@jbrowse/plugin-alignments 3.0.5 → 3.1.0

package/dist/BamAdapter/configSchema.js

@@ -6,7 +6,10 @@ function x() { }
 const configSchema = (0, configuration_1.ConfigurationSchema)('BamAdapter', {
     bamLocation: {
         type: 'fileLocation',
-        defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
+        defaultValue: {
+            uri: '/path/to/my.bam',
+            locationType: 'UriLocation',
+        },
     },
     index: (0, configuration_1.ConfigurationSchema)('BamIndex', {
         indexType: {
@@ -32,5 +35,24 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('BamAdapter', {
         description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
         defaultValue: null,
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                bamLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+                index: {
+                    location: {
+                        uri: `${snap.uri}.bai`,
+                        baseUri: snap.baseUri,
+                    },
+                },
+            }
+            : snap;
+    },
+});
 exports.default = configSchema;

package/dist/CramAdapter/configSchema.js

@@ -27,5 +27,22 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('CramAdapter', {
         description: 'sequence data adapter',
         defaultValue: null,
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                cramLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+                craiLocation: {
+                    uri: `${snap.uri}.crai`,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 exports.default = configSchema;

package/dist/PileupRenderer/makeImageData.js

@@ -16,8 +16,8 @@ function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
     const hideSmallIndels = (0, configuration_1.readConfObject)(config, 'hideSmallIndels');
     const defaultColor = (0, configuration_1.readConfObject)(config, 'color') === '#f0f';
     const theme = (0, ui_1.createJBrowseTheme)(configTheme);
-    const colorForBase = (0, util_1.getColorBaseMap)(theme);
-    const contrastForBase = (0, util_1.getContrastBaseMap)(theme);
+    const colorMap = (0, util_1.getColorBaseMap)(theme);
+    const colorContrastMap = (0, util_1.getContrastBaseMap)(theme);
     ctx.font = 'bold 10px Courier New,monospace';
     const { charWidth, charHeight } = (0, util_1.getCharWidthHeight)();
     const drawSNPsMuted = (0, util_1.shouldDrawSNPsMuted)(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
@@ -33,8 +33,8 @@ function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
             feat,
             renderArgs,
             defaultColor,
-            colorForBase,
-            contrastForBase,
+            colorMap,
+            colorContrastMap,
             charWidth,
             charHeight,
             canvasWidth,
@@ -51,8 +51,8 @@ function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
             minSubfeatureWidth,
             charWidth,
             charHeight,
-            colorForBase,
-            contrastForBase,
+            colorMap,
+            colorContrastMap,
             canvasWidth,
         });
         if (showSoftClip) {
@@ -60,7 +60,7 @@ function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
                 ctx,
                 feat,
                 renderArgs,
-                colorForBase,
+                colorMap,
                 config,
                 theme,
                 canvasWidth,

package/dist/PileupRenderer/renderAlignment.d.ts

@@ -1,11 +1,11 @@
 import type { ProcessedRenderArgs } from './types';
 import type { LayoutFeature } from './util';
-export declare function renderAlignment({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }: {
+export declare function renderAlignment({ ctx, feat, renderArgs, colorMap, colorContrastMap, charWidth, charHeight, defaultColor, canvasWidth, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
     renderArgs: ProcessedRenderArgs;
-    colorForBase: Record<string, string>;
-    contrastForBase: Record<string, string>;
+    colorMap: Record<string, string>;
+    colorContrastMap: Record<string, string>;
     charWidth: number;
     charHeight: number;
     defaultColor: boolean;

package/dist/PileupRenderer/renderAlignment.js

@@ -8,7 +8,7 @@ const renderPerBaseLettering_1 = require("./renderPerBaseLettering");
 const renderPerBaseQuality_1 = require("./renderPerBaseQuality");
 const MismatchParser_1 = require("../MismatchParser");
 const renderMethylation_1 = require("./renderMethylation");
-function renderAlignment({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }) {
+function renderAlignment({ ctx, feat, renderArgs, colorMap, colorContrastMap, charWidth, charHeight, defaultColor, canvasWidth, }) {
     const { config, bpPerPx, regions, colorBy, colorTagMap = {} } = renderArgs;
     const { tag = '', type: colorType = '' } = colorBy || {};
     const { feature } = feat;
@@ -42,8 +42,8 @@ function renderAlignment({ ctx, feat, renderArgs, colorForBase, contrastForBase,
                 feat,
                 region,
                 bpPerPx,
-                colorForBase,
-                contrastForBase,
+                colorMap,
+                colorContrastMap,
                 charWidth,
                 charHeight,
                 canvasWidth,

