npm - @jbrowse/plugin-alignments - Versions diffs - 2.2.2 → 2.3.1 - Mend

@jbrowse/plugin-alignments 2.2.2 → 2.3.1

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 (308) hide show

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +1 -1
package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
package/dist/AlignmentsTrack/index.js +1 -0
package/dist/AlignmentsTrack/index.js.map +1 -1
package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts +3 -4
package/dist/BamAdapter/BamSlightlyLazyFeature.js +11 -18
package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
package/dist/BamAdapter/index.js +1 -0
package/dist/BamAdapter/index.js.map +1 -1
package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts +5 -7
package/dist/CramAdapter/CramSlightlyLazyFeature.js +6 -8
package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
package/dist/CramAdapter/index.js +1 -0
package/dist/CramAdapter/index.js.map +1 -1
package/dist/GuessAlignmentsTypes/index.d.ts +3 -0
package/dist/GuessAlignmentsTypes/index.js +56 -0
package/dist/GuessAlignmentsTypes/index.js.map +1 -0
package/dist/HtsgetBamAdapter/index.js +11 -11
package/dist/HtsgetBamAdapter/index.js.map +1 -1
package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +10 -13
package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
package/dist/LinearAlignmentsDisplay/index.js +1 -0
package/dist/LinearAlignmentsDisplay/index.js.map +1 -1
package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts +6 -3
package/dist/LinearAlignmentsDisplay/models/configSchema.js +2 -3
package/dist/LinearAlignmentsDisplay/models/configSchema.js.map +1 -1
package/dist/LinearAlignmentsDisplay/models/model.d.ts +22 -36
package/dist/LinearAlignmentsDisplay/models/model.js +166 -151
package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts +2 -2
package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +2 -4
package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
package/dist/LinearPileupDisplay/configSchema.d.ts +0 -3
package/dist/LinearPileupDisplay/configSchema.js.map +1 -1
package/dist/LinearPileupDisplay/index.js +2 -0
package/dist/LinearPileupDisplay/index.js.map +1 -1
package/dist/LinearPileupDisplay/model.d.ts +19 -16
package/dist/LinearPileupDisplay/model.js +28 -13
package/dist/LinearPileupDisplay/model.js.map +1 -1
package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts +6 -0
package/dist/LinearReadArcsDisplay/components/ReactComponent.js +49 -0
package/dist/LinearReadArcsDisplay/components/ReactComponent.js.map +1 -0
package/dist/LinearReadArcsDisplay/configSchema.d.ts +6 -0
package/dist/LinearReadArcsDisplay/configSchema.js +52 -0
package/dist/LinearReadArcsDisplay/configSchema.js.map +1 -0
package/dist/LinearReadArcsDisplay/drawFeats.d.ts +14 -0
package/dist/LinearReadArcsDisplay/drawFeats.js +162 -0
package/dist/LinearReadArcsDisplay/drawFeats.js.map +1 -0
package/dist/LinearReadArcsDisplay/index.d.ts +2 -0
package/dist/LinearReadArcsDisplay/index.js +27 -0
package/dist/LinearReadArcsDisplay/index.js.map +1 -0
package/dist/LinearReadArcsDisplay/model.d.ts +342 -0
package/dist/LinearReadArcsDisplay/model.js +327 -0
package/dist/LinearReadArcsDisplay/model.js.map +1 -0
package/dist/LinearReadCloudDisplay/components/ReactComponent.d.ts +6 -0
package/dist/LinearReadCloudDisplay/components/ReactComponent.js +49 -0
package/dist/LinearReadCloudDisplay/components/ReactComponent.js.map +1 -0
package/dist/LinearReadCloudDisplay/configSchema.d.ts +6 -0
package/dist/LinearReadCloudDisplay/configSchema.js +51 -0
package/dist/LinearReadCloudDisplay/configSchema.js.map +1 -0
package/dist/LinearReadCloudDisplay/drawFeats.d.ts +10 -0
package/dist/LinearReadCloudDisplay/drawFeats.js +159 -0
package/dist/LinearReadCloudDisplay/drawFeats.js.map +1 -0
package/dist/LinearReadCloudDisplay/index.d.ts +2 -0
package/dist/LinearReadCloudDisplay/index.js +27 -0
package/dist/LinearReadCloudDisplay/index.js.map +1 -0
package/dist/LinearReadCloudDisplay/model.d.ts +320 -0
package/dist/LinearReadCloudDisplay/model.js +252 -0
package/dist/LinearReadCloudDisplay/model.js.map +1 -0
package/dist/LinearSNPCoverageDisplay/index.js +1 -0
