npm - @jbrowse/plugin-alignments - Versions diffs - 2.4.0 → 2.4.2 - Mend

@jbrowse/plugin-alignments 2.4.0 → 2.4.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (145) hide show

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +4 -4
package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +88 -126
package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts +6 -0
package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js +44 -0
package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map +1 -0
package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts +6 -0
package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js +37 -0
package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js.map +1 -0
package/dist/AlignmentsFeatureDetail/index.d.ts +1 -1
package/dist/AlignmentsFeatureDetail/util.d.ts +8 -0
package/dist/AlignmentsFeatureDetail/util.js +27 -0
package/dist/AlignmentsFeatureDetail/util.js.map +1 -0
package/dist/BamAdapter/BamAdapter.js +2 -2
package/dist/BamAdapter/BamAdapter.js.map +1 -1
package/dist/BamAdapter/BamSlightlyLazyFeature.js +2 -2
package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
package/dist/CramAdapter/CramAdapter.js +2 -2
package/dist/CramAdapter/CramAdapter.js.map +1 -1
package/dist/CramAdapter/CramSlightlyLazyFeature.js +2 -2
package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
package/dist/CramAdapter/util.js +10 -10
package/dist/CramAdapter/util.js.map +1 -1
package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +4 -4
package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
package/dist/LinearAlignmentsDisplay/models/model.d.ts +2 -4
package/dist/LinearAlignmentsDisplay/models/model.js +3 -4
package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
package/dist/LinearPileupDisplay/index.d.ts +2 -3
package/dist/LinearPileupDisplay/index.js +4 -2
package/dist/LinearPileupDisplay/index.js.map +1 -1
package/dist/LinearPileupDisplay/model.d.ts +30 -31
package/dist/LinearPileupDisplay/model.js +4 -4
package/dist/LinearPileupDisplay/model.js.map +1 -1
package/dist/LinearReadArcsDisplay/model.d.ts +13 -21
package/dist/LinearReadCloudDisplay/model.d.ts +13 -21
package/dist/LinearSNPCoverageDisplay/models/model.d.ts +22 -24
package/dist/MismatchParser/index.js +6 -8
package/dist/MismatchParser/index.js.map +1 -1
package/dist/PileupRPC/rpcMethods.d.ts +3 -4
package/dist/PileupRPC/rpcMethods.js +6 -6
package/dist/PileupRPC/rpcMethods.js.map +1 -1
package/dist/PileupRenderer/PileupRenderer.d.ts +5 -3
package/dist/PileupRenderer/PileupRenderer.js +29 -33
package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
package/dist/PileupRenderer/components/PileupRendering.js +2 -2
package/dist/PileupRenderer/components/PileupRendering.js.map +1 -1
package/dist/PileupRenderer/configSchema.js +1 -1
package/dist/PileupRenderer/configSchema.js.map +1 -1
package/dist/PileupRenderer/sortUtil.js +5 -4
package/dist/PileupRenderer/sortUtil.js.map +1 -1
package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
package/dist/index.d.ts +3 -5
package/dist/index.js +6 -6
package/dist/index.js.map +1 -1
package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +4 -4
package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +88 -126
package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts +6 -0
package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js +38 -0
package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map +1 -0
package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts +6 -0
package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js +31 -0
package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js.map +1 -0
package/esm/AlignmentsFeatureDetail/index.d.ts +1 -1
package/esm/AlignmentsFeatureDetail/util.d.ts +8 -0
package/esm/AlignmentsFeatureDetail/util.js +22 -0
package/esm/AlignmentsFeatureDetail/util.js.map +1 -0