package/dist/PileupRenderer/renderMismatches.d.ts

@@ -1,11 +1,11 @@
 import type { ProcessedRenderArgs } from './types';
 import type { LayoutFeature } from './util';
-export declare function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels, }: {
+export declare function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorMap, colorContrastMap, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
     renderArgs: ProcessedRenderArgs;
-    colorForBase: Record<string, string>;
-    contrastForBase: Record<string, string>;
+    colorMap: Record<string, string>;
+    colorContrastMap: Record<string, string>;
     mismatchAlpha?: boolean;
     drawIndels?: boolean;
     drawSNPsMuted?: boolean;

package/dist/PileupRenderer/renderMismatches.js

@@ -4,7 +4,7 @@ exports.renderMismatches = renderMismatches;
 const util_1 = require("@jbrowse/core/util");
 const colord_1 = require("@jbrowse/core/util/colord");
 const util_2 = require("./util");
-function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
+function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorMap, colorContrastMap, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
     const { bpPerPx, regions } = renderArgs;
     const { heightPx, topPx, feature } = feat;
     const region = regions[0];
@@ -24,7 +24,7 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
         const widthPx = Math.max(minSubfeatureWidth, rightPx - leftPx);
         if (mismatch.type === 'mismatch') {
             if (!drawSNPsMuted) {
-                const baseColor = colorForBase[mismatch.base] || '#888';
+                const baseColor = colorMap[mismatch.base] || '#888';
                 const c = mismatchAlpha && mismatch.qual !== undefined
                     ? (0, colord_1.colord)(baseColor)
                         .alpha(Math.min(1, mismatch.qual / 50))
@@ -35,7 +35,7 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
             if (widthPx >= charWidth && heightPx >= heightLim) {
                 const contrastColor = drawSNPsMuted
                     ? 'black'
-                    : contrastForBase[mismatch.base] || 'black';
+                    : colorContrastMap[mismatch.base] || 'black';
                 ctx.fillStyle =
                     mismatchAlpha && mismatch.qual !== undefined
                         ? (0, colord_1.colord)(contrastColor)
@@ -48,11 +48,11 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
         else if (mismatch.type === 'deletion' && drawIndels) {
             const len = mismatch.length;
             if (!hideSmallIndels || len >= 10) {
-                (0, util_2.fillRect)(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorForBase.deletion);
+                (0, util_2.fillRect)(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorMap.deletion);
                 const txt = `${mismatch.length}`;
                 const rwidth = (0, util_1.measureText)(txt, 10);
                 if (widthPx >= rwidth && heightPx >= heightLim) {
-                    ctx.fillStyle = contrastForBase.deletion;
+                    ctx.fillStyle = colorContrastMap.deletion;
                     ctx.fillText(txt, (leftPx + rightPx) / 2 - rwidth / 2, topPx + heightPx);
                 }
             }
@@ -63,7 +63,7 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
             const insW = Math.max(0, Math.min(1.2, 1 / bpPerPx));
             if (len < 10) {
                 if (!hideSmallIndels) {
-                    (0, util_2.fillRect)(ctx, pos, topPx, insW, heightPx, canvasWidth, 'purple');
+                    (0, util_2.fillRect)(ctx, pos, topPx, insW, heightPx, canvasWidth, colorMap.insertion);
                     if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
                         const l = Math.round(pos - insW);
                         (0, util_2.fillRect)(ctx, l, topPx, insW * 3, 1, canvasWidth);
@@ -75,7 +75,7 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
         }
         else if (mismatch.type === 'hardclip' || mismatch.type === 'softclip') {
             const pos = leftPx + extraHorizontallyFlippedOffset;
-            const c = mismatch.type === 'hardclip' ? 'red' : 'blue';
+            const c = colorMap[mismatch.type];
             const clipW = Math.max(minSubfeatureWidth, pxPerBp);
             (0, util_2.fillRect)(ctx, pos, topPx, clipW, heightPx, canvasWidth, c);
             if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
@@ -92,7 +92,7 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
                 const t = topPx + heightPx / 2 - 1;
                 const w = adjustPx + Math.min(leftPx, 0);
                 const h = 1;
-                (0, util_2.fillRect)(ctx, l, t, w, h, canvasWidth, 'rgb(151,184,201)');
+                (0, util_2.fillRect)(ctx, l, t, w, h, canvasWidth, colorMap.skip);
             }
         }
     }
@@ -105,18 +105,18 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
                 const [leftPx] = (0, util_1.bpSpanPx)(mstart, mstart + mlen, region, bpPerPx);
                 const txt = `${len}`;
                 if (bpPerPx > largeInsertionIndicatorScale) {
-                    (0, util_2.fillRect)(ctx, leftPx - 1, topPx, 2, heightPx, canvasWidth, 'purple');
+                    (0, util_2.fillRect)(ctx, leftPx - 1, topPx, 2, heightPx, canvasWidth, colorMap.insertion);
                 }
                 else if (heightPx > charHeight) {
                     const rwidth = (0, util_1.measureText)(txt);
                     const padding = 5;
                     (0, util_2.fillRect)(ctx, leftPx - rwidth / 2 - padding, topPx, rwidth + 2 * padding, heightPx, canvasWidth, 'purple');
-                    ctx.fillStyle = 'white';
+                    ctx.fillStyle = colorContrastMap.insertion;
                     ctx.fillText(txt, leftPx - rwidth / 2, topPx + heightPx);
                 }
                 else {
                     const padding = 2;
-                    (0, util_2.fillRect)(ctx, leftPx - padding, topPx, 2 * padding, heightPx, canvasWidth, 'purple');
+                    (0, util_2.fillRect)(ctx, leftPx - padding, topPx, 2 * padding, heightPx, canvasWidth, colorMap.insertion);
                 }
             }
         }