package/dist/LinearSNPCoverageDisplay/index.js.map +1 -1
package/dist/LinearSNPCoverageDisplay/models/model.d.ts +19 -20
package/dist/LinearSNPCoverageDisplay/models/model.js +1 -6
package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
package/dist/{BamAdapter/MismatchParser.d.ts → MismatchParser/index.d.ts} +23 -0
package/dist/{BamAdapter/MismatchParser.js → MismatchParser/index.js} +116 -3
package/dist/MismatchParser/index.js.map +1 -0
package/dist/PileupRPC/base.d.ts +8 -0
package/dist/PileupRPC/base.js +22 -0
package/dist/PileupRPC/base.js.map +1 -0
package/dist/PileupRPC/index.d.ts +3 -0
package/dist/PileupRPC/index.js +9 -0
package/dist/PileupRPC/index.js.map +1 -0
package/dist/PileupRPC/methods/GetGlobalValueForTag.d.ts +14 -0
package/dist/PileupRPC/methods/GetGlobalValueForTag.js +29 -0
package/dist/PileupRPC/methods/GetGlobalValueForTag.js.map +1 -0
package/dist/PileupRPC/methods/GetReducedFeatures.d.ts +25 -0
package/dist/PileupRPC/methods/GetReducedFeatures.js +61 -0
package/dist/PileupRPC/methods/GetReducedFeatures.js.map +1 -0
package/dist/PileupRPC/methods/GetVisibleModifications.d.ts +14 -0
package/dist/PileupRPC/methods/GetVisibleModifications.js +32 -0
package/dist/PileupRPC/methods/GetVisibleModifications.js.map +1 -0
package/dist/PileupRPC/rpcMethods.d.ts +4 -34
package/dist/PileupRPC/rpcMethods.js +7 -77
package/dist/PileupRPC/rpcMethods.js.map +1 -1
package/dist/PileupRPC/util.d.ts +8 -0
package/dist/PileupRPC/util.js +20 -0
package/dist/PileupRPC/util.js.map +1 -0
package/dist/PileupRenderer/PileupRenderer.d.ts +1 -1
package/dist/PileupRenderer/PileupRenderer.js +5 -5
package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
package/dist/PileupRenderer/index.js +1 -0
package/dist/PileupRenderer/index.js.map +1 -1
package/dist/PileupRenderer/sortUtil.d.ts +1 -1
package/dist/PileupRenderer/sortUtil.js +2 -2
package/dist/PileupRenderer/sortUtil.js.map +1 -1
package/dist/SNPCoverageAdapter/generateCoverageBins.js +1 -1
package/dist/SNPCoverageAdapter/generateCoverageBins.js.map +1 -1
package/dist/SNPCoverageAdapter/index.js +1 -3
package/dist/SNPCoverageAdapter/index.js.map +1 -1
package/dist/index.d.ts +2 -2
package/dist/index.js +12 -58
package/dist/index.js.map +1 -1
package/dist/{LinearPileupDisplay/components → shared}/FilterByTag.d.ts +0 -0
package/dist/{LinearPileupDisplay/components → shared}/FilterByTag.js +3 -9
package/dist/shared/FilterByTag.js.map +1 -0
package/dist/shared/color.d.ts +17 -0
package/dist/shared/color.js +43 -0
package/dist/shared/color.js.map +1 -0
package/dist/shared/fetchChains.d.ts +27 -0
package/dist/shared/fetchChains.js +30 -0
package/dist/shared/fetchChains.js.map +1 -0
package/dist/shared/index.d.ts +36 -0
package/dist/{shared.js → shared/index.js} +12 -2
package/dist/shared/index.js.map +1 -0
package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +1 -1
package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
package/esm/AlignmentsTrack/index.js +1 -0
package/esm/AlignmentsTrack/index.js.map +1 -1
package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts +3 -4
package/esm/BamAdapter/BamSlightlyLazyFeature.js +11 -18
package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
package/esm/BamAdapter/index.js +1 -0
package/esm/BamAdapter/index.js.map +1 -1
package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +5 -7
package/esm/CramAdapter/CramSlightlyLazyFeature.js +6 -8
package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
package/esm/CramAdapter/index.js +1 -0
package/esm/CramAdapter/index.js.map +1 -1
package/esm/GuessAlignmentsTypes/index.d.ts +3 -0
package/esm/GuessAlignmentsTypes/index.js +54 -0
package/esm/GuessAlignmentsTypes/index.js.map +1 -0
package/esm/HtsgetBamAdapter/index.js +11 -11
package/esm/HtsgetBamAdapter/index.js.map +1 -1
package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +10 -13
package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
package/esm/LinearAlignmentsDisplay/index.js +1 -0
package/esm/LinearAlignmentsDisplay/index.js.map +1 -1
package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +6 -3
package/esm/LinearAlignmentsDisplay/models/configSchema.js +2 -4