package/esm/BamAdapter/BamAdapter.js +2 -2
package/esm/BamAdapter/BamAdapter.js.map +1 -1
package/esm/BamAdapter/BamSlightlyLazyFeature.js +2 -2
package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
package/esm/CramAdapter/CramAdapter.js +2 -2
package/esm/CramAdapter/CramAdapter.js.map +1 -1
package/esm/CramAdapter/CramSlightlyLazyFeature.js +2 -2
package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
package/esm/CramAdapter/util.js +10 -10
package/esm/CramAdapter/util.js.map +1 -1
package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +4 -4
package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
package/esm/LinearAlignmentsDisplay/models/model.d.ts +2 -4
package/esm/LinearAlignmentsDisplay/models/model.js +3 -4
package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
package/esm/LinearPileupDisplay/index.d.ts +2 -3
package/esm/LinearPileupDisplay/index.js +2 -1
package/esm/LinearPileupDisplay/index.js.map +1 -1
package/esm/LinearPileupDisplay/model.d.ts +30 -31
package/esm/LinearPileupDisplay/model.js +4 -4
package/esm/LinearPileupDisplay/model.js.map +1 -1
package/esm/LinearReadArcsDisplay/model.d.ts +13 -21
package/esm/LinearReadCloudDisplay/model.d.ts +13 -21
package/esm/LinearSNPCoverageDisplay/models/model.d.ts +22 -24
package/esm/MismatchParser/index.js +6 -8
package/esm/MismatchParser/index.js.map +1 -1
package/esm/PileupRPC/rpcMethods.d.ts +3 -4
package/esm/PileupRPC/rpcMethods.js +3 -4
package/esm/PileupRPC/rpcMethods.js.map +1 -1
package/esm/PileupRenderer/PileupRenderer.d.ts +5 -3
package/esm/PileupRenderer/PileupRenderer.js +29 -33
package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
package/esm/PileupRenderer/components/PileupRendering.js +2 -2
package/esm/PileupRenderer/components/PileupRendering.js.map +1 -1
package/esm/PileupRenderer/configSchema.js +1 -1
package/esm/PileupRenderer/configSchema.js.map +1 -1
package/esm/PileupRenderer/sortUtil.js +5 -4
package/esm/PileupRenderer/sortUtil.js.map +1 -1
package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
package/esm/index.d.ts +3 -5
package/esm/index.js +3 -3
package/esm/index.js.map +1 -1
package/package.json +2 -2
package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +109 -183
package/src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx +62 -0
package/src/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.tsx +51 -0
package/src/AlignmentsFeatureDetail/__snapshots__/index.test.tsx.snap +3 -2
package/src/AlignmentsFeatureDetail/index.test.tsx +1 -1
package/src/AlignmentsFeatureDetail/util.ts +27 -0
package/src/BamAdapter/BamAdapter.ts +2 -2
package/src/BamAdapter/BamSlightlyLazyFeature.ts +2 -2
package/src/CramAdapter/CramAdapter.ts +2 -2
package/src/CramAdapter/CramSlightlyLazyFeature.ts +2 -2
package/src/CramAdapter/util.ts +10 -10
package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +4 -4
package/src/LinearAlignmentsDisplay/models/configSchema.test.ts +1 -1
package/src/LinearAlignmentsDisplay/models/model.tsx +4 -5
package/src/LinearPileupDisplay/index.ts +2 -4
package/src/LinearPileupDisplay/model.ts +4 -4
package/src/LinearSNPCoverageDisplay/models/configSchema.test.ts +1 -1
package/src/MismatchParser/index.ts +5 -7
package/src/PileupRPC/rpcMethods.ts +3 -9
package/src/PileupRenderer/PileupRenderer.ts +46 -61
package/src/PileupRenderer/components/PileupRendering.tsx +2 -2
package/src/PileupRenderer/configSchema.ts +1 -1
package/src/PileupRenderer/sortUtil.ts +5 -4
package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +14 -13
package/src/index.ts +5 -10
package/dist/NestedFrequencyTable.d.ts +0 -14
package/dist/NestedFrequencyTable.js +0 -104
package/dist/NestedFrequencyTable.js.map +0 -1
package/esm/NestedFrequencyTable.d.ts +0 -14
package/esm/NestedFrequencyTable.js +0 -101
package/esm/NestedFrequencyTable.js.map +0 -1
package/src/NestedFrequencyTable.ts +0 -121