package/dist/PileupRenderer/renderPerBaseLettering.d.ts

@@ -1,12 +1,12 @@
 import type { LayoutFeature } from './util';
 import type { Region } from '@jbrowse/core/util';
-export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, cigarOps, }: {
+export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorMap, colorContrastMap, charWidth, charHeight, canvasWidth, cigarOps, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
     region: Region;
     bpPerPx: number;
-    colorForBase: Record<string, string>;
-    contrastForBase: Record<string, string>;
+    colorMap: Record<string, string>;
+    colorContrastMap: Record<string, string>;
     charWidth: number;
     charHeight: number;
     canvasWidth: number;

package/dist/PileupRenderer/renderPerBaseLettering.js

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderPerBaseLettering = renderPerBaseLettering;
 const util_1 = require("@jbrowse/core/util");
 const util_2 = require("./util");
-function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, cigarOps, }) {
+function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorMap, colorContrastMap, charWidth, charHeight, canvasWidth, cigarOps, }) {
     const heightLim = charHeight - 2;
     const { feature, topPx, heightPx } = feat;
     const seq = feature.get('seq');
@@ -28,10 +28,10 @@ function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, cont
                 const letter = seq[soffset + m];
                 const r = start + roffset + m;
                 const [leftPx] = (0, util_1.bpSpanPx)(r, r + 1, region, bpPerPx);
-                const c = colorForBase[letter];
+                const c = colorMap[letter];
                 (0, util_2.fillRect)(ctx, leftPx, topPx, w + 0.5, heightPx, canvasWidth, c);
                 if (w >= charWidth && heightPx >= heightLim) {
-                    ctx.fillStyle = contrastForBase[letter];
+                    ctx.fillStyle = colorContrastMap[letter];
                     ctx.fillText(letter, leftPx + (w - charWidth) / 2 + 1, topPx + heightPx);
                 }
             }

package/dist/PileupRenderer/renderSoftClipping.d.ts

@@ -2,12 +2,12 @@ import type { ProcessedRenderArgs } from './types';
 import type { LayoutFeature } from './util';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Theme } from '@mui/material';
-export declare function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase, canvasWidth, }: {
+export declare function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorMap, canvasWidth, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
     renderArgs: ProcessedRenderArgs;
     config: AnyConfigurationModel;
-    colorForBase: Record<string, string>;
+    colorMap: Record<string, string>;
     theme: Theme;
     canvasWidth: number;
 }): void;

package/dist/PileupRenderer/renderSoftClipping.js

@@ -5,7 +5,7 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const util_2 = require("./util");
 const MismatchParser_1 = require("../MismatchParser");
-function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase, canvasWidth, }) {
+function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorMap, canvasWidth, }) {
     const { feature, topPx, heightPx } = feat;
     const { regions, bpPerPx } = renderArgs;
     const region = regions[0];
@@ -30,7 +30,7 @@ function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase
                 const s0 = feature.get('start') - (i === 0 ? len : 0) + refOffset + k;
                 const [leftPx, rightPx] = (0, util_1.bpSpanPx)(s0, s0 + 1, region, bpPerPx);
                 const widthPx = Math.max(minFeatWidth, rightPx - leftPx);
-                const baseColor = colorForBase[base] || '#000000';
+                const baseColor = colorMap[base] || '#000000';
                 ctx.fillStyle = baseColor;
                 (0, util_2.fillRect)(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth);
                 if (widthPx >= charWidth && heightPx >= heightLim) {

package/dist/PileupRenderer/util.d.ts

@@ -7,6 +7,10 @@ export declare function getColorBaseMap(theme: Theme): {
     G: string;
     T: string;
     deletion: string;
+    insertion: string;
+    hardclip: string;
+    softclip: string;
+    skip: string;
 };
 export declare function getContrastBaseMap(theme: Theme): {
     [k: string]: string;