package/esm/LinearAlignmentsDisplay/models/configSchema.js.map +1 -1
package/esm/LinearAlignmentsDisplay/models/model.d.ts +22 -36
package/esm/LinearAlignmentsDisplay/models/model.js +167 -152
package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +2 -2
package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +2 -4
package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
package/esm/LinearPileupDisplay/configSchema.d.ts +0 -3
package/esm/LinearPileupDisplay/configSchema.js.map +1 -1
package/esm/LinearPileupDisplay/index.js +2 -0
package/esm/LinearPileupDisplay/index.js.map +1 -1
package/esm/LinearPileupDisplay/model.d.ts +19 -16
package/esm/LinearPileupDisplay/model.js +29 -14
package/esm/LinearPileupDisplay/model.js.map +1 -1
package/esm/LinearReadArcsDisplay/components/ReactComponent.d.ts +6 -0
package/esm/LinearReadArcsDisplay/components/ReactComponent.js +44 -0
package/esm/LinearReadArcsDisplay/components/ReactComponent.js.map +1 -0
package/esm/LinearReadArcsDisplay/configSchema.d.ts +6 -0
package/esm/LinearReadArcsDisplay/configSchema.js +50 -0
package/esm/LinearReadArcsDisplay/configSchema.js.map +1 -0
package/esm/LinearReadArcsDisplay/drawFeats.d.ts +14 -0
package/esm/LinearReadArcsDisplay/drawFeats.js +157 -0
package/esm/LinearReadArcsDisplay/drawFeats.js.map +1 -0
package/esm/LinearReadArcsDisplay/index.d.ts +2 -0
package/esm/LinearReadArcsDisplay/index.js +21 -0
package/esm/LinearReadArcsDisplay/index.js.map +1 -0
package/esm/LinearReadArcsDisplay/model.d.ts +342 -0
package/esm/LinearReadArcsDisplay/model.js +299 -0
package/esm/LinearReadArcsDisplay/model.js.map +1 -0
package/esm/LinearReadCloudDisplay/components/ReactComponent.d.ts +6 -0
package/esm/LinearReadCloudDisplay/components/ReactComponent.js +44 -0
package/esm/LinearReadCloudDisplay/components/ReactComponent.js.map +1 -0
package/esm/LinearReadCloudDisplay/configSchema.d.ts +6 -0
package/esm/LinearReadCloudDisplay/configSchema.js +49 -0
package/esm/LinearReadCloudDisplay/configSchema.js.map +1 -0
package/esm/LinearReadCloudDisplay/drawFeats.d.ts +10 -0
package/esm/LinearReadCloudDisplay/drawFeats.js +156 -0
package/esm/LinearReadCloudDisplay/drawFeats.js.map +1 -0
package/esm/LinearReadCloudDisplay/index.d.ts +2 -0
package/esm/LinearReadCloudDisplay/index.js +21 -0
package/esm/LinearReadCloudDisplay/index.js.map +1 -0
package/esm/LinearReadCloudDisplay/model.d.ts +320 -0
package/esm/LinearReadCloudDisplay/model.js +224 -0
package/esm/LinearReadCloudDisplay/model.js.map +1 -0
package/esm/LinearSNPCoverageDisplay/index.js +1 -0
package/esm/LinearSNPCoverageDisplay/index.js.map +1 -1
package/esm/LinearSNPCoverageDisplay/models/model.d.ts +19 -20
package/esm/LinearSNPCoverageDisplay/models/model.js +2 -7
package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
package/esm/{BamAdapter/MismatchParser.d.ts → MismatchParser/index.d.ts} +23 -0
package/esm/{BamAdapter/MismatchParser.js → MismatchParser/index.js} +107 -2
package/esm/MismatchParser/index.js.map +1 -0
package/esm/PileupRPC/base.d.ts +8 -0
package/esm/PileupRPC/base.js +16 -0
package/esm/PileupRPC/base.js.map +1 -0
package/esm/PileupRPC/index.d.ts +3 -0
package/esm/PileupRPC/index.js +7 -0
package/esm/PileupRPC/index.js.map +1 -0
package/esm/PileupRPC/methods/GetGlobalValueForTag.d.ts +14 -0
package/esm/PileupRPC/methods/GetGlobalValueForTag.js +23 -0
package/esm/PileupRPC/methods/GetGlobalValueForTag.js.map +1 -0
package/esm/PileupRPC/methods/GetReducedFeatures.d.ts +25 -0
package/esm/PileupRPC/methods/GetReducedFeatures.js +55 -0
package/esm/PileupRPC/methods/GetReducedFeatures.js.map +1 -0
package/esm/PileupRPC/methods/GetVisibleModifications.d.ts +14 -0
package/esm/PileupRPC/methods/GetVisibleModifications.js +26 -0
package/esm/PileupRPC/methods/GetVisibleModifications.js.map +1 -0
package/esm/PileupRPC/rpcMethods.d.ts +4 -34
package/esm/PileupRPC/rpcMethods.js +4 -74
package/esm/PileupRPC/rpcMethods.js.map +1 -1
package/esm/PileupRPC/util.d.ts +8 -0
package/esm/PileupRPC/util.js +15 -0
package/esm/PileupRPC/util.js.map +1 -0
package/esm/PileupRenderer/PileupRenderer.d.ts +1 -1
package/esm/PileupRenderer/PileupRenderer.js +5 -5
package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
