACrC,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;gBACrC,MAAM,KAAK,GAAG,SAAS,IAAI,SAAS,CAAC,IAAI,CAAC,WAAW,EAAE,CAAA;gBACvD,MAAM,KAAK,GAAG,SAAS,IAAI,SAAS,CAAC,IAAI,CAAC,WAAW,EAAE,CAAA;gBACvD,IAAI,KAAK,KAAK,KAAK,IAAI,KAAK,KAAK,GAAG,EAAE;oBACpC,mBAAmB;oBACnB,OAAO,SAAS,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;iBAC3C;gBACD,OAAO,CACL,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACtE,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,MAAK;SACN;QAED,+CAA+C;QAC/C,KAAK,aAAa,CAAC,CAAC;YAClB,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACjC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC5C,CAAA;YACD,MAAK;SACN;KACF;IAED,MAAM,SAAS,GAAG,IAAI,GAAG,CACvB,CAAC,GAAG,oBAAoB,EAAE,GAAG,qBAAqB,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC;QACjE,OAAO,CAAC,EAAE,EAAE;QACZ,OAAO;KACR,CAAC,CACH,CAAA;IAED,OAAO,SAAS,CAAA;AAClB,CAAC,CAAA;AApGY,QAAA,WAAW,eAoGvB"}

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -4,6 +4,7 @@ const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+const fudgeFactor = 0.6;
 class SNPCoverageRenderer extends plugin_wiggle_1.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
@@ -30,6 +31,7 @@ class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
             scaleType: 'linear',
         });
         const originY = (0, plugin_wiggle_1.getOrigin)(scaleOpts.scaleType);
+        const originLinear = (0, plugin_wiggle_1.getOrigin)('linear');
         const indicatorThreshold = (0, configuration_1.readConfObject)(cfg, 'indicatorThreshold');
         const drawInterbaseCounts = (0, configuration_1.readConfObject)(cfg, 'drawInterbaseCounts');
         const drawArcs = (0, configuration_1.readConfObject)(cfg, 'drawArcs');
@@ -37,8 +39,9 @@ class SNPCoverageRenderer extends plugin_wiggle_1.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((0, plugin_wiggle_1.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,
@@ -51,7 +54,6 @@ class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
             hardclip: 'red',
             meth: 'red',
             unmeth: 'blue',
-            ref: 'lightgrey',
         };
         const feats = [...features.values()];
         const coverage = feats.filter(f => f.get('type') !== 'skip');
@@ -62,7 +64,7 @@ class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
         for (let i = 0; i < coverage.length; i++) {
             const feature = coverage[i];
             const [leftPx, rightPx] = (0, util_1.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));
         }
@@ -83,7 +85,7 @@ class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
             const [leftPx, rightPx] = (0, util_1.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;
@@ -96,7 +98,7 @@ class SNPCoverageRenderer extends plugin_wiggle_1.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);
@@ -106,8 +108,9 @@ class SNPCoverageRenderer extends plugin_wiggle_1.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/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map

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

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MismatchParser = exports.linearPileupDisplayStateModelFactory = exports.linearPileupDisplayConfigSchemaFactory = void 0;
+exports.MismatchParser = exports.linearPileupDisplayConfigSchemaFactory = exports.linearPileupDisplayStateModelFactory = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const CramAdapter_1 = __importDefault(require("./CramAdapter"));
 const BamAdapter_1 = __importDefault(require("./BamAdapter"));
@@ -42,11 +42,7 @@ const AlignmentsTrack_1 = __importDefault(require("./AlignmentsTrack"));
 const AlignmentsFeatureDetail_1 = __importDefault(require("./AlignmentsFeatureDetail"));
 const PileupRPC_1 = __importDefault(require("./PileupRPC"));
 const GuessAlignmentsTypes_1 = __importDefault(require("./GuessAlignmentsTypes"));
-const LinearPileupDisplay_1 = __importStar(require("./LinearPileupDisplay"));
-Object.defineProperty(exports, "linearPileupDisplayStateModelFactory", { enumerable: true, get: function () { return LinearPileupDisplay_1.linearPileupDisplayStateModelFactory; } });
-Object.defineProperty(exports, "linearPileupDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearPileupDisplay_1.linearPileupDisplayConfigSchemaFactory; } });
-const MismatchParser = __importStar(require("./MismatchParser"));
-exports.MismatchParser = MismatchParser;
+const LinearPileupDisplay_1 = __importDefault(require("./LinearPileupDisplay"));
 class AlignmentsPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -74,4 +70,8 @@ class AlignmentsPlugin extends Plugin_1.default {
     }
 }
 exports.default = AlignmentsPlugin;
+var LinearPileupDisplay_2 = require("./LinearPileupDisplay");
+Object.defineProperty(exports, "linearPileupDisplayStateModelFactory", { enumerable: true, get: function () { return LinearPileupDisplay_2.linearPileupDisplayStateModelFactory; } });
+Object.defineProperty(exports, "linearPileupDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearPileupDisplay_2.linearPileupDisplayConfigSchemaFactory; } });
+exports.MismatchParser = __importStar(require("./MismatchParser"));
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kEAAyC;AAEzC,gEAAuC;AACvC,8DAAuC;AACvC,0EAAkD;AAClD,8EAAsD;AACtD,gFAAwD;AACxD,sEAA8C;AAC9C,wFAAgE;AAChE,0FAAkE;AAClE,oFAA4D;AAC5D,sFAA8D;AAC9D,wEAAgD;AAChD,wFAAgE;AAChE,4DAA2C;AAC3C,kFAA0D;AAC1D,gFAAwD;AAExD,MAAqB,gBAAiB,SAAQ,gBAAM;IAApD;;QACE,SAAI,GAAG,kBAAkB,CAAA;IAqB3B,CAAC;IAnBC,OAAO,CAAC,aAA4B;QAClC,CAAC;QAAA;YACC,oBAAY;YACZ,qBAAW;YACX,6BAAoB;YACpB,kCAAyB;YACzB,yBAAgB;YAChB,4BAAmB;YACnB,0BAAiB;YACjB,wBAAe;YACf,mBAAiB;YACjB,6BAAoB;YACpB,+BAAsB;YACtB,gCAAuB;YACvB,iCAAwB;YACxB,iCAAwB;YACxB,8BAAqB;SACtB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAA;IAC9B,CAAC;CACF;AAtBD,mCAsBC;AAED,6DAG8B;AAF5B,2IAAA,oCAAoC,OAAA;AACpC,6IAAA,sCAAsC,OAAA;AAGxC,mEAAkD"}

package/esm/BamAdapter/BamAdapter.js

@@ -116,7 +116,7 @@ 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) {
             throw new Error(`sequence fetch failed: fetching ${refName}:${(start - 1).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(end - start).toLocaleString()}`);
@@ -159,7 +159,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     async estimateRegionsStats(regions, opts) {
         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');