package/dist/PileupRenderer/util.js

@@ -17,13 +17,17 @@ function fillRect(ctx, l, t, w, h, cw, color) {
     ctx.fillRect(l, t, w, h);
 }
 function getColorBaseMap(theme) {
-    const { bases } = theme.palette;
+    const { skip, deletion, insertion, hardclip, softclip, bases } = theme.palette;
     return {
         A: bases.A.main,
         C: bases.C.main,
         G: bases.G.main,
         T: bases.T.main,
-        deletion: '#808080',
+        deletion,
+        insertion,
+        hardclip,
+        softclip,
+        skip,
     };
 }
 function getContrastBaseMap(theme) {

package/dist/SNPCoverageRenderer/makeImage.js

@@ -42,22 +42,22 @@ async function makeImage(ctx, props) {
     const toHeight = (n) => toY(originY) - toY(n);
     const toY2 = (n) => height - (indicatorViewScale(n) || 0) + offset;
     const toHeight2 = (n) => toY2(originLinear) - toY2(n);
-    const { bases } = theme.palette;
-    const colorForBase = {
+    const { bases, softclip, hardclip, insertion } = theme.palette;
+    const colorMap = {
         A: bases.A.main,
         C: bases.C.main,
         G: bases.G.main,
         T: bases.T.main,
-        insertion: 'purple',
-        softclip: 'blue',
-        hardclip: 'red',
+        insertion,
+        softclip,
+        hardclip,
         total: (0, configuration_1.readConfObject)(cfg, 'color'),
         mod_NONE: 'blue',
         cpg_meth: 'red',
         cpg_unmeth: 'blue',
     };
     const feats = [...features.values()];
-    ctx.fillStyle = colorForBase.total;
+    ctx.fillStyle = colorMap.total;
     let start = performance.now();
     for (const feature of feats) {
         if (feature.get('type') === 'skip') {
@@ -167,7 +167,7 @@ async function makeImage(ctx, props) {
                 const { entryDepth } = mods[base];
                 const height = toHeight(score0);
                 const bottom = toY(score0) + height;
-                ctx.fillStyle = colorForBase[base] || 'black';
+                ctx.fillStyle = colorMap[base] || 'black';
                 ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
                 curr += entryDepth;
             }
@@ -175,7 +175,7 @@ async function makeImage(ctx, props) {
                 const { entryDepth } = nonmods[base];
                 const height = toHeight(score0);
                 const bottom = toY(score0) + height;
-                ctx.fillStyle = colorForBase[base] || 'black';
+                ctx.fillStyle = colorMap[base] || 'black';
                 ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
                 curr += entryDepth;
             }
@@ -187,7 +187,7 @@ async function makeImage(ctx, props) {
                 const { entryDepth } = snps[base];
                 const height = toHeight(score0);
                 const bottom = toY(score0) + height;
-                ctx.fillStyle = colorForBase[base] || 'black';
+                ctx.fillStyle = colorMap[base] || 'black';
                 ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
                 curr += entryDepth;
             }
@@ -198,7 +198,7 @@ async function makeImage(ctx, props) {
             for (const base of interbaseEvents) {
                 const { entryDepth } = snpinfo.noncov[base];
                 const r = 0.6;
-                ctx.fillStyle = colorForBase[base];
+                ctx.fillStyle = colorMap[base];
                 ctx.fillRect(leftPx - r + extraHorizontallyFlippedOffset, INTERBASE_INDICATOR_HEIGHT + toHeight2(curr), r * 2, toHeight2(entryDepth));
                 curr += entryDepth;
             }
@@ -218,7 +218,7 @@ async function makeImage(ctx, props) {
             const indicatorComparatorScore = Math.max(score0, prevTotal);
             if (accum > indicatorComparatorScore * indicatorThreshold &&
                 indicatorComparatorScore > MINIMUM_INTERBASE_INDICATOR_READ_DEPTH) {
-                ctx.fillStyle = colorForBase[maxBase];
+                ctx.fillStyle = colorMap[maxBase];
                 ctx.beginPath();
                 const l = leftPx + extraHorizontallyFlippedOffset;
                 ctx.moveTo(l - INTERBASE_INDICATOR_WIDTH / 2, 0);

package/dist/shared/util.js

@@ -18,7 +18,7 @@ function hasPairedReads(features) {
 function alphaColor(baseColor, p) {
     return p !== 1
         ? (0, colord_1.colord)(baseColor)
-            .alpha(p * p)
+            .alpha(Math.min(1, p * p + 0.1))
             .toHslString()
         : baseColor;
 }