package/esm/PileupRenderer/index.js +1 -0
package/esm/PileupRenderer/index.js.map +1 -1
package/esm/PileupRenderer/sortUtil.d.ts +1 -1
package/esm/PileupRenderer/sortUtil.js +1 -1
package/esm/PileupRenderer/sortUtil.js.map +1 -1
package/esm/SNPCoverageAdapter/generateCoverageBins.js +1 -1
package/esm/SNPCoverageAdapter/generateCoverageBins.js.map +1 -1
package/esm/SNPCoverageAdapter/index.js +1 -3
package/esm/SNPCoverageAdapter/index.js.map +1 -1
package/esm/index.d.ts +2 -2
package/esm/index.js +10 -56
package/esm/index.js.map +1 -1
package/esm/{LinearPileupDisplay/components → shared}/FilterByTag.d.ts +0 -0
package/esm/{LinearPileupDisplay/components → shared}/FilterByTag.js +3 -9
package/esm/shared/FilterByTag.js.map +1 -0
package/esm/shared/color.d.ts +17 -0
package/esm/shared/color.js +37 -0
package/esm/shared/color.js.map +1 -0
package/esm/shared/fetchChains.d.ts +27 -0
package/esm/shared/fetchChains.js +26 -0
package/esm/shared/fetchChains.js.map +1 -0
package/esm/shared/index.d.ts +36 -0
package/esm/{shared.js → shared/index.js} +11 -1
package/esm/shared/index.js.map +1 -0
package/package.json +4 -4
package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +1 -1
package/src/AlignmentsTrack/index.ts +1 -0
package/src/BamAdapter/BamSlightlyLazyFeature.ts +13 -19
package/src/BamAdapter/index.ts +1 -0
package/src/CramAdapter/CramSlightlyLazyFeature.ts +13 -15
package/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap +0 -10
package/src/CramAdapter/index.ts +1 -0
package/src/GuessAlignmentsTypes/index.ts +79 -0
package/src/HtsgetBamAdapter/index.ts +11 -15
package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +21 -29
package/src/LinearAlignmentsDisplay/index.ts +1 -0
package/src/LinearAlignmentsDisplay/models/configSchema.ts +2 -6
package/src/LinearAlignmentsDisplay/models/model.tsx +238 -199
package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +4 -6
package/src/LinearPileupDisplay/configSchema.ts +1 -3
package/src/LinearPileupDisplay/index.ts +2 -0
package/src/LinearPileupDisplay/model.ts +36 -23
package/src/LinearReadArcsDisplay/components/ReactComponent.tsx +86 -0
package/src/LinearReadArcsDisplay/configSchema.ts +58 -0
package/src/LinearReadArcsDisplay/declare.d.ts +1 -0
package/src/LinearReadArcsDisplay/drawFeats.ts +199 -0
package/src/LinearReadArcsDisplay/index.ts +23 -0
package/src/LinearReadArcsDisplay/model.tsx +370 -0
package/src/LinearReadCloudDisplay/components/ReactComponent.tsx +86 -0
package/src/LinearReadCloudDisplay/configSchema.ts +57 -0
package/src/LinearReadCloudDisplay/drawFeats.ts +201 -0
package/src/LinearReadCloudDisplay/index.ts +23 -0
package/src/LinearReadCloudDisplay/model.tsx +289 -0
package/src/LinearSNPCoverageDisplay/index.ts +1 -0
package/src/LinearSNPCoverageDisplay/models/model.ts +3 -13
package/src/{BamAdapter/MismatchParser.test.ts → MismatchParser/index.test.ts} +1 -1
package/src/{BamAdapter/MismatchParser.ts → MismatchParser/index.ts} +129 -2
package/src/PileupRPC/base.ts +24 -0
package/src/PileupRPC/index.ts +12 -0
package/src/PileupRPC/methods/GetGlobalValueForTag.ts +41 -0
package/src/PileupRPC/methods/GetReducedFeatures.ts +76 -0
package/src/PileupRPC/methods/GetVisibleModifications.ts +45 -0
package/src/PileupRPC/rpcMethods.ts +8 -113
package/src/PileupRPC/util.ts +19 -0
package/src/PileupRenderer/PileupRenderer.ts +5 -8
package/src/PileupRenderer/index.ts +1 -0
package/src/PileupRenderer/sortUtil.ts +2 -3
package/src/SNPCoverageAdapter/generateCoverageBins.ts +1 -1
package/src/SNPCoverageAdapter/index.ts +1 -3
package/src/index.ts +12 -93
package/src/{LinearPileupDisplay/components → shared}/FilterByTag.tsx +3 -9
package/src/shared/color.ts +47 -0
package/src/shared/fetchChains.ts +63 -0
package/src/{shared.ts → shared/index.ts} +17 -4
package/dist/BamAdapter/MismatchParser.js.map +0 -1
package/dist/LinearPileupDisplay/components/FilterByTag.js.map +0 -1
package/dist/shared.d.ts +0 -25
package/dist/shared.js.map +0 -1
package/esm/BamAdapter/MismatchParser.js.map +0 -1
package/esm/LinearPileupDisplay/components/FilterByTag.js.map +0 -1
package/esm/shared.d.ts +0 -25
package/esm/shared.js.map +0 -1

