@jbrowse/plugin-alignments 2.2.1 → 2.3.0

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

@@ -22,26 +22,17 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
+const ui_1 = require("@jbrowse/core/ui");
 const mui_1 = require("tss-react/mui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     paper: {
         padding: theme.spacing(2),
         margin: theme.spacing(2),
     },
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
     field: {
         margin: theme.spacing(2),
     },
@@ -91,11 +82,7 @@ function FilterByTagDlg(props) {
     const [readName, setReadName] = (0, react_1.useState)((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || '');
     const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
     const site = 'https://broadinstitute.github.io/picard/explain-flags.html';
-    return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
-        react_1.default.createElement(material_1.DialogTitle, null,
-            "Filter options",
-            react_1.default.createElement(material_1.IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
-                react_1.default.createElement(Close_1.default, null))),
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options" },
         react_1.default.createElement(material_1.DialogContent, null,
             react_1.default.createElement(material_1.Typography, null,
                 "Set filter bitmask options. Refer to ",
@@ -112,22 +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

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package/dist/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/dist/shared/color.js

@@ -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

@@ -0,0 +1 @@
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package/dist/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/dist/shared/fetchChains.js

@@ -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

@@ -0,0 +1 @@
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package/dist/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/dist/{shared.js → shared/index.js}

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getUniqueModificationValues = exports.getUniqueTagValues = void 0;
+exports.FilterModel = exports.getUniqueModificationValues = exports.getUniqueTagValues = void 0;
+const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 async function getUniqueTagValues(self, colorScheme, blocks, opts) {
@@ -30,4 +31,13 @@ async function getUniqueModificationValues(self, adapterConfig, colorScheme, blo
     return values;
 }
 exports.getUniqueModificationValues = getUniqueModificationValues;
-//# sourceMappingURL=shared.js.map
+exports.FilterModel = mobx_state_tree_1.types.model({
+    flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
+    flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
+    readName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+    tagFilter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({
+        tag: mobx_state_tree_1.types.string,
+        value: mobx_state_tree_1.types.string,
+    })),
+});
+//# sourceMappingURL=index.js.map

package/dist/shared/index.js.map

@@ -0,0 +1 @@
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package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -6,7 +6,7 @@ import { getSession } from '@jbrowse/core/util';
 import copy from 'copy-to-clipboard';
 import clone from 'clone';
 import { FeatureDetails, BaseCard, SimpleValue, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
-import { parseCigar } from '../BamAdapter/MismatchParser';
+import { parseCigar } from '../MismatchParser';
 const useStyles = makeStyles()({
     compact: {
         paddingRight: 0,

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map

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

@@ -19,6 +19,7 @@ export default function register(pm) {
         const configSchema = configSchemaFactory(pm);
         const track = new TrackType({
             name: 'AlignmentsTrack',
+            displayName: 'Alignments track',
             configSchema,
             stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema),
         });

package/esm/AlignmentsTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EACL,qBAAqB,EACrB,oBAAoB,GACrB,MAAM,4CAA4C,CAAA;AAEnD;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,mBAAmB,CACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AACD,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EACL,qBAAqB,EACrB,oBAAoB,GACrB,MAAM,4CAA4C,CAAA;AAEnD;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,OAAO,mBAAmB,CACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AACD,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -13,9 +13,8 @@ export default class BamSlightlyLazyFeature implements Feature {
     _get_flags(): string;
     _get_strand(): number;
     _get_pair_orientation(): string | null | undefined;
-    _get_next_seq_id(): number;
-    _get_seq_id(): number;
-    _get_next_refName(): string | undefined;
+    _get_next_ref(): string | undefined;
+    _get_next_pos(): number | undefined;
     _get_next_segment_position(): string | undefined;
     _get_seq(): string;
     qualRaw(): Buffer | undefined;
@@ -28,6 +27,6 @@ export default class BamSlightlyLazyFeature implements Feature {
     children(): undefined;
     pairedFeature(): boolean;
     toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): import("./MismatchParser").Mismatch[];
+    _get_mismatches(): import("../MismatchParser").Mismatch[];
     _get_clipPos(): number;
 }