package/esm/BamAdapter/configSchema.js

@@ -4,7 +4,10 @@ function x() { }
 const configSchema = ConfigurationSchema('BamAdapter', {
     bamLocation: {
         type: 'fileLocation',
-        defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
+        defaultValue: {
+            uri: '/path/to/my.bam',
+            locationType: 'UriLocation',
+        },
     },
     index: ConfigurationSchema('BamIndex', {
         indexType: {
@@ -30,5 +33,24 @@ const configSchema = ConfigurationSchema('BamAdapter', {
         description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
         defaultValue: null,
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                bamLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+                index: {
+                    location: {
+                        uri: `${snap.uri}.bai`,
+                        baseUri: snap.baseUri,
+                    },
+                },
+            }
+            : snap;
+    },
+});
 export default configSchema;

package/esm/CramAdapter/configSchema.js

@@ -25,5 +25,22 @@ const configSchema = ConfigurationSchema('CramAdapter', {
         description: 'sequence data adapter',
         defaultValue: null,
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                cramLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+                craiLocation: {
+                    uri: `${snap.uri}.crai`,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 export default configSchema;

package/esm/PileupRenderer/makeImageData.js

@@ -13,8 +13,8 @@ export function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, })
     const hideSmallIndels = readConfObject(config, 'hideSmallIndels');
     const defaultColor = readConfObject(config, 'color') === '#f0f';
     const theme = createJBrowseTheme(configTheme);
-    const colorForBase = getColorBaseMap(theme);
-    const contrastForBase = getContrastBaseMap(theme);
+    const colorMap = getColorBaseMap(theme);
+    const colorContrastMap = getContrastBaseMap(theme);
     ctx.font = 'bold 10px Courier New,monospace';
     const { charWidth, charHeight } = getCharWidthHeight();
     const drawSNPsMuted = shouldDrawSNPsMuted(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
@@ -30,8 +30,8 @@ export function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, })
             feat,
             renderArgs,
             defaultColor,
-            colorForBase,
-            contrastForBase,
+            colorMap,
+            colorContrastMap,
             charWidth,
             charHeight,
             canvasWidth,
@@ -48,8 +48,8 @@ export function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, })
             minSubfeatureWidth,
             charWidth,
             charHeight,
-            colorForBase,
-            contrastForBase,
+            colorMap,
+            colorContrastMap,
             canvasWidth,
         });
         if (showSoftClip) {
@@ -57,7 +57,7 @@ export function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, })
                 ctx,
                 feat,
                 renderArgs,
-                colorForBase,
+                colorMap,
                 config,
                 theme,
                 canvasWidth,

package/esm/PileupRenderer/renderAlignment.d.ts

@@ -1,11 +1,11 @@
 import type { ProcessedRenderArgs } from './types';
 import type { LayoutFeature } from './util';
-export declare function renderAlignment({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }: {
+export declare function renderAlignment({ ctx, feat, renderArgs, colorMap, colorContrastMap, charWidth, charHeight, defaultColor, canvasWidth, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
     renderArgs: ProcessedRenderArgs;
-    colorForBase: Record<string, string>;
-    contrastForBase: Record<string, string>;
+    colorMap: Record<string, string>;
+    colorContrastMap: Record<string, string>;
     charWidth: number;
     charHeight: number;
     defaultColor: boolean;

package/esm/PileupRenderer/renderAlignment.js

@@ -5,7 +5,7 @@ import { renderPerBaseLettering } from './renderPerBaseLettering';
 import { renderPerBaseQuality } from './renderPerBaseQuality';
 import { parseCigar } from '../MismatchParser';
 import { renderMethylation } from './renderMethylation';
-export function renderAlignment({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }) {
+export function renderAlignment({ ctx, feat, renderArgs, colorMap, colorContrastMap, charWidth, charHeight, defaultColor, canvasWidth, }) {
     const { config, bpPerPx, regions, colorBy, colorTagMap = {} } = renderArgs;
     const { tag = '', type: colorType = '' } = colorBy || {};
     const { feature } = feat;
@@ -39,8 +39,8 @@ export function renderAlignment({ ctx, feat, renderArgs, colorForBase, contrastF
                 feat,
                 region,
                 bpPerPx,
-                colorForBase,
-                contrastForBase,
+                colorMap,
+                colorContrastMap,
                 charWidth,
                 charHeight,
                 canvasWidth,

package/esm/PileupRenderer/renderMismatches.d.ts

@@ -1,11 +1,11 @@
 import type { ProcessedRenderArgs } from './types';
 import type { LayoutFeature } from './util';
-export declare function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels, }: {
+export declare function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorMap, colorContrastMap, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
     renderArgs: ProcessedRenderArgs;
-    colorForBase: Record<string, string>;
-    contrastForBase: Record<string, string>;
+    colorMap: Record<string, string>;
+    colorContrastMap: Record<string, string>;
     mismatchAlpha?: boolean;
     drawIndels?: boolean;
     drawSNPsMuted?: boolean;