package/dist/PileupRenderer/PileupRenderer.js.map CHANGED Viewed

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

@@ -10,6 +10,7 @@ function register(pluginManager) {
     pluginManager.addRendererType(() => {
         return new PileupRenderer_1.default({
             name: 'PileupRenderer',
+            displayName: 'Pileup renderer',
             ReactComponent: PileupRendering_1.default,
             configSchema: configSchema_1.default,
             pluginManager,

package/dist/PileupRenderer/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":";;;;;AACA,sEAA6C;AAC7C,mFAAyD;AACzD,kEAAyC;AAEzC,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAAC,GAAG,EAAE;QACjC,OAAO,IAAI,wBAAc,CAAC;YACxB,IAAI,EAAE,gBAAgB;YACtB,WAAW,EAAE,iBAAiB;YAC9B,cAAc,EAAd,yBAAc;YACd,YAAY,EAAZ,sBAAY;YACZ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAVD,2BAUC"}

package/dist/PileupRenderer/sortUtil.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Feature } from '@jbrowse/core/util';
 interface SortObject {
     pos: number;
     type: string;

package/dist/PileupRenderer/sortUtil.js CHANGED Viewed

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.sortFeature = void 0;
-const range_1 = require("@jbrowse/core/util/range");
+const util_1 = require("@jbrowse/core/util");
 const sortFeature = (features, sortedBy) => {
     const featureArray = Array.from(features.values());
     const featuresInCenterLine = [];
@@ -12,7 +12,7 @@ const sortFeature = (features, sortedBy) => {
         const feature = innerArray;
         const start = feature.get('start');
         const end = feature.get('end');
-        if ((0, range_1.doesIntersect2)(pos - 1, pos, start, end)) {
+        if ((0, util_1.doesIntersect2)(pos - 1, pos, start, end)) {
             featuresInCenterLine.push(innerArray);
         }
         else {

package/dist/PileupRenderer/sortUtil.js.map CHANGED Viewed

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package/dist/SNPCoverageAdapter/generateCoverageBins.js CHANGED Viewed

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const util_1 = require("../util");
-const MismatchParser_1 = require("../BamAdapter/MismatchParser");
+const MismatchParser_1 = require("../MismatchParser");
 function mismatchLen(mismatch) {
     return !isInterbase(mismatch.type) ? mismatch.length : 1;
 }

package/dist/SNPCoverageAdapter/generateCoverageBins.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/SNPCoverageAdapter/index.js CHANGED Viewed

@@ -33,11 +33,9 @@ function default_1(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'SNPCoverageAdapter',
+            displayName: 'SNPCoverage adapter',
             adapterMetadata: {
-                category: null,
-                displayName: null,
                 hiddenFromGUI: true,
-                description: null,
             },
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SNPCoverageAdapter'))).then(r => r.default),
             configSchema: configSchema_1.default,

package/dist/SNPCoverageAdapter/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AACzC,6DAAmD;AAEnD,mBAAyB,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,oBAAoB;YAC1B,~~eAAe~~,EAAE~~;gBACf~~,~~QAAQ,EAAE,IAAI~~;~~gBACd~~,~~WAAW~~,EAAE~~,IAAI~~;~~gBACjB~~,aAAa,EAAE,IAAI;~~gBACnB,WAAW,EAAE,IAAI~~;~~aAClB;~~YACD,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,sBAAsB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;YACrD,YAAY,EAAZ,sBAAY;YACZ,mBAAmB,EAAE,iCAAY;SAClC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;~~AAhBD~~,~~4BAgBC~~"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AACzC,6DAAmD;AAEnD,mBAAyB,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,oBAAoB;YAC1B,WAAW,EAAE,qBAAqB;YAClC,eAAe,EAAE;gBACf,aAAa,EAAE,IAAI;aACpB;YACD,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,sBAAsB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;YACrD,YAAY,EAAZ,sBAAY;YACZ,mBAAmB,EAAE,iCAAY;SAClC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAdD,4BAcC"}

