@jbrowse/plugin-alignments 2.0.0 → 2.1.2

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -1,15 +1,4 @@
 "use strict";
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -33,48 +22,32 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var react_1 = __importStar(require("react"));
-var material_1 = require("@mui/material");
-var mui_1 = require("tss-react/mui");
-var mobx_react_1 = require("mobx-react");
-var util_1 = require("@jbrowse/core/util");
-var copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-var BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
-var MismatchParser_1 = require("../BamAdapter/MismatchParser");
-var useStyles = (0, mui_1.makeStyles)()(function () { return ({
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("@jbrowse/core/util");
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const MismatchParser_1 = require("../BamAdapter/MismatchParser");
+const useStyles = (0, mui_1.makeStyles)()(() => ({
     compact: {
         paddingRight: 0,
         paddingTop: 0,
         paddingBottom: 0,
     },
-}); });
-var omit = ['clipPos', 'flags'];
+}));
+const omit = ['clipPos', 'flags'];
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function AlignmentFlags(props) {
-    var classes = useStyles().classes;
-    var feature = props.feature;
-    var flags = feature.flags;
-    var flagNames = [
+    const { classes } = useStyles();
+    const { feature } = props;
+    const { flags } = feature;
+    const flagNames = [
         'read paired',
         'read mapped in proper pair',
         'read unmapped',
@@ -88,40 +61,39 @@ function AlignmentFlags(props) {
         'read is PCR or optical duplicate',
         'supplementary alignment',
     ];
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, __assign({}, props, { title: "Flags" }),
+    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Flags" },
         react_1.default.createElement(BaseFeatureDetail_1.SimpleValue, { name: 'Flag', value: flags }),
-        react_1.default.createElement(material_1.FormGroup, null, flagNames.map(function (name, index) {
-            var val = flags & (1 << index);
-            var key = "".concat(name, "_").concat(val);
+        react_1.default.createElement(material_1.FormGroup, null, flagNames.map((name, index) => {
+            const val = flags & (1 << index);
+            const key = `${name}_${val}`;
             return (react_1.default.createElement(material_1.FormControlLabel, { key: key, control: react_1.default.createElement(material_1.Checkbox, { className: classes.compact, checked: Boolean(val), name: name, readOnly: true }), label: name }));
         }))));
 }
-function Formatter(_a) {
-    var value = _a.value;
-    var _b = __read((0, react_1.useState)(false), 2), show = _b[0], setShow = _b[1];
-    var _c = __read((0, react_1.useState)(false), 2), copied = _c[0], setCopied = _c[1];
-    var display = String(value);
+function Formatter({ value }) {
+    const [show, setShow] = (0, react_1.useState)(false);
+    const [copied, setCopied] = (0, react_1.useState)(false);
+    const display = String(value);
     if (display.length > 100) {
         return (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement("button", { type: "button", onClick: function () {
+            react_1.default.createElement("button", { type: "button", onClick: () => {
                     (0, copy_to_clipboard_1.default)(display);
                     setCopied(true);
-                    setTimeout(function () {
+                    setTimeout(() => {
                         setCopied(false);
                     }, 700);
                 } }, copied ? 'Copied to clipboard' : 'Copy'),
-            react_1.default.createElement("button", { type: "button", onClick: function () { return setShow(function (val) { return !val; }); } }, show ? 'Show less' : 'Show more'),
-            react_1.default.createElement("div", null, show ? display : "".concat(display.slice(0, 100), "..."))));
+            react_1.default.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
+            react_1.default.createElement("div", null, show ? display : `${display.slice(0, 100)}...`)));
     }
     return react_1.default.createElement("div", null, display);
 }
 // utility function to get length of alignment from cigar
 function getLengthOnRef(cigar) {
-    var cigarOps = (0, MismatchParser_1.parseCigar)(cigar);
-    var lengthOnRef = 0;
-    for (var i = 0; i < cigarOps.length; i += 2) {
-        var len = +cigarOps[i];
-        var op = cigarOps[i + 1];
+    const cigarOps = (0, MismatchParser_1.parseCigar)(cigar);
+    let lengthOnRef = 0;
+    for (let i = 0; i < cigarOps.length; i += 2) {
+        const len = +cigarOps[i];
+        const op = cigarOps[i + 1];
         if (op !== 'H' && op !== 'S' && op !== 'I') {
             lengthOnRef += len;
         }
@@ -130,27 +102,27 @@ function getLengthOnRef(cigar) {
 }
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function SupplementaryAlignments(props) {
-    var tag = props.tag, model = props.model;
-    var session = (0, util_1.getSession)(model);