package/esm/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,5 +1,5 @@
 // locals
-import { getMismatches } from './MismatchParser';
+import { getClip, getMismatches } from '../MismatchParser';
 export default class BamSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class
     // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
@@ -26,20 +26,17 @@ export default class BamSlightlyLazyFeature {
     _get_pair_orientation() {
         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;
     }
     _get_seq() {
@@ -55,9 +52,7 @@ export default class BamSlightlyLazyFeature {
             ...new Set(properties
                 .filter(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())),
         ];
@@ -100,9 +95,7 @@ export default class BamSlightlyLazyFeature {
     }
     _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'));
     }
 }
 //# sourceMappingURL=BamSlightlyLazyFeature.js.map

package/esm/BamAdapter/BamSlightlyLazyFeature.js.map

@@ -1 +1 @@
-{"version":3,"file":"BamSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/BamAdapter/BamSlightlyLazyFeature.ts"],"names":[],"mappings":"AAOA,SAAS;AACT,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAGhD,MAAM,CAAC,OAAO,OAAO,sBAAsB;IACzC,wEAAwE;IACxE,iFAAiF;IACjF,YACU,MAAiB,EACjB,OAAmB,EACnB,GAAY;QAFZ,WAAM,GAAN,MAAM,CAAW;QACjB,YAAO,GAAP,OAAO,CAAY;QACnB,QAAG,GAAH,GAAG,CAAS;IACnB,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,gBAAgB;QACd,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAA;IAClC,CAAC;IAED,WAAW;QACT,aAAa;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,MAAM,CAAA;IAC3B,CAAC;IAED,iBAAiB;QACf,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;IAC5D,CAAC;IAED,0BAA0B;QACxB,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;QAChC,OAAO,MAAM,CAAC,QAAQ,EAAE;YACtB,CAAC,CAAC,GAAG,OAAO,CAAC,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IAAI,MAAM,CAAC,SAAS,EAAE,GAAG,CAAC,EAAE;YAC1E,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAA;IAC9B,CAAC;IAED,GAAG,KAAI,CAAC;IAER,IAAI;QACF,MAAM,UAAU,GAAG,MAAM,CAAC,mBAAmB,CAC3C,sBAAsB,CAAC,SAAS,CACjC,CAAA;QAED,OAAO;YACL,GAAG,IAAI,GAAG,CACR,UAAU;iBACP,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;gBACxB,IAAI,KAAK,iBAAiB;gBAC1B,IAAI,KAAK,WAAW;gBACpB,IAAI,KAAK,kBAAkB;gBAC3B,IAAI,KAAK,aAAa,CACzB;iBACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;iBAClD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAC/B;SACF,CAAA;IACH,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,CAAA;IACjD,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC/B,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;IACvD,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,OAAO,aAAa,CAClB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EACjB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EACd,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EACf,IAAI,CAAC,GAAG,EACR,IAAI,CAAC,OAAO,EAAE,CACf,CAAA;IACH,CAAC;IAED,YAAY;QACV,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;QACrC,OAAO,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;YAC9B,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;YAC5C,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAClD,CAAC;CACF"}
+{"version":3,"file":"BamSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/BamAdapter/BamSlightlyLazyFeature.ts"],"names":[],"mappings":"AAOA,SAAS;AACT,OAAO,EAAE,OAAO,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAA;AAG1D,MAAM,CAAC,OAAO,OAAO,sBAAsB;IACzC,wEAAwE;IACxE,iFAAiF;IACjF,YACU,MAAiB,EACjB,OAAmB,EACnB,GAAY;QAFZ,WAAM,GAAN,MAAM,CAAW;QACjB,YAAO,GAAP,OAAO,CAAY;QACnB,QAAG,GAAH,GAAG,CAAS;IACnB,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;YACrD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IACrE,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IACpD,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,CAC5B,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAA;IAC9B,CAAC;IAED,GAAG,KAAI,CAAC;IAER,IAAI;QACF,MAAM,UAAU,GAAG,MAAM,CAAC,mBAAmB,CAC3C,sBAAsB,CAAC,SAAS,CACjC