package/dist/index.d.ts CHANGED Viewed

@@ -1,8 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
-import * as MismatchParser from './BamAdapter/MismatchParser';
-import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
 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;

package/dist/index.js CHANGED Viewed

@@ -28,8 +28,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MismatchParser = exports.linearPileupDisplayStateModelFactory = exports.linearPileupDisplayConfigSchemaFactory = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const MismatchParser = __importStar(require("./BamAdapter/MismatchParser"));
-exports.MismatchParser = MismatchParser;
 const CramAdapter_1 = __importDefault(require("./CramAdapter"));
 const BamAdapter_1 = __importDefault(require("./BamAdapter"));
 const HtsgetBamAdapter_1 = __importDefault(require("./HtsgetBamAdapter"));
@@ -38,13 +36,17 @@ const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
 const PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
 const LinearAlignmentsDisplay_1 = __importDefault(require("./LinearAlignmentsDisplay"));
 const LinearSNPCoverageDisplay_1 = __importDefault(require("./LinearSNPCoverageDisplay"));
+const LinearReadArcsDisplay_1 = __importDefault(require("./LinearReadArcsDisplay"));
+const LinearReadCloudDisplay_1 = __importDefault(require("./LinearReadCloudDisplay"));
+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 AlignmentsTrack_1 = __importDefault(require("./AlignmentsTrack"));
-const AlignmentsFeatureDetail_1 = __importDefault(require("./AlignmentsFeatureDetail"));
-const rpcMethods_1 = require("./PileupRPC/rpcMethods");
-const tracks_1 = require("@jbrowse/core/util/tracks");
+const MismatchParser = __importStar(require("./MismatchParser"));
+exports.MismatchParser = MismatchParser;
 class AlignmentsPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -61,62 +63,14 @@ class AlignmentsPlugin extends Plugin_1.default {
             SNPCoverageAdapter_1.default,
             HtsgetBamAdapter_1.default,
             PileupRenderer_1.default,
+            PileupRPC_1.default,
             SNPCoverageRenderer_1.default,
+            LinearReadArcsDisplay_1.default,
+            LinearReadCloudDisplay_1.default,
             LinearAlignmentsDisplay_1.default,
             AlignmentsFeatureDetail_1.default,
+            GuessAlignmentsTypes_1.default,
         ].map(f => f(pluginManager));
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.cram$/i;
-                const adapterName = 'CramAdapter';
-                const fileName = (0, tracks_1.getFileName)(file);
-                const obj = {
-                    type: adapterName,
-                    cramLocation: file,
-                    craiLocation: index || (0, tracks_1.makeIndex)(file, '.crai'),
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.bam$/i;
-                const adapterName = 'BamAdapter';
-                const fileName = (0, tracks_1.getFileName)(file);
-                const indexName = index && (0, tracks_1.getFileName)(index);
-                const obj = {
-                    type: adapterName,
-                    bamLocation: file,
-                    index: {
-                        location: index || (0, tracks_1.makeIndex)(file, '.bai'),
-                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'BAI'),
-                    },
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-            return (adapterName) => {
-                if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
-                    return 'AlignmentsTrack';
-                }
-                return trackTypeGuesser(adapterName);
-            };
-        });
-        pluginManager.addRpcMethod(() => new rpcMethods_1.PileupGetGlobalValueForTag(pluginManager));
-        pluginManager.addRpcMethod(() => new rpcMethods_1.PileupGetVisibleModifications(pluginManager));
     }
 }
 exports.default = AlignmentsPlugin;

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,6EAG8B;AA8B5B,qHAhCA,0DAAoC,OAgCA;AADpC,uHA9BA,4DAAsC,OA8BA;AA3BxC,iEAAkD;AA6BhD,wCAAc;AA3BhB,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"}

package/dist/{LinearPileupDisplay/components → shared}/FilterByTag.d.ts RENAMED Viewed

File without changes

package/dist/{LinearPileupDisplay/components → shared}/FilterByTag.js RENAMED Viewed