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package/dist/PileupRenderer/components/PileupRendering.js CHANGED Viewed

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

	@@ -1 +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"}
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,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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js CHANGED Viewed

@@ -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, 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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"SNPCoverageRenderer.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/SNPCoverageRenderer.ts"],"names":[],"mappings":";;AAAA,yCAAqD;AACrD,6CAAqE;AACrE,+DAA4D;AAE5D,0DAM+B;AA2B/B,MAAM,WAAW,GAAG,GAAG,CAAA;AAEvB,MAAqB,mBAAoB,SAAQ,kCAAkB;IACjE,4EAA4E;IAC5E,kDAAkD;IAClD,KAAK,CAAC,IAAI,CACR,GAA6B,EAC7B,KAAyC;QAEzC,MAAM,EACJ,QAAQ,EACR,OAAO,EACP,OAAO,EACP,mBAAmB,EACnB,kBAAkB,GAAG,EAAE,EACvB,SAAS,EACT,MAAM,EAAE,gBAAgB,EACxB,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,GAAG,EACX,KAAK,GACN,GAAG,KAAK,CAAA;QACT,MAAM,KAAK,GAAG,IAAA,uBAAkB,EAAC,WAAW,CAAC,CAAA;QAC7C,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;QACxB,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QAEnD,yEAAyE;QACzE,oEAAoE;QACpE,iDAAiD;QACjD,MAAM,MAAM,GAAG,sCAAsB,CAAA;QACrC,MAAM,MAAM,GAAG,gBAAgB,GAAG,MAAM,GAAG,CAAC,CAAA;QAE5C,MAAM,EAAE,MAAM,EAAE,GAAG,SAAS,CAAA;QAC5B,IAAI,CAAC,MAAM,EAAE;YACX,OAAM;SACP;QACD,MAAM,IAAI,GAAG,EAAE,GAAG,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,CAAC,EAAE,CAAA;QACjD,MAAM,SAAS,GAAG,IAAA,wBAAQ,EAAC,IAAI,CAAC,CAAA;QAEhC,mEAAmE;QACnE,MAAM,kBAAkB,GAAG,IAAA,wBAAQ,EAAC;YAClC,GAAG,IAAI;YACP,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,GAAG,CAAC,CAAC;YACtB,SAAS,EAAE,QAAQ;SACpB,CAAC,CAAA;QACF,MAAM,OAAO,GAAG,IAAA,yBAAS,EAAC,SAAS,CAAC,SAAS,CAAC,CAAA;QAC9C,MAAM,YAAY,GAAG,IAAA,yBAAS,EAAC,QAAQ,CAAC,CAAA;QAExC,MAAM,kBAAkB,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,oBAAoB,CAAC,CAAA;QACpE,MAAM,mBAAmB,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,qBAAqB,CAAC,CAAA;QACtE,MAAM,QAAQ,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,UAAU,CAAC,CAAA;QAChD,MAAM,cAAc,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,gBAAgB,CAAC,CAAA;QAE5D,sEAAsE;QACtE,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAChE,MAAM,QAAQ,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QACrD,kCAAkC;QAClC,MAAM,IAAI,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,kBAAkB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAC1E,MAAM,SAAS,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QAE7D,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,OAAO,CAAA;QAC/B,MAAM,YAAY,GAA8B;YAC9C,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,KAAK,EAAE,WAAW;YAClB,SAAS,EAAE,QAAQ;YACnB,QAAQ,EAAE,MAAM;YAChB,QAAQ,EAAE,KAAK;YACf,IAAI,EAAE,KAAK;YACX,MAAM,EAAE,MAAM;SACf,CAAA;QAED,MAAM,KAAK,GAAG,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;QACpC,MAAM,QAAQ,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAC5D,MAAM,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAEzD,wEAAwE;QACxE,+CAA+C;QAC/C,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,KAAK,CAAA;QAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAA,oBAAa,EAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YACjE,MAAM,CAAC,GAAG,OAAO,GAAG,MAAM,GAAG,WAAW,CAAA;YACxC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAA;SACrD;QAED,0EAA0E;QAC1E,2EAA2E;QAC3E,0EAA0E;QAC1E,0EAA0E;QAC1E,wEAAwE;QACxE,IAAI,SAAS,GAAG,CAAC,CAAA;QAEjB,wEAAwE;QACxE,+DAA+D;QAC/D,MAAM,8BAA8B,GAAG,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAExE,yEAAyE;QACzE,yEAAyE;QACzE,oCAAoC;QAEpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAA,oBAAa,EAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YAEjE,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAY,CAAA;YACjD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,GAAG,MAAM,EAAE,CAAC,CAAC,CAAA;YACvC,MAAM,UAAU,GAAG,OAAO,CAAC,KAAK,CAAA;YAChC,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAA;YAE5C,IAAI,IAAI,GAAG,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACpC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;gBACpB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;gBACnC,GAAG,CAAC,SAAS;oBACX,YAAY,CAAC,IAAI,CAAC;wBAClB,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;wBAC5C,MAAM,CAAA;gBAER,MAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;gBAC9B,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,MAAM,CAAA;gBAClC,GAAG,CAAC,QAAQ,CACV,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,EAClB,MAAM,GAAG,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,KAAK,CAAC,GAAG,MAAM,EAC1C,CAAC,EACD,CAAC,KAAK,GAAG,KAAK,CAAC,GAAG,MAAM,CACzB,CAAA;gBACD,IAAI,IAAI,KAAK,CAAA;aACd;YAED,MAAM,eAAe,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YACnD,MAAM,eAAe,GAAG,GAAG,CAAA;YAC3B,IAAI,mBAAmB,EAAE;gBACvB,IAAI,IAAI,GAAG,CAAC,CAAA;gBACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/C,MAAM,IAAI,GAAG,eAAe,CAAC,CAAC,CAAC,CAAA;oBAC/B,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;oBACtC,MAAM,CAAC,GAAG,GAAG,CAAA;oBAC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package/dist/index.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"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/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 /// <reference types="react" />
-declare function AlignmentFeatureDetails(props: {
-    model: any;
-}): JSX.Element;
-declare const _default: typeof AlignmentFeatureDetails;
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+declare const _default: (props: {
+    model: IAnyStateTreeNode;
+}) => JSX.Element;
 export default _default;