package/esm/PileupRenderer/renderMismatches.js

@@ -1,7 +1,7 @@
 import { bpSpanPx, measureText } from '@jbrowse/core/util';
 import { colord } from '@jbrowse/core/util/colord';
 import { fillRect } from './util';
-export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
+export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorMap, colorContrastMap, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
     const { bpPerPx, regions } = renderArgs;
     const { heightPx, topPx, feature } = feat;
     const region = regions[0];
@@ -21,7 +21,7 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
         const widthPx = Math.max(minSubfeatureWidth, rightPx - leftPx);
         if (mismatch.type === 'mismatch') {
             if (!drawSNPsMuted) {
-                const baseColor = colorForBase[mismatch.base] || '#888';
+                const baseColor = colorMap[mismatch.base] || '#888';
                 const c = mismatchAlpha && mismatch.qual !== undefined
                     ? colord(baseColor)
                         .alpha(Math.min(1, mismatch.qual / 50))
@@ -32,7 +32,7 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
             if (widthPx >= charWidth && heightPx >= heightLim) {
                 const contrastColor = drawSNPsMuted
                     ? 'black'
-                    : contrastForBase[mismatch.base] || 'black';
+                    : colorContrastMap[mismatch.base] || 'black';
                 ctx.fillStyle =
                     mismatchAlpha && mismatch.qual !== undefined
                         ? colord(contrastColor)
@@ -45,11 +45,11 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
         else if (mismatch.type === 'deletion' && drawIndels) {
             const len = mismatch.length;
             if (!hideSmallIndels || len >= 10) {
-                fillRect(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorForBase.deletion);
+                fillRect(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorMap.deletion);
                 const txt = `${mismatch.length}`;
                 const rwidth = measureText(txt, 10);
                 if (widthPx >= rwidth && heightPx >= heightLim) {
-                    ctx.fillStyle = contrastForBase.deletion;
+                    ctx.fillStyle = colorContrastMap.deletion;
                     ctx.fillText(txt, (leftPx + rightPx) / 2 - rwidth / 2, topPx + heightPx);
                 }
             }
@@ -60,7 +60,7 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
             const insW = Math.max(0, Math.min(1.2, 1 / bpPerPx));
             if (len < 10) {
                 if (!hideSmallIndels) {
-                    fillRect(ctx, pos, topPx, insW, heightPx, canvasWidth, 'purple');
+                    fillRect(ctx, pos, topPx, insW, heightPx, canvasWidth, colorMap.insertion);
                     if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
                         const l = Math.round(pos - insW);
                         fillRect(ctx, l, topPx, insW * 3, 1, canvasWidth);
@@ -72,7 +72,7 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
         }
         else if (mismatch.type === 'hardclip' || mismatch.type === 'softclip') {
             const pos = leftPx + extraHorizontallyFlippedOffset;
-            const c = mismatch.type === 'hardclip' ? 'red' : 'blue';
+            const c = colorMap[mismatch.type];
             const clipW = Math.max(minSubfeatureWidth, pxPerBp);
             fillRect(ctx, pos, topPx, clipW, heightPx, canvasWidth, c);
             if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
@@ -89,7 +89,7 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
                 const t = topPx + heightPx / 2 - 1;
                 const w = adjustPx + Math.min(leftPx, 0);
                 const h = 1;
-                fillRect(ctx, l, t, w, h, canvasWidth, 'rgb(151,184,201)');
+                fillRect(ctx, l, t, w, h, canvasWidth, colorMap.skip);
             }
         }
     }
@@ -102,18 +102,18 @@ export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, la
                 const [leftPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx);
                 const txt = `${len}`;
                 if (bpPerPx > largeInsertionIndicatorScale) {
-                    fillRect(ctx, leftPx - 1, topPx, 2, heightPx, canvasWidth, 'purple');
+                    fillRect(ctx, leftPx - 1, topPx, 2, heightPx, canvasWidth, colorMap.insertion);
                 }
                 else if (heightPx > charHeight) {
                     const rwidth = measureText(txt);
                     const padding = 5;
                     fillRect(ctx, leftPx - rwidth / 2 - padding, topPx, rwidth + 2 * padding, heightPx, canvasWidth, 'purple');
-                    ctx.fillStyle = 'white';
+                    ctx.fillStyle = colorContrastMap.insertion;
                     ctx.fillText(txt, leftPx - rwidth / 2, topPx + heightPx);
                 }
                 else {
                     const padding = 2;
-                    fillRect(ctx, leftPx - padding, topPx, 2 * padding, heightPx, canvasWidth, 'purple');
+                    fillRect(ctx, leftPx - padding, topPx, 2 * padding, heightPx, canvasWidth, colorMap.insertion);
                 }
             }
         }