@@ -99,22 +99,16 @@ function FilterByTagDlg(props) {
                         react_1.default.createElement(Bitmask, { flag: flagExclude, setFlag: setFlagExclude })))),
             react_1.default.createElement(material_1.Paper, { className: classes.paper, variant: "outlined" },
                 react_1.default.createElement(material_1.Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"),
-                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tag, onChange: event => {
-                        setTag(event.target.value);
-                    }, placeholder: "Enter tag name", inputProps: {
+                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: {
                         maxLength: 2,
                         'data-testid': 'color-tag-name-input',
                     }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', "data-testid": "color-tag-name" }),
-                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tagValue, onChange: event => {
-                        setTagValue(event.target.value);
-                    }, placeholder: "Enter tag value", inputProps: {
+                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tagValue, onChange: event => setTagValue(event.target.value), placeholder: "Enter tag value", inputProps: {
                         'data-testid': 'color-tag-name-input',
                     }, "data-testid": "color-tag-value" })),
             react_1.default.createElement(material_1.Paper, { className: classes.paper, variant: "outlined" },
                 react_1.default.createElement(material_1.Typography, null, "Filter by read name"),
-                react_1.default.createElement(material_1.TextField, { className: classes.field, value: readName, onChange: event => {
-                        setReadName(event.target.value);
-                    }, placeholder: "Enter read name", inputProps: {
+                react_1.default.createElement(material_1.TextField, { className: classes.field, value: readName, onChange: event => setReadName(event.target.value), placeholder: "Enter read name", inputProps: {
                         'data-testid': 'color-tag-readname-input',
                     }, "data-testid": "color-tag-readname" })),
             react_1.default.createElement(material_1.DialogActions, null,

package/dist/shared/FilterByTag.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"FilterByTag.js","sourceRoot":"","sources":["../../src/shared/FilterByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAQsB;AACtB,yCAAyC;AACzC,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACzB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,SAAS,GAAG;IAChB,aAAa;IACb,4BAA4B;IAC5B,eAAe;IACf,eAAe;IACf,qBAAqB;IACrB,qBAAqB;IACrB,eAAe;IACf,gBAAgB;IAChB,uBAAuB;IACvB,2CAA2C;IAC3C,kCAAkC;IAClC,yBAAyB;CAC1B,CAAA;AAED,SAAS,OAAO,CAAC,KAA2C;IAC1D,MAAM,EAAE,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACnC,OAAO,CACL;QACE,8BAAC,oBAAS,IACR,IAAI,EAAC,QAAQ,EACb,KAAK,EAAE,IAAI,EACX,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GAC/C;QACD,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE;YAC7B,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAA;YAC/B,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,uCAAK,GAAG,EAAE,GAAG;gBACX,yCACE,IAAI,EAAC,UAAU,EACf,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,EAAE;4BACxB,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC7B;6BAAM;4BACL,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC9B;oBACH,CAAC,GACD;gBACF,yCAAO,OAAO,EAAE,GAAG,IAAG,IAAI,CAAS,CAC/B,CACP,CAAA;QACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAS,cAAc,CAAC,KAWvB;;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,EAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,EAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,GAAG,KAAI,EAAE,CAAC,CAAA;IAC9D,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,KAAK,KAAI,EAAE,CAAC,CAAA;IAC1E,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,QAAQ,KAAI,EAAE,CAAC,CAAA;IAClE,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,MAAM,IAAI,GAAG,4DAA4D,CAAA;IAEzE,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa;YACZ,8BAAC,qBAAU;;gBAC4B,8BAAC,eAAI,IAAC,IAAI,EAAE,IAAI,IAAG,IAAI,CAAQ;gBAAC,GAAG;8BAE7D;YACb,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,uCAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;oBAC7B;wBACE,8BAAC,qBAAU,yCAA4C;wBACvD,8BAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD;oBACN;wBACE,8BAAC,qBAAU,6CAAgD;wBAC3D,8BAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD,CACF,CACA;YACR,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,8BAAC,qBAAU,kQAKE;gBACb,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;wBACV,SAAS,EAAE,CAAC;wBACZ,aAAa,EAAE,sBAAsB;qBACtC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,iBACtD,gBAAgB,GAC5B;gBACF,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAClD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,sBAAsB;qBACtC,iBACW,iBAAiB,GAC7B,CACI;YACR,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,8BAAC,qBAAU,8BAAiC;gBAC5C,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAClD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,0BAA0B;qBAC1C,iBACW,oBAAoB,GAChC,CACI;YACR,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,QACT,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC;4BAChB,WAAW;4BACX,WAAW;4BACX,QAAQ;4BACR,SAAS,EACP,GAAG,KAAK,EAAE;gCACR,CAAC,CAAC;oCACE,GAAG;oCACH,KAAK,EAAE,QAAQ;iCAChB;gCACH,CAAC,CAAC,SAAS;yBAChB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,cAAc,CAAC,CAAA"}

package/dist/shared/color.d.ts ADDED Viewed

@@ -0,0 +1,17 @@
+import { ChainStats } from './fetchChains';
+export declare function getInsertSizeColor(f1: {
+    refName: string;
+    tlen?: number;
+}, f2: {
+    refName: string;
+}, stats?: ChainStats): "" | "red" | "purple" | "#f0f";
+export declare function getInsertSizeAndOrientationColor(f1: {
+    refName: string;
+    pair_orientation?: string;
+    tlen?: number;
+}, f2: {
+    refName: string;
+}, stats?: ChainStats): string;
+export declare function getOrientationColor(f: {
+    pair_orientation?: string;
+}): string;

