@jbrowse/plugin-alignments 2.4.1 → 2.4.2

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

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

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -28,145 +28,107 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 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 clone_1 = __importDefault(require("clone"));
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
-const MismatchParser_1 = require("../MismatchParser");
-const useStyles = (0, mui_1.makeStyles)()({
-    compact: {
-        paddingRight: 0,
-        paddingTop: 0,
-        paddingBottom: 0,
-    },
-});
+// locals
+const util_1 = require("./util");
+const AlignmentsFeatureSuppAligns_1 = __importDefault(require("./AlignmentsFeatureSuppAligns"));
+const AlignmentsFeatureFlags_1 = __importDefault(require("./AlignmentsFeatureFlags"));
 const omit = ['clipPos', 'flags'];
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function AlignmentFlags(props) {
-    const { classes } = useStyles();
-    const { feature } = props;
-    const { flags } = feature;
-    const flagNames = [
-        'read paired',
-        'read mapped in proper pair',
-        'read unmapped',
-        'mate unmapped',
-        'read reverse strand',
-        'mate reverse strand',
-        'first in pair',
-        'second in pair',
-        'not primary alignment',
-        'read fails platform/vendor quality checks',
-        'read is PCR or optical duplicate',
-        'supplementary alignment',
-    ];
-    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((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 }));
-        }))));
-}
+const tags = {
+    AM: 'The smallest template-independent mapping quality in the template',
+    AS: 'Alignment score generated by aligner',
+    BC: 'Barcode sequence identifying the sample',
+    BQ: 'Offset to base alignment quality (BAQ)',
+    BZ: 'Phred quality of the unique molecular barcode bases in the {OX} tag',
+    CB: 'Cell identifier',
+    CC: 'Reference name of the next hit',
+    CM: 'Edit distance between the color sequence and the color reference (see also {NM})',
+    CO: 'Free-text comments',
+    CP: 'Leftmost coordinate of the next hit',
+    CQ: 'Color read base qualities',
+    CR: 'Cellular barcode sequence bases (uncorrected)',
+    CS: 'Color read sequence',
+    CT: 'Complete read annotation tag, used for consensus annotation dummy features',
+    CY: 'Phred quality of the cellular barcode sequence in the {CR} tag',
+    E2: 'The 2nd most likely base calls',
+    FI: 'The index of segment in the template',
+    FS: 'Segment suffix',
+    FZ: 'Flow signal intensities',
+    GC: 'Reserved for backwards compatibility reasons',
+    GQ: 'Reserved for backwards compatibility reasons',
+    GS: 'Reserved for backwards compatibility reasons',
+    H0: 'Number of perfect hits',
+    H1: 'Number of 1-difference hits (see also {NM})',
+    H2: 'Number of 2-difference hits',
+    HI: 'Query hit index',
+    IH: 'Query hit total count',
+    LB: 'Library',
+    MC: 'CIGAR string for mate/next segment',
+    MD: 'String encoding mismatched and deleted reference bases',
+    MF: 'Reserved for backwards compatibility reasons',
+    MI: 'Molecular identifier; a string that uniquely identifies the molecule from which the record was derived',
+    ML: 'Base modification probabilities',
+    MM: 'Base modifications / methylation ',
+    MQ: 'Mapping quality of the mate/next segment',
+    NH: 'Number of reported alignments that contain the query in the current record',
+    NM: 'Edit distance to the reference',
+    OA: 'Original alignment',
+    OC: 'Original CIGAR (deprecated; use {OA} instead)',
+    OP: 'Original mapping position (deprecated; use {OA} instead)',
+    OQ: 'Original base quality',
+    OX: 'Original unique molecular barcode bases',
+    PG: 'Program',
+    PQ: 'Phred likelihood of the template',
+    PT: 'Read annotations for parts of the padded read sequence',
+    PU: 'Platform unit',
+    Q2: 'Phred quality of the mate/next segment sequence in the {R2} tag',
+    QT: 'Phred quality of the sample barcode sequence in the {BC} tag',
+    QX: 'Quality score of the unique molecular identifier in the {RX} tag',
+    R2: 'Sequence of the mate/next segment in the template',
+    RG: 'Read group',
+    RT: 'Reserved for backwards compatibility reasons',
+    RX: 'Sequence bases of the (possibly corrected) unique molecular identifier',
+    S2: 'Reserved for backwards compatibility reasons',
+    SA: 'Other canonical alignments in a chimeric alignment',
+    SM: 'Template-independent mapping quality',
+    SQ: 'Reserved for backwards compatibility reasons',
+    TC: 'The number of segments in the template',
+    TS: 'Transcript strand',