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, __assign({}, props, { title: "Supplementary alignments" }),
+    const { tag, model } = props;
+    const session = (0, util_1.getSession)(model);
+    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Supplementary alignments" },
         react_1.default.createElement(material_1.Typography, null, "List of supplementary alignment locations"),
         react_1.default.createElement("ul", null, tag
             .split(';')
-            .filter(function (SA) { return !!SA; })
-            .map(function (SA, index) {
-            var _a = __read(SA.split(','), 4), saRef = _a[0], saStart = _a[1], saStrand = _a[2], saCigar = _a[3];
-            var saLength = getLengthOnRef(saCigar);
-            var extra = Math.floor(saLength / 5);
-            var start = +saStart;
-            var end = +saStart + saLength;
-            var locString = "".concat(saRef, ":").concat(Math.max(1, start - extra), "-").concat(end + extra);
-            var displayStart = start.toLocaleString('en-US');
-            var displayEnd = end.toLocaleString('en-US');
-            var displayString = "".concat(saRef, ":").concat(displayStart, "-").concat(displayEnd, " (").concat(saStrand, ")");
-            return (react_1.default.createElement("li", { key: "".concat(locString, "-").concat(index) },
-                react_1.default.createElement(material_1.Link, { onClick: function (event) {
+            .filter(SA => !!SA)
+            .map((SA, index) => {
+            const [saRef, saStart, saStrand, saCigar] = SA.split(',');
+            const saLength = getLengthOnRef(saCigar);
+            const extra = Math.floor(saLength / 5);
+            const start = +saStart;
+            const end = +saStart + saLength;
+            const locString = `${saRef}:${Math.max(1, start - extra)}-${end + extra}`;
+            const displayStart = start.toLocaleString('en-US');
+            const displayEnd = end.toLocaleString('en-US');
+            const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand})`;
+            return (react_1.default.createElement("li", { key: `${locString}-${index}` },
+                react_1.default.createElement(material_1.Link, { onClick: event => {
                         event.preventDefault();
-                        var view = model.view;
+                        const { view } = model;
                         try {
                             if (view) {
                                 view.navToLocString(locString);
@@ -161,17 +133,16 @@ function SupplementaryAlignments(props) {
                         }
                         catch (e) {
                             console.error(e);
-                            session.notify("".concat(e));
+                            session.notify(`${e}`);
                         }
                     }, href: "#" }, displayString)));
         }))));
 }
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
-function PairLink(_a) {
-    var locString = _a.locString, model = _a.model;
-    var session = (0, util_1.getSession)(model);
-    return (react_1.default.createElement(material_1.Link, { onClick: function () {
-            var view = model.view;
+function PairLink({ locString, model }) {
+    const session = (0, util_1.getSession)(model);
+    return (react_1.default.createElement(material_1.Link, { onClick: () => {
+            const { view } = model;
             try {
                 if (view) {
                     view.navToLocString(locString);
@@ -182,21 +153,21 @@ function PairLink(_a) {
             }
             catch (e) {
                 console.error(e);
-                session.notify("".concat(e));
+                session.notify(`${e}`);
             }
         }, href: "#" }, locString));
 }
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function AlignmentFeatureDetails(props) {
-    var model = props.model;
-    var feat = JSON.parse(JSON.stringify(model.featureData));
-    var SA = (feat.tags && feat.tags.SA) || feat.SA;
+    const { model } = props;
+    const feat = JSON.parse(JSON.stringify(model.featureData));
+    const SA = (feat.tags && feat.tags.SA) || feat.SA;
     return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
-        react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, __assign({}, props, { omit: omit, feature: feat, formatter: function (value, key) {
+        react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, { ...props, omit: omit, feature: feat, formatter: (value, key) => {
                 return key === 'next_segment_position' ? (react_1.default.createElement(PairLink, { model: model, locString: value })) : (react_1.default.createElement(Formatter, { value: value }));
-            } })),
+            } }),
         SA ? react_1.default.createElement(SupplementaryAlignments, { model: model, tag: SA }) : null,
-        react_1.default.createElement(AlignmentFlags, __assign({ feature: feat }, props))));
+        react_1.default.createElement(AlignmentFlags, { feature: feat, ...props })));
 }
 exports.default = (0, mobx_react_1.observer)(AlignmentFeatureDetails);
 //# sourceMappingURL=AlignmentsFeatureDetail.js.map