package/esm/PileupRenderer/renderPerBaseLettering.d.ts

@@ -1,12 +1,12 @@
 import type { LayoutFeature } from './util';
 import type { Region } from '@jbrowse/core/util';
-export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, cigarOps, }: {
+export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorMap, colorContrastMap, charWidth, charHeight, canvasWidth, cigarOps, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
     region: Region;
     bpPerPx: number;
-    colorForBase: Record<string, string>;
-    contrastForBase: Record<string, string>;
+    colorMap: Record<string, string>;
+    colorContrastMap: Record<string, string>;
     charWidth: number;
     charHeight: number;
     canvasWidth: number;

package/esm/PileupRenderer/renderPerBaseLettering.js

@@ -1,6 +1,6 @@
 import { bpSpanPx } from '@jbrowse/core/util';
 import { fillRect } from './util';
-export function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, cigarOps, }) {
+export function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorMap, colorContrastMap, charWidth, charHeight, canvasWidth, cigarOps, }) {
     const heightLim = charHeight - 2;
     const { feature, topPx, heightPx } = feat;
     const seq = feature.get('seq');
@@ -25,10 +25,10 @@ export function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBas
                 const letter = seq[soffset + m];
                 const r = start + roffset + m;
                 const [leftPx] = bpSpanPx(r, r + 1, region, bpPerPx);
-                const c = colorForBase[letter];
+                const c = colorMap[letter];
                 fillRect(ctx, leftPx, topPx, w + 0.5, heightPx, canvasWidth, c);
                 if (w >= charWidth && heightPx >= heightLim) {
-                    ctx.fillStyle = contrastForBase[letter];
+                    ctx.fillStyle = colorContrastMap[letter];
                     ctx.fillText(letter, leftPx + (w - charWidth) / 2 + 1, topPx + heightPx);
                 }
             }

package/esm/PileupRenderer/renderSoftClipping.d.ts

@@ -2,12 +2,12 @@ import type { ProcessedRenderArgs } from './types';
 import type { LayoutFeature } from './util';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Theme } from '@mui/material';
-export declare function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase, canvasWidth, }: {
+export declare function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorMap, canvasWidth, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
     renderArgs: ProcessedRenderArgs;
     config: AnyConfigurationModel;
-    colorForBase: Record<string, string>;
+    colorMap: Record<string, string>;
     theme: Theme;
     canvasWidth: number;
 }): void;

package/esm/PileupRenderer/renderSoftClipping.js

@@ -2,7 +2,7 @@ import { readConfObject } from '@jbrowse/core/configuration';
 import { bpSpanPx } from '@jbrowse/core/util';
 import { fillRect, getCharWidthHeight } from './util';
 import { parseCigar } from '../MismatchParser';
-export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase, canvasWidth, }) {
+export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorMap, canvasWidth, }) {
     const { feature, topPx, heightPx } = feat;
     const { regions, bpPerPx } = renderArgs;
     const region = regions[0];
@@ -27,7 +27,7 @@ export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, color
                 const s0 = feature.get('start') - (i === 0 ? len : 0) + refOffset + k;
                 const [leftPx, rightPx] = bpSpanPx(s0, s0 + 1, region, bpPerPx);
                 const widthPx = Math.max(minFeatWidth, rightPx - leftPx);
-                const baseColor = colorForBase[base] || '#000000';
+                const baseColor = colorMap[base] || '#000000';
                 ctx.fillStyle = baseColor;
                 fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth);
                 if (widthPx >= charWidth && heightPx >= heightLim) {

package/esm/PileupRenderer/util.d.ts

@@ -7,6 +7,10 @@ export declare function getColorBaseMap(theme: Theme): {
     G: string;
     T: string;
     deletion: string;
+    insertion: string;
+    hardclip: string;
+    softclip: string;
+    skip: string;
 };
 export declare function getContrastBaseMap(theme: Theme): {
     [k: string]: string;

package/esm/PileupRenderer/util.js

@@ -9,13 +9,17 @@ export function fillRect(ctx, l, t, w, h, cw, color) {
     ctx.fillRect(l, t, w, h);
 }
 export function getColorBaseMap(theme) {
-    const { bases } = theme.palette;
+    const { skip, deletion, insertion, hardclip, softclip, bases } = theme.palette;
     return {
         A: bases.A.main,
         C: bases.C.main,
         G: bases.G.main,
         T: bases.T.main,
-        deletion: '#808080',
+        deletion,
+        insertion,
+        hardclip,
+        softclip,
+        skip,
     };
 }
 export function getContrastBaseMap(theme) {