+    U2: 'Phred probability of the 2nd call being wrong conditional on the best being wrong',
+    UQ: 'Phred likelihood of the segment, conditional on the mapping being correct',
+};
 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: () => {
-                    (0, copy_to_clipboard_1.default)(display);
-                    setCopied(true);
-                    setTimeout(() => {
-                        setCopied(false);
-                    }, 700);
-                } }, copied ? 'Copied to clipboard' : 'Copy'),
-            react_1.default.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
-            react_1.default.createElement("div", null, show ? display : `${display.slice(0, 100)}...`)));
-    }
-    return react_1.default.createElement("div", null, display);
+    return display.length > 100 ? (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement("button", { type: "button", onClick: () => {
+                (0, copy_to_clipboard_1.default)(display);
+                setCopied(true);
+                setTimeout(() => setCopied(false), 700);
+            } }, copied ? 'Copied to clipboard' : 'Copy'),
+        react_1.default.createElement("button", { type: "button", onClick: () => setShow(val => !val) }, show ? 'Show less' : 'Show more'),
+        react_1.default.createElement("div", null, show ? display : `${display.slice(0, 100)}...`))) : (react_1.default.createElement("div", null, display));
 }
-// utility function to get length of alignment from cigar
-function getLengthOnRef(cigar) {
-    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;
-        }
-    }
-    return lengthOnRef;
-}
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function SupplementaryAlignments(props) {
-    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(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}-${index}` },
-                react_1.default.createElement(material_1.Link, { onClick: async (event) => {
-                        event.preventDefault();
-                        const { view } = model;
-                        try {
-                            if (view) {
-                                await view.navToLocString(locString);
-                            }
-                            else {
-                                throw new Error('No view associated with this view anymore');
-                            }
-                        }
-                        catch (e) {
-                            console.error(e);
-                            session.notify(`${e}`);
-                        }
-                    }, href: "#" }, displayString)));
-        }))));
-}
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function PairLink({ locString, model }) {
-    const session = (0, util_1.getSession)(model);
-    return (react_1.default.createElement(material_1.Link, { onClick: async () => {
-            const { view } = model;
-            if (!view) {
-                throw new Error('No view associated with this feature detail panel anymore');
-            }
-            try {
-                await view.navToLocString(locString);
-            }
-            catch (e) {
-                console.error(e);
-                session.notify(`${e}`);
-            }
+function PairLink({ locString, model, }) {
+    return (react_1.default.createElement(material_1.Link, { onClick: event => {
+            event.preventDefault();
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            (0, util_1.navToLoc)(locString, model);
         }, href: "#" }, locString));
 }
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function AlignmentFeatureDetails(props) {
+exports.default = (0, mobx_react_1.observer)(function AlignmentFeatureDetails(props) {
     const { model } = props;
     const feat = (0, clone_1.default)(model.featureData);
-    const SA = (feat.tags && feat.tags.SA) || feat.SA;
+    const SA = (0, util_1.getTag)('SA', feat);
     return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
-        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,
-        feat.flags !== undefined ? (react_1.default.createElement(AlignmentFlags, { feature: feat, ...props })) : null));
-}
-exports.default = (0, mobx_react_1.observer)(AlignmentFeatureDetails);
+        react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, { ...props, omit: omit, 
+            // @ts-expect-error
+            descriptions: { ...tags, tags }, feature: feat, formatter: (value, key) => 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(AlignmentsFeatureSuppAligns_1.default, { model: model, tag: SA }) : null,
+        feat.flags !== undefined ? (react_1.default.createElement(AlignmentsFeatureFlags_1.default, { feature: feat, ...props })) : null));
+});
 //# sourceMappingURL=AlignmentsFeatureDetail.js.map

