@jbrowse/plugin-alignments 2.2.2 → 2.3.0

package/esm/SNPCoverageAdapter/generateCoverageBins.js.map

@@ -1 +1 @@
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package/esm/SNPCoverageAdapter/index.js

@@ -5,11 +5,9 @@ export default function (pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'SNPCoverageAdapter',
+            displayName: 'SNPCoverage adapter',
             adapterMetadata: {
-                category: null,
-                displayName: null,
                 hiddenFromGUI: true,
-                description: null,
             },
             getAdapterClass: () => import('./SNPCoverageAdapter').then(r => r.default),
             configSchema,

package/esm/SNPCoverageAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,EAAE,YAAY,EAAE,MAAM,sBAAsB,CAAA;AAEnD,MAAM,CAAC,OAAO,WAAW,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,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,MAAM,CAAC,sBAAsB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;YACrD,YAAY;YACZ,mBAAmB,EAAE,YAAY;SAClC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,EAAE,YAAY,EAAE,MAAM,sBAAsB,CAAA;AAEnD,MAAM,CAAC,OAAO,WAAW,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,oBAAoB;YAC1B,WAAW,EAAE,qBAAqB;YAClC,eAAe,EAAE;gBACf,aAAa,EAAE,IAAI;aACpB;YACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,sBAAsB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;YACrD,YAAY;YACZ,mBAAmB,EAAE,YAAY;SAClC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/index.d.ts

@@ -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/esm/index.js

@@ -1,5 +1,4 @@
 import Plugin from '@jbrowse/core/Plugin';
-import * as MismatchParser from './BamAdapter/MismatchParser';
 import BamAdapterF from './CramAdapter';
 import CramAdapterF from './BamAdapter';
 import HtsgetBamAdapterF from './HtsgetBamAdapter';
@@ -8,11 +7,14 @@ import SNPCoverageRendererF from './SNPCoverageRenderer';
 import PileupRendererF from './PileupRenderer';
 import LinearAlignmentsDisplayF from './LinearAlignmentsDisplay';
 import LinearSNPCoverageDisplayF from './LinearSNPCoverageDisplay';
-import LinearPileupDisplayF, { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, } from './LinearPileupDisplay';
+import LinearReadArcsDisplayF from './LinearReadArcsDisplay';
+import LinearReadCloudDisplayF from './LinearReadCloudDisplay';
 import AlignmentsTrackF from './AlignmentsTrack';
 import AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail';
-import { PileupGetGlobalValueForTag, PileupGetVisibleModifications, } from './PileupRPC/rpcMethods';
-import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
+import PileupRPCMethodsF from './PileupRPC';
+import GuessAlignmentsTypesF from './GuessAlignmentsTypes';
+import LinearPileupDisplayF, { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, } from './LinearPileupDisplay';
+import * as MismatchParser from './MismatchParser';
 export default class AlignmentsPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -29,62 +31,14 @@ export default class AlignmentsPlugin extends Plugin {
             SNPCoverageAdapterF,
             HtsgetBamAdapterF,
             PileupRendererF,
+            PileupRPCMethodsF,
             SNPCoverageRendererF,
+            LinearReadArcsDisplayF,
+            LinearReadCloudDisplayF,
             LinearAlignmentsDisplayF,
             AlignmentsFeatureWidgetF,
+            GuessAlignmentsTypesF,
         ].map(f => f(pluginManager));
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.cram$/i;
-                const adapterName = 'CramAdapter';
-                const fileName = getFileName(file);
-                const obj = {
-                    type: adapterName,
-                    cramLocation: file,
-                    craiLocation: index || makeIndex(file, '.crai'),
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.bam$/i;
-                const adapterName = 'BamAdapter';
-                const fileName = getFileName(file);
-                const indexName = index && getFileName(index);
-                const obj = {
-                    type: adapterName,
-                    bamLocation: file,
-                    index: {
-                        location: index || makeIndex(file, '.bai'),
-                        indexType: 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 PileupGetGlobalValueForTag(pluginManager));
-        pluginManager.addRpcMethod(() => new PileupGetVisibleModifications(pluginManager));
     }
 }
 export { linearPileupDisplayConfigSchemaFactory, linearPileupDisplayStateModelFactory, MismatchParser, };