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map

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

@@ -27,30 +27,28 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.configSchema = exports.stateModelFactory = void 0;
-var react_1 = require("react");
-var configuration_1 = require("@jbrowse/core/configuration");
-var mobx_state_tree_1 = require("mobx-state-tree");
-var WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
-var BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
-var configSchema = (0, configuration_1.ConfigurationSchema)('AlignmentsFeatureWidget', {});
+const react_1 = require("react");
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
+const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
+const configSchema = (0, configuration_1.ConfigurationSchema)('AlignmentsFeatureWidget', {});
 exports.configSchema = configSchema;
 function stateModelFactory(pluginManager) {
-    var baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
+    const baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
     return mobx_state_tree_1.types.compose(baseModel, mobx_state_tree_1.types.model('AlignmentsFeatureWidget', {
         type: mobx_state_tree_1.types.literal('AlignmentsFeatureWidget'),
     }));
 }
 exports.stateModelFactory = stateModelFactory;
 function register(pluginManager) {
-    pluginManager.addWidgetType(function () {
-        return new WidgetType_1.default({
-            name: 'AlignmentsFeatureWidget',
-            heading: 'Feature details',
-            configSchema: configSchema,
-            stateModel: stateModelFactory(pluginManager),
-            ReactComponent: (0, react_1.lazy)(function () { return Promise.resolve().then(function () { return __importStar(require('./AlignmentsFeatureDetail')); }); }),
-        });
-    });
+    pluginManager.addWidgetType(() => new WidgetType_1.default({
+        name: 'AlignmentsFeatureWidget',
+        heading: 'Feature details',
+        configSchema,
+        stateModel: stateModelFactory(pluginManager),
+        ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AlignmentsFeatureDetail')))),
+    }));
 }
 exports.default = register;
 //# sourceMappingURL=index.js.map

package/dist/AlignmentsFeatureDetail/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,iCAA4B;AAE5B,+DAAiE;AACjE,qDAAuC;AACvC,gGAAuE;AACvE,uEAAuF;AAEvF,MAAM,YAAY,GAAG,IAAA,mCAAmB,EAAC,yBAAyB,EAAE,EAAE,CAAC,CAAA;AAyB9D,oCAAY;AAvBrB,SAAgB,iBAAiB,CAAC,aAA4B;IAC5D,MAAM,SAAS,GAAG,IAAA,qCAAgB,EAAC,aAAa,CAAC,CAAA;IACjD,OAAO,uBAAK,CAAC,OAAO,CAClB,SAAS,EACT,uBAAK,CAAC,KAAK,CAAC,yBAAyB,EAAE;QACrC,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,yBAAyB,CAAC;KAC/C,CAAC,CACH,CAAA;AACH,CAAC;AARD,8CAQC;AAED,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,aAAa,CACzB,GAAG,EAAE,CACH,IAAI,oBAAU,CAAC;QACb,IAAI,EAAE,yBAAyB;QAC/B,OAAO,EAAE,iBAAiB;QAC1B,YAAY;QACZ,UAAU,EAAE,iBAAiB,CAAC,aAAa,CAAC;QAC5C,cAAc,EAAE,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,2BAA2B,GAAC,CAAC;KAChE,CAAC,CACL,CAAA;AACH,CAAC;AAXD,2BAWC"}