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map

@@ -1 +1 @@
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package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+export default function AlignmentFlags(props: {
+    feature: {
+        flags: number;
+    };
+}): JSX.Element;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js

@@ -0,0 +1,44 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const useStyles = (0, mui_1.makeStyles)()({
+    compact: {
+        paddingRight: 0,
+        paddingTop: 0,
+        paddingBottom: 0,
+    },
+});
+const flagNames = [
+    'read paired',
+    'read mapped in proper pair',
+    'read unmapped',
+    'mate unmapped',
+    'read reverse strand',
+    'mate reverse strand',
+    'first in pair',
+    'second in pair',
+    'not primary alignment',
+    'read fails platform/vendor quality checks',
+    'read is PCR or optical duplicate',
+    'supplementary alignment',
+];
+function AlignmentFlags(props) {
+    const { classes } = useStyles();
+    const { feature } = props;
+    const { flags } = feature;
+    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((name, idx) => {
+            const val = flags & (1 << idx);
+            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 }));
+        }))));
+}
+exports.default = AlignmentFlags;
+//# sourceMappingURL=AlignmentsFeatureFlags.js.map

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"AlignmentsFeatureFlags.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAqE;AACrE,uCAA0C;AAC1C,yFAG0D;AAE1D,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,OAAO,EAAE;QACP,YAAY,EAAE,CAAC;QACf,UAAU,EAAE,CAAC;QACb,aAAa,EAAE,CAAC;KACjB;CACF,CAAC,CAAA;AAEF,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,SAAwB,cAAc,CAAC,KAAqC;IAC1E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACzB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAA;IAEzB,OAAO,CACL,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,OAAO;QAChC,8BAAC,+BAAW,IAAC,IAAI,EAAC,MAAM,EAAC,KAAK,EAAE,KAAK,GAAI;QACzC,8BAAC,oBAAS,QACP,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,GAAG,EAAE,EAAE;YAC3B,MAAM,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,IAAI,GAAG,CAAC,CAAA;YAC9B,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,8BAAC,2BAAgB,IACf,GAAG,EAAE,GAAG,EACR,OAAO,EACL,8BAAC,mBAAQ,IACP,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,IAAI,EAAE,IAAI,EACV,QAAQ,SACR,EAEJ,KAAK,EAAE,IAAI,GACX,CACH,CAAA;QACH,CAAC,CAAC,CACQ,CACH,CACZ,CAAA;AACH,CAAC;AA9BD,iCA8BC"}

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+export default function SupplementaryAlignments(props: {
+    tag: string;
+    model: IAnyStateTreeNode;
+}): JSX.Element;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js

@@ -0,0 +1,37 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const MismatchParser_1 = require("../MismatchParser");
+const util_1 = require("./util");
+function SupplementaryAlignments(props) {
+    const { tag, model } = props;
+    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(SA => !!SA)
+            .map((SA, index) => {
+            const [saRef, saStart, saStrand, saCigar] = SA.split(',');
+            const saLength = (0, MismatchParser_1.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} (${saStrand}) [${saLength}bp]`;
+            return (react_1.default.createElement("li", { key: `${locString}-${index}` },
+                react_1.default.createElement(material_1.Link, { onClick: async (event) => {
+                        event.preventDefault();
+                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                        (0, util_1.navToLoc)(locString, model);
+                    }, href: "#" }, displayString)));
+        }))));
+}
+exports.default = SupplementaryAlignments;
+//# sourceMappingURL=AlignmentsFeatureSuppAligns.js.map

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"AlignmentsFeatureSuppAligns.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAgD;AAChD,yFAA4E;AAC5E,sDAAkD;AAElD,iCAAiC;AAEjC,SAAwB,uBAAuB,CAAC,KAG/C;IACC,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAC5B,OAAO,CACL,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,0BAA0B;QACnD,8BAAC,qBAAU,oDAAuD;QAClE,0CACG,GAAG;aACD,KAAK,CAAC,GAAG,CAAC;aACV,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;aAClB,GAAG,CAAC,CAAC,EAAE,EAAE,KAAK,EAAE,EAAE;YACjB,MAAM,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;YACzD,MAAM,QAAQ,GAAG,IAAA,+BAAc,EAAC,OAAO,CAAC,CAAA;YACxC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,GAAG,CAAC,CAAC,CAAA;YACtC,MAAM,KAAK,GAAG,CAAC,OAAO,CAAA;YACtB,MAAM,GAAG,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAA;YAC/B,MAAM,SAAS,GAAG,GAAG,KAAK,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC,IACtD,GAAG,GAAG,KACR,EAAE,CAAA;YACF,MAAM,YAAY,GAAG,KAAK,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;YAClD,MAAM,UAAU,GAAG,GAAG,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;YAC9C,MAAM,aAAa,GAAG,GAAG,KAAK,IAAI,YAAY,IAAI,UAAU,KAAK,QAAQ,MAAM,QAAQ,KAAK,CAAA;YAC5F,OAAO,CACL,sCAAI,GAAG,EAAE,GAAG,SAAS,IAAI,KAAK,EAAE;gBAC9B,8BAAC,eAAI,IACH,OAAO,EAAE,KAAK,EAAC,KAAK,EAAC,EAAE;wBACrB,KAAK,CAAC,cAAc,EAAE,CAAA;wBAEtB,mEAAmE;wBACnE,IAAA,eAAQ,EAAC,SAAS,EAAE,KAAK,CAAC,CAAA;oBAC5B,CAAC,EACD,IAAI,EAAC,GAAG,IAEP,aAAa,CACT,CACJ,CACN,CAAA;QACH,CAAC,CAAC,CACD,CACI,CACZ,CAAA;AACH,CAAC;AA3CD,0CA2CC"}

package/dist/AlignmentsFeatureDetail/index.d.ts

@@ -32,8 +32,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    id: string;
     type: "BaseFeatureWidget";
+    id: string;
     track: import("mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;

package/dist/AlignmentsFeatureDetail/util.d.ts

@@ -0,0 +1,8 @@
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+export declare function getTag(tag: string, feat: {
+    tags?: {
+        [key: string]: unknown;
+    };
+    [key: string]: unknown;
+}): unknown;
+export declare function navToLoc(locString: string, model: IAnyStateTreeNode): Promise<void>;