package/esm/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,WAAW,MAAM,eAAe,CAAA;AACvC,OAAO,YAAY,MAAM,cAAc,CAAA;AACvC,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,mBAAmB,MAAM,sBAAsB,CAAA;AACtD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAC9C,OAAO,wBAAwB,MAAM,2BAA2B,CAAA;AAChE,OAAO,yBAAyB,MAAM,4BAA4B,CAAA;AAClE,OAAO,sBAAsB,MAAM,yBAAyB,CAAA;AAC5D,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,wBAAwB,MAAM,2BAA2B,CAAA;AAChE,OAAO,iBAAiB,MAAM,aAAa,CAAA;AAC3C,OAAO,qBAAqB,MAAM,wBAAwB,CAAA;AAC1D,OAAO,oBAAoB,EAAE,EAC3B,oCAAoC,EACpC,sCAAsC,GACvC,MAAM,uBAAuB,CAAA;AAE9B,OAAO,KAAK,cAAc,MAAM,kBAAkB,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,gBAAiB,SAAQ,MAAM;IAApD;;QACE,SAAI,GAAG,kBAAkB,CAAA;IAqB3B,CAAC;IAnBC,OAAO,CAAC,aAA4B;QAClC,CAAC;QAAA;YACC,YAAY;YACZ,WAAW;YACX,oBAAoB;YACpB,yBAAyB;YACzB,gBAAgB;YAChB,mBAAmB;YACnB,iBAAiB;YACjB,eAAe;YACf,iBAAiB;YACjB,oBAAoB;YACpB,sBAAsB;YACtB,uBAAuB;YACvB,wBAAwB;YACxB,wBAAwB;YACxB,qBAAqB;SACtB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAA;IAC9B,CAAC;CACF;AAED,OAAO,EACL,sCAAsC,EACtC,oCAAoC,EACpC,cAAc,GACf,CAAA"}

package/esm/{LinearPileupDisplay/components → shared}/FilterByTag.js

@@ -74,22 +74,16 @@ function FilterByTagDlg(props) {
                         React.createElement(Bitmask, { flag: flagExclude, setFlag: setFlagExclude })))),
             React.createElement(Paper, { className: classes.paper, variant: "outlined" },
                 React.createElement(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.createElement(TextField, { className: classes.field, value: tag, onChange: event => {
-                        setTag(event.target.value);
-                    }, placeholder: "Enter tag name", inputProps: {
+                React.createElement(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.createElement(TextField, { className: classes.field, value: tagValue, onChange: event => {
-                        setTagValue(event.target.value);
-                    }, placeholder: "Enter tag value", inputProps: {
+                React.createElement(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.createElement(Paper, { className: classes.paper, variant: "outlined" },
                 React.createElement(Typography, null, "Filter by read name"),
-                React.createElement(TextField, { className: classes.field, value: readName, onChange: event => {
-                        setReadName(event.target.value);
-                    }, placeholder: "Enter read name", inputProps: {
+                React.createElement(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.createElement(DialogActions, null,

package/esm/shared/FilterByTag.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"FilterByTag.js","sourceRoot":"","sources":["../../src/shared/FilterByTag.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,IAAI,EACJ,KAAK,EACL,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,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,oBAAC,SAAS,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,6BAAK,GAAG,EAAE,GAAG;gBACX,+BACE,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,+BAAO,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,QAAQ,CAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,GAAG,KAAI,EAAE,CAAC,CAAA;IAC9D,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,KAAK,KAAI,EAAE,CAAC,CAAA;IAC1E,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,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,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,oBAAC,aAAa;YACZ,oBAAC,UAAU;;gBAC4B,oBAAC,IAAI,IAAC,IAAI,EAAE,IAAI,IAAG,IAAI,CAAQ;gBAAC,GAAG;8BAE7D;YACb,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;oBAC7B;wBACE,oBAAC,UAAU,yCAA4C;wBACvD,oBAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD;oBACN;wBACE,oBAAC,UAAU,6CAAgD;wBAC3D,oBAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD,CACF,CACA;YACR,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,oBAAC,UAAU,kQAKE;gBACb,oBAAC,SAAS,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,oBAAC,SAAS,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,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,oBAAC,UAAU,8BAAiC;gBAC5C,oBAAC,SAAS,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,oBAAC,aAAa;gBACZ,oBAAC,MAAM,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,oBAAC,MAAM,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,eAAe,QAAQ,CAAC,cAAc,CAAC,CAAA"}