package/esm/SNPCoverageRenderer/makeImage.js

@@ -39,22 +39,22 @@ export async function makeImage(ctx, props) {
     const toHeight = (n) => toY(originY) - toY(n);
     const toY2 = (n) => height - (indicatorViewScale(n) || 0) + offset;
     const toHeight2 = (n) => toY2(originLinear) - toY2(n);
-    const { bases } = theme.palette;
-    const colorForBase = {
+    const { bases, softclip, hardclip, insertion } = theme.palette;
+    const colorMap = {
         A: bases.A.main,
         C: bases.C.main,
         G: bases.G.main,
         T: bases.T.main,
-        insertion: 'purple',
-        softclip: 'blue',
-        hardclip: 'red',
+        insertion,
+        softclip,
+        hardclip,
         total: readConfObject(cfg, 'color'),
         mod_NONE: 'blue',
         cpg_meth: 'red',
         cpg_unmeth: 'blue',
     };
     const feats = [...features.values()];
-    ctx.fillStyle = colorForBase.total;
+    ctx.fillStyle = colorMap.total;
     let start = performance.now();
     for (const feature of feats) {
         if (feature.get('type') === 'skip') {
@@ -164,7 +164,7 @@ export async function makeImage(ctx, props) {
                 const { entryDepth } = mods[base];
                 const height = toHeight(score0);
                 const bottom = toY(score0) + height;
-                ctx.fillStyle = colorForBase[base] || 'black';
+                ctx.fillStyle = colorMap[base] || 'black';
                 ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
                 curr += entryDepth;
             }
@@ -172,7 +172,7 @@ export async function makeImage(ctx, props) {
                 const { entryDepth } = nonmods[base];
                 const height = toHeight(score0);
                 const bottom = toY(score0) + height;
-                ctx.fillStyle = colorForBase[base] || 'black';
+                ctx.fillStyle = colorMap[base] || 'black';
                 ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
                 curr += entryDepth;
             }
@@ -184,7 +184,7 @@ export async function makeImage(ctx, props) {
                 const { entryDepth } = snps[base];
                 const height = toHeight(score0);
                 const bottom = toY(score0) + height;
-                ctx.fillStyle = colorForBase[base] || 'black';
+                ctx.fillStyle = colorMap[base] || 'black';
                 ctx.fillRect(Math.round(leftPx), bottom - ((entryDepth + curr) / depth) * height, w, (entryDepth / depth) * height);
                 curr += entryDepth;
             }
@@ -195,7 +195,7 @@ export async function makeImage(ctx, props) {
             for (const base of interbaseEvents) {
                 const { entryDepth } = snpinfo.noncov[base];
                 const r = 0.6;
-                ctx.fillStyle = colorForBase[base];
+                ctx.fillStyle = colorMap[base];
                 ctx.fillRect(leftPx - r + extraHorizontallyFlippedOffset, INTERBASE_INDICATOR_HEIGHT + toHeight2(curr), r * 2, toHeight2(entryDepth));
                 curr += entryDepth;
             }
@@ -215,7 +215,7 @@ export async function makeImage(ctx, props) {
             const indicatorComparatorScore = Math.max(score0, prevTotal);
             if (accum > indicatorComparatorScore * indicatorThreshold &&
                 indicatorComparatorScore > MINIMUM_INTERBASE_INDICATOR_READ_DEPTH) {
-                ctx.fillStyle = colorForBase[maxBase];
+                ctx.fillStyle = colorMap[maxBase];
                 ctx.beginPath();
                 const l = leftPx + extraHorizontallyFlippedOffset;
                 ctx.moveTo(l - INTERBASE_INDICATOR_WIDTH / 2, 0);

package/esm/shared/util.js

@@ -10,7 +10,7 @@ export function hasPairedReads(features) {
 export function alphaColor(baseColor, p) {
     return p !== 1
         ? colord(baseColor)
-            .alpha(p * p)
+            .alpha(Math.min(1, p * p + 0.1))
             .toHslString()
         : baseColor;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "3.0.5",
+  "version": "3.1.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,10 +38,10 @@
   "dependencies": {
     "@gmod/bam": "^5.0.0",
     "@gmod/cram": "^4.0.1",
-    "@jbrowse/core": "^3.0.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.0.5",
-    "@jbrowse/plugin-wiggle": "^3.0.5",
-    "@jbrowse/sv-core": "^3.0.5",
+    "@jbrowse/core": "^3.1.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.1.0",
+    "@jbrowse/plugin-wiggle": "^3.1.0",
+    "@jbrowse/sv-core": "^3.1.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "canvas2svg": "^1.0.16",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "a03749efe19e51609922272b845a331897346789"
+  "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
 }