package/dist/AlignmentsFeatureDetail/util.js

@@ -0,0 +1,27 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.navToLoc = exports.getTag = void 0;
+const util_1 = require("@jbrowse/core/util");
+function getTag(tag, feat) {
+    var _a;
+    return ((_a = feat.tags) === null || _a === void 0 ? void 0 : _a[tag]) || feat[tag];
+}
+exports.getTag = getTag;
+async function navToLoc(locString, model) {
+    const session = (0, util_1.getSession)(model);
+    const { view } = model;
+    try {
+        if (view) {
+            await view.navToLocString(locString);
+        }
+        else {
+            throw new Error('No view associated with this view anymore');
+        }
+    }
+    catch (e) {
+        console.error(e);
+        session.notify(`${e}`);
+    }
+}
+exports.navToLoc = navToLoc;
+//# sourceMappingURL=util.js.map

package/dist/AlignmentsFeatureDetail/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/util.ts"],"names":[],"mappings":";;;AAAA,6CAA+C;AAG/C,SAAgB,MAAM,CACpB,GAAW,EACX,IAGC;;IAED,OAAO,CAAA,MAAA,IAAI,CAAC,IAAI,0CAAG,GAAG,CAAC,KAAI,IAAI,CAAC,GAAG,CAAC,CAAA;AACtC,CAAC;AARD,wBAQC;AAEM,KAAK,UAAU,QAAQ,CAAC,SAAiB,EAAE,KAAwB;IACxE,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IACtB,IAAI;QACF,IAAI,IAAI,EAAE;YACR,MAAM,IAAI,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;SACrC;aAAM;YACL,MAAM,IAAI,KAAK,CAAC,2CAA2C,CAAC,CAAA;SAC7D;KACF;IAAC,OAAO,CAAC,EAAE;QACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;KACvB;AACH,CAAC;AAbD,4BAaC"}

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -10,7 +10,7 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const useStyles = (0, mui_1.makeStyles)()({
     resizeHandle: {
-        height: 2,
+        height: 5,
         position: 'absolute',
         zIndex: 2,
     },
@@ -25,7 +25,7 @@ function AlignmentsDisplay({ model }) {
         react_1.default.createElement(ui_1.ResizeHandle, { onDrag: delta => {
                 SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
                 return delta;
-            }, className: classes.resizeHandle, style: { top } }),
+            }, className: classes.resizeHandle, style: { top: top - 4 } }),
         react_1.default.createElement("div", { "data-testid": "Blockset-pileup", style: {
                 position: 'absolute',
                 top,

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map

@@ -1 +1 @@
-{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,uCAA0C;AAC1C,+DAAqD;AACrD,yCAA+C;AAK/C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAA;AAEF,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAAqC;IACrE,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,kBAAkB,CAAC,MAAM,CAAA;IACrC,OAAO,CACL,sDACe,WAAW,IAAA,uBAAO,EAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE/B,sDAAiB,sBAAsB;YACrC,8BAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;QACN,8BAAC,iBAAY,IACX,MAAM,EAAE,KAAK,CAAC,EAAE;gBACd,kBAAkB,CAAC,SAAS,CAAC,kBAAkB,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;gBAC/D,OAAO,KAAK,CAAA;YACd,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE,EAAE,GAAG,EAAE,GACd;QAEF,sDACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG;aACJ;YAED,8BAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACF,CACP,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,iBAAiB,CAAC,CAAA"}
+{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,uCAA0C;AAC1C,+DAAqD;AACrD,yCAA+C;AAK/C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAA;AAEF,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAAqC;IACrE,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,kBAAkB,CAAC,MAAM,CAAA;IACrC,OAAO,CACL,sDACe,WAAW,IAAA,uBAAO,EAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE/B,sDAAiB,sBAAsB;YACrC,8BAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;QACN,8BAAC,iBAAY,IACX,MAAM,EAAE,KAAK,CAAC,EAAE;gBACd,kBAAkB,CAAC,SAAS,CAAC,kBAAkB,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;gBAC/D,OAAO,KAAK,CAAA;YACd,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE,EAAE,GAAG,EAAE,GAAG,GAAG,CAAC,EAAE,GACvB;QAEF,sDACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG;aACJ;YAED,8BAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACF,CACP,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,iBAAiB,CAAC,CAAA"}

package/dist/LinearAlignmentsDisplay/models/model.d.ts

@@ -125,7 +125,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #action
      */
-    updateStatsLimit(stats: unknown): void;
+    updateStatsLimit(stats?: unknown): void;
     /**
      * #action
      */

package/dist/LinearAlignmentsDisplay/models/model.js.map

@@ -1 +1 @@
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