package/esm/shared/color.d.ts

@@ -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/esm/shared/color.js

@@ -0,0 +1,37 @@
+import { orientationTypes } from '../util';
+const alignmentColoring = {
+    color_pair_lr: '#c8c8c8',
+    color_pair_rr: 'navy',
+    color_pair_rl: 'teal',
+    color_pair_ll: 'green',
+};
+export 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 '';
+}
+export function getInsertSizeAndOrientationColor(f1, f2, stats) {
+    return getInsertSizeColor(f1, f2, stats) || getOrientationColor(f1);
+}
+export function getOrientationColor(f) {
+    const type = 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';
+}
+//# sourceMappingURL=color.js.map

package/esm/shared/color.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"color.js","sourceRoot":"","sources":["../../src/shared/color.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,MAAM,SAAS,CAAA;AAG1C,MAAM,iBAAiB,GAA8B;IACnD,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,MAAM;IACrB,aAAa,EAAE,MAAM;IACrB,aAAa,EAAE,OAAO;CACvB,CAAA;AAED,MAAM,UAAU,kBAAkB,CAChC,EAAsC,EACtC,EAAuB,EACvB,KAAkB;IAElB,MAAM,OAAO,GAAG,EAAE,CAAC,OAAO,KAAK,EAAE,CAAC,OAAO,CAAA;IACzC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,IAAI,CAAC,CAAC,CAAA;IACnC,IAAI,OAAO,IAAI,IAAI,GAAG,CAAC,CAAA,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,KAAK,KAAI,CAAC,CAAC,EAAE;QACzC,OAAO,KAAK,CAAA;KACb;SAAM,IAAI,OAAO,IAAI,IAAI,GAAG,CAAC,CAAA,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,KAAK,KAAI,CAAC,CAAC,EAAE;QAChD,OAAO,MAAM,CAAA;KACd;SAAM,IAAI,CAAC,OAAO,EAAE;QACnB,OAAO,QAAQ,CAAA;KAChB;IACD,OAAO,EAAE,CAAA;AACX,CAAC;AAED,MAAM,UAAU,gCAAgC,CAC9C,EAAiE,EACjE,EAAuB,EACvB,KAAkB;IAElB,OAAO,kBAAkB,CAAC,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,mBAAmB,CAAC,EAAE,CAAC,CAAA;AACrE,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,CAAgC;IAClE,MAAM,IAAI,GAAG,gBAAgB,CAAC,IAAI,CAAC,CAAA;IACnC,MAAM,WAAW,GAAG,IAAI,CAAC,CAAC,CAAC,gBAAgB,IAAI,EAAE,CAAC,CAAA;IAClD,MAAM,GAAG,GAAG;QACV,EAAE,EAAE,eAAe;QACnB,EAAE,EAAE,eAAe;QACnB,EAAE,EAAE,eAAe;QACnB,EAAE,EAAE,eAAe;KACpB,CAAA;IACD,MAAM,GAAG,GAAG,GAAG,CAAC,WAA+B,CAAC,CAAA;IAChD,OAAO,iBAAiB,CAAC,GAAG,CAAC,IAAI,MAAM,CAAA;AACzC,CAAC"}

package/esm/shared/fetchChains.d.ts

@@ -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/esm/shared/fetchChains.js

@@ -0,0 +1,26 @@
+import { getContainingTrack, getContainingView, getSession, } from '@jbrowse/core/util';
+import { getSnapshot } from 'mobx-state-tree';
+export async function fetchChains(self) {
+    try {
+        const { rpcSessionId: sessionId } = getContainingTrack(self);
+        const { rpcManager } = getSession(self);
+        const view = getContainingView(self);
+        if (!view.initialized || self.error) {
+            return;
+        }
+        self.setLoading(true);
+        const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
+            sessionId,
+            regions: view.staticBlocks.contentBlocks,
+            filterBy: getSnapshot(self.filterBy),
+            adapterConfig: self.adapterConfig,
+        }));
+        self.setChainData(ret);
+        self.setLoading(false);
+    }
+    catch (e) {
+        console.error(e);
+        self.setError(e);
+    }
+}
+//# sourceMappingURL=fetchChains.js.map

package/esm/shared/fetchChains.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"fetchChains.js","sourceRoot":"","sources":["../../src/shared/fetchChains.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,kBAAkB,EAClB,iBAAiB,EACjB,UAAU,GACX,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,WAAW,EAAqB,MAAM,iBAAiB,CAAA;AAiChE,MAAM,CAAC,KAAK,UAAU,WAAW,CAAC,IAAuB;IACvD,IAAI;QACF,MAAM,EAAE,YAAY,EAAE,SAAS,EAAE,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;QAC5D,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;QACvC,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;QAE3C,IAAI,CAAC,IAAI,CAAC,WAAW,IAAI,IAAI,CAAC,KAAK,EAAE;YACnC,OAAM;SACP;QACD,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QAErB,MAAM,GAAG,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,0BAA0B,EAAE;YACxE,SAAS;YACT,OAAO,EAAE,IAAI,CAAC,YAAY,CAAC,aAAa;YACxC,QAAQ,EAAE,WAAW,CAAC,IAAI,CAAC,QAAQ,CAAC;YACpC,aAAa,EAAE,IAAI,CAAC,aAAa;SAClC,CAAC,CAAc,CAAA;QAEhB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;QACtB,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;KACvB;IAAC,OAAO,CAAC,EAAE;QACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;KACjB;AACH,CAAC"}

package/esm/shared/index.d.ts

@@ -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 {};

package/esm/{shared.js → shared/index.js}

@@ -1,3 +1,4 @@
+import { types } from 'mobx-state-tree';
 import { getSession } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 export async function getUniqueTagValues(self, colorScheme, blocks, opts) {
@@ -25,4 +26,13 @@ export async function getUniqueModificationValues(self, adapterConfig, colorSche
     });
     return values;
 }
-//# sourceMappingURL=shared.js.map
+export const FilterModel = types.model({
+    flagInclude: types.optional(types.number, 0),
+    flagExclude: types.optional(types.number, 1540),
+    readName: types.maybe(types.string),
+    tagFilter: types.maybe(types.model({
+        tag: types.string,
+        value: types.string,
+    })),
+});
+//# sourceMappingURL=index.js.map

package/esm/shared/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/shared/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAqB,MAAM,iBAAiB,CAAA;AAE1D,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAG3D,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,IAAkE,EAClE,WAA2C,EAC3C,MAAgB,EAChB,IAIC;IAED,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IACvC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IAC9B,MAAM,SAAS,GAAG,eAAe,CAAC,IAAI,CAAC,CAAA;IACvC,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,IAAI,CAClC,eAAe,CAAC,IAAI,CAAC,EACrB,4BAA4B,EAC5B;QACE,aAAa;QACb,GAAG,EAAE,WAAW,CAAC,GAAG;QACpB,SAAS;QACT,OAAO,EAAE,MAAM,CAAC,aAAa;QAC7B,GAAG,IAAI;KACR,CACF,CAAA;IACD,OAAO,MAAkB,CAAA;AAC3B,CAAC;AAID,MAAM,CAAC,KAAK,UAAU,2BAA2B,CAC/C,IAEC,EACD,aAAoC,EACpC,WAA2C,EAC3C,MAAgB,EAChB,IAIC;IAED,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IACvC,MAAM,SAAS,GAAG,eAAe,CAAC,IAAI,CAAC,CAAA;IACvC,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,IAAI,CAClC,SAAS,EACT,+BAA+B,EAC/B;QACE,aAAa;QACb,GAAG,EAAE,WAAW,CAAC,GAAG;QACpB,SAAS;QACT,OAAO,EAAE,MAAM,CAAC,aAAa;QAC7B,GAAG,IAAI;KACR,CACF,CAAA;IACD,OAAO,MAAkB,CAAA;AAC3B,CAAC;AAED,MAAM,CAAC,MAAM,WAAW,GAAG,KAAK,CAAC,KAAK,CAAC;IACrC,WAAW,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5C,WAAW,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC;IAC/C,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;IACnC,SAAS,EAAE,KAAK,CAAC,KAAK,CACpB,KAAK,CAAC,KAAK,CAAC;QACV,GAAG,EAAE,KAAK,CAAC,MAAM;QACjB,KAAK,EAAE,KAAK,CAAC,MAAM;KACpB,CAAC,CACH;CACF,CAAC,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.2.2",
+  "version": "2.3.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -40,6 +40,7 @@
     "@gmod/bam": "^1.1.15",
     "@gmod/cram": "^1.7.1",
     "@mui/icons-material": "^5.0.1",
+    "canvas2svg": "^1.0.16",
     "clone": "^2.1.2",
     "color": "^3.1.2",
     "copy-to-clipboard": "^3.3.1",
@@ -54,10 +55,9 @@
     "mobx": "^6.0.0",
     "mobx-react": "^7.0.0",
     "mobx-state-tree": "^5.0.0",
-    "prop-types": "^15.0.0",
     "react": ">=16.8.0",
     "rxjs": "^6.0.0",
-    "tss-react": "^3.0.0"
+    "tss-react": "^4.0.0"
   },
   "publishConfig": {
     "access": "public"
@@ -65,5 +65,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "abbc00e8feedbc58de84a7a3e735ec0224909b29"
+  "gitHead": "a85b280a8af4d1a11e81ab42913f5f6049e6e580"
 }

package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx

@@ -17,7 +17,7 @@ import {
   BaseCard,
   SimpleValue,
 } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
-import { parseCigar } from '../BamAdapter/MismatchParser'
+import { parseCigar } from '../MismatchParser'
 
 const useStyles = makeStyles()({
   compact: {

package/src/AlignmentsTrack/index.ts

@@ -29,6 +29,7 @@ export default function register(pm: PluginManager) {
     const configSchema = configSchemaFactory(pm)
     const track = new TrackType({
       name: 'AlignmentsTrack',
+      displayName: 'Alignments track',
       configSchema,
       stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema),
     })

package/src/BamAdapter/BamSlightlyLazyFeature.ts

@@ -6,7 +6,7 @@ import {
 import { BamRecord } from '@gmod/bam'
 
 // locals
-import { getMismatches } from './MismatchParser'
+import { getClip, getMismatches } from '../MismatchParser'
 import BamAdapter from './BamAdapter'
 
 export default class BamSlightlyLazyFeature implements Feature {
@@ -42,23 +42,21 @@ export default class BamSlightlyLazyFeature implements Feature {
     return this.record.isPaired() ? this.record.getPairOrientation() : undefined
   }
 
-  _get_next_seq_id() {
-    return this.record._next_refid()
-  }
-
-  _get_seq_id() {
-    // @ts-ignore
-    return this.record._refID
+  _get_next_ref() {
+    return this.record.isPaired()
+      ? this.adapter.refIdToName(this.record._next_refid())
+      : undefined
   }
 
-  _get_next_refName() {
-    return this.adapter.refIdToName(this.record._next_refid())
+  _get_next_pos() {
+    return this.record.isPaired() ? this.record._next_pos() : undefined
   }
 