package/dist/shared/color.js ADDED Viewed

@@ -0,0 +1,43 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getOrientationColor = exports.getInsertSizeAndOrientationColor = exports.getInsertSizeColor = void 0;
+const util_1 = require("../util");
+const alignmentColoring = {
+    color_pair_lr: '#c8c8c8',
+    color_pair_rr: 'navy',
+    color_pair_rl: 'teal',
+    color_pair_ll: 'green',
+};
+function getInsertSizeColor(f1, f2, stats) {
+    const sameRef = f1.refName === f2.refName;
+    const tlen = Math.abs(f1.tlen || 0);
+    if (sameRef && tlen > ((stats === null || stats === void 0 ? void 0 : stats.upper) || 0)) {
+        return 'red';
+    }
+    else if (sameRef && tlen < ((stats === null || stats === void 0 ? void 0 : stats.lower) || 0)) {
+        return '#f0f';
+    }
+    else if (!sameRef) {
+        return 'purple';
+    }
+    return '';
+}
+exports.getInsertSizeColor = getInsertSizeColor;
+function getInsertSizeAndOrientationColor(f1, f2, stats) {
+    return getInsertSizeColor(f1, f2, stats) || getOrientationColor(f1);
+}
+exports.getInsertSizeAndOrientationColor = getInsertSizeAndOrientationColor;
+function getOrientationColor(f) {
+    const type = util_1.orientationTypes['fr'];
+    const orientation = type[f.pair_orientation || ''];
+    const map = {
+        LR: 'color_pair_lr',
+        RR: 'color_pair_rr',
+        RL: 'color_pair_rl',
+        LL: 'color_pair_ll',
+    };
+    const val = map[orientation];
+    return alignmentColoring[val] || 'grey';
+}
+exports.getOrientationColor = getOrientationColor;
+//# sourceMappingURL=color.js.map

package/dist/shared/color.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/shared/fetchChains.d.ts ADDED Viewed

@@ -0,0 +1,27 @@
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+export interface ReducedFeature {
+    name: string;
+    strand: number;
+    refName: string;
+    start: number;
+    end: number;
+    id: string;
+    flags: number;
+    tlen: number;
+    pair_orientation: string;
+    next_ref?: string;
+    next_pos?: number;
+    clipPos: number;
+    SA?: string;
+}
+export interface ChainStats {
+    max: number;
+    min: number;
+    upper: number;
+    lower: number;
+}
+export interface ChainData {
+    chains: ReducedFeature[][];
+    stats?: ChainStats;
+}
+export declare function fetchChains(self: IAnyStateTreeNode): Promise<void>;

package/dist/shared/fetchChains.js ADDED Viewed

@@ -0,0 +1,30 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fetchChains = void 0;
+const util_1 = require("@jbrowse/core/util");
+const mobx_state_tree_1 = require("mobx-state-tree");
+async function fetchChains(self) {
+    try {
+        const { rpcSessionId: sessionId } = (0, util_1.getContainingTrack)(self);
+        const { rpcManager } = (0, util_1.getSession)(self);
+        const view = (0, util_1.getContainingView)(self);
+        if (!view.initialized || self.error) {
+            return;
+        }
+        self.setLoading(true);
+        const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
+            sessionId,
+            regions: view.staticBlocks.contentBlocks,
+            filterBy: (0, mobx_state_tree_1.getSnapshot)(self.filterBy),
+            adapterConfig: self.adapterConfig,
+        }));
+        self.setChainData(ret);
+        self.setLoading(false);
+    }
+    catch (e) {
+        console.error(e);
+        self.setError(e);
+    }
+}
+exports.fetchChains = fetchChains;
+//# sourceMappingURL=fetchChains.js.map

package/dist/shared/fetchChains.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/shared/index.d.ts ADDED Viewed

@@ -0,0 +1,36 @@
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { BlockSet } from '@jbrowse/core/util/blockTypes';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function getUniqueTagValues(self: IAnyStateTreeNode & {
+    adapterConfig: AnyConfigurationModel;
+}, colorScheme: {
+    type: string;
+    tag?: string;
+}, blocks: BlockSet, opts?: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<string[]>;
+type Track = IAnyStateTreeNode & {
+    configuration: AnyConfigurationModel;
+};
+export declare function getUniqueModificationValues(self: IAnyStateTreeNode & {
+    parentTrack: Track;
+}, adapterConfig: AnyConfigurationModel, colorScheme: {
+    type: string;
+    tag?: string;
+}, blocks: BlockSet, opts?: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<string[]>;
+export declare const FilterModel: import("mobx-state-tree").IModelType<{
+    flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+        tag: import("mobx-state-tree").ISimpleType<string>;
+        value: import("mobx-state-tree").ISimpleType<string>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export {};