package/dist/AlignmentsTrack/index.js

@@ -3,21 +3,21 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
-var configuration_1 = require("@jbrowse/core/configuration");
-var models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
+const configuration_1 = require("@jbrowse/core/configuration");
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 function configSchemaFactory(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('AlignmentsTrack', {}, { baseConfiguration: (0, models_1.createBaseTrackConfig)(pluginManager) });
 }
 function register(pluginManager) {
-    pluginManager.addTrackType(function () {
-        var configSchema = configSchemaFactory(pluginManager);
-        var track = new TrackType_1.default({
+    pluginManager.addTrackType(() => {
+        const configSchema = configSchemaFactory(pluginManager);
+        const track = new TrackType_1.default({
             name: 'AlignmentsTrack',
-            configSchema: configSchema,
+            configSchema,
             stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'AlignmentsTrack', configSchema),
         });
-        var linearAlignmentsDisplay = pluginManager.getDisplayType('LinearAlignmentsDisplay');
+        const linearAlignmentsDisplay = pluginManager.getDisplayType('LinearAlignmentsDisplay');
         // Add LinearAlignmentsDisplay here so that it has priority over the other
         // linear displays (defaults to order the displays are added, but we have
         // to add the Pileup and SNPCoverage displays first).

package/dist/AlignmentsTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,4FAAqE;AACrE,6DAAiE;AACjE,qEAGmD;AACnD,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,IAAA,mCAAmB,EACxB,iBAAiB,EACjB,EAAE,EACF,EAAE,iBAAiB,EAAE,IAAA,8BAAqB,EAAC,aAAa,CAAC,EAAE,CAC5D,CAAA;AACH,CAAC;AACD,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,YAAY,CAAC;QACzB,IAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,IAAM,KAAK,GAAG,IAAI,mBAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,YAAY,cAAA;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAC9B,aAAa,EACb,iBAAiB,EACjB,YAAY,CACb;SACF,CAAC,CAAA;QACF,IAAM,uBAAuB,GAAG,aAAa,CAAC,cAAc,CAC1D,yBAAyB,CAC1B,CAAA;QACD,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AArBD,2BAqBC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,+DAAiE;AACjE,uEAGmD;AACnD,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,IAAA,mCAAmB,EACxB,iBAAiB,EACjB,EAAE,EACF,EAAE,iBAAiB,EAAE,IAAA,8BAAqB,EAAC,aAAa,CAAC,EAAE,CAC5D,CAAA;AACH,CAAC;AACD,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,MAAM,KAAK,GAAG,IAAI,mBAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAC9B,aAAa,EACb,iBAAiB,EACjB,YAAY,CACb;SACF,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,aAAa,CAAC,cAAc,CAC1D,yBAAyB,CAC1B,CAAA;QACD,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AArBD,2BAqBC"}

package/dist/BamAdapter/BamAdapter.d.ts

@@ -2,6 +2,10 @@ import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
+interface Header {
+    idToName: string[];
+    nameToId: Record<string, number>;
+}
 export default class BamAdapter extends BaseFeatureDataAdapter {
     private samHeader?;
     private setupP?;
@@ -15,7 +19,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     }>;
     getHeader(opts?: BaseOptions): Promise<any>;
     private setupPre;
-    private setup;
+    setup(opts?: BaseOptions): Promise<Header>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     private seqFetch;
     getFeatures(region: Region & {
@@ -38,3 +42,4 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     freeResources(): void;
     refIdToName(refId: number): string | undefined;
 }
+export {};