   _get_next_segment_position() {
-    const { record, adapter } = this
-    return record.isPaired()
-      ? `${adapter.refIdToName(record._next_refid())}:${record._next_pos() + 1}`
+    return this.record.isPaired()
+      ? `${this.adapter.refIdToName(this.record._next_refid())}:${
+          this.record._next_pos() + 1
+        }`
       : undefined
   }
 
@@ -84,9 +82,7 @@ export default class BamSlightlyLazyFeature implements Feature {
             prop =>
               prop.startsWith('_get_') &&
               prop !== '_get_mismatches' &&
-              prop !== '_get_tags' &&
-              prop !== '_get_next_seq_id' &&
-              prop !== '_get_seq_id',
+              prop !== '_get_tags',
           )
           .map(methodName => methodName.replace('_get_', ''))
           .concat(this.record._tags()),
@@ -148,8 +144,6 @@ export default class BamSlightlyLazyFeature implements Feature {
 
   _get_clipPos() {
     const cigar = this.get('CIGAR') || ''
-    return this.get('strand') === -1
-      ? +(cigar.match(/(\d+)[SH]$/) || [])[1] || 0
-      : +(cigar.match(/^(\d+)([SH])/) || [])[1] || 0
+    return getClip(cigar, this.get('strand'))
   }
 }

package/src/BamAdapter/index.ts

@@ -6,6 +6,7 @@ export default (pluginManager: PluginManager) => {
   pluginManager.addAdapterType(() => {
     return new AdapterType({
       name: 'BamAdapter',
+      displayName: 'BAM adapter',
       configSchema,
       getAdapterClass: () => import('./BamAdapter').then(r => r.default),
     })

package/src/CramAdapter/CramSlightlyLazyFeature.ts

@@ -4,8 +4,10 @@ import {
   SimpleFeatureSerialized,
 } from '@jbrowse/core/util/simpleFeature'
 import { CramRecord } from '@gmod/cram'
+
+// locals
 import CramAdapter from './CramAdapter'
-import { Mismatch, readFeaturesToCIGAR, readFeaturesToMismatches } from './util'
+import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util'
 
 export default class CramSlightlyLazyFeature implements Feature {
   // uses parameter properties to automatically create fields on the class
@@ -57,12 +59,8 @@ export default class CramSlightlyLazyFeature implements Feature {
     return this.record.qualityScores
   }
 
-  _get_seq_id() {
-    return this._store.refIdToName(this.record.sequenceId)
-  }
-
   _get_refName() {
-    return this._get_seq_id()
+    return this._store.refIdToName(this.record.sequenceId)
   }
 
   _get_is_paired() {
@@ -77,16 +75,12 @@ export default class CramSlightlyLazyFeature implements Feature {
     return this.record.templateLength || this.record.templateSize
   }
 
-  _get_next_seq_id() {
+  _get_next_ref() {
     return this.record.mate
       ? this._store.refIdToName(this.record.mate.sequenceId)
       : undefined
   }
 
-  _get_next_pos() {
-    return this.record.mate ? this.record.mate.alignmentStart : undefined
-  }
-
   _get_next_segment_position() {
     return this.record.mate
       ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${
@@ -95,6 +89,10 @@ export default class CramSlightlyLazyFeature implements Feature {
       : undefined
   }
 
+  _get_next_pos() {
+    return this.record.mate?.alignmentStart
+  }
+
   _get_tags() {
     const RG = this._read_group_id()
     const { tags } = this.record
@@ -141,15 +139,15 @@ export default class CramSlightlyLazyFeature implements Feature {
     return undefined
   }
 
-  parent(): undefined | Feature {
+  parent() {
     return undefined
   }
 
-  children(): undefined | Feature[] {
+  children() {
     return undefined
   }
 
-  set(): void {}
+  set() {}
 
   pairedFeature() {
     return false
@@ -181,7 +179,7 @@ export default class CramSlightlyLazyFeature implements Feature {
     }
   }
 
-  _get_mismatches(): Mismatch[] {
+  _get_mismatches() {
     const readFeatures = this.record.readFeatures
     const qual = this.qualRaw()
     const start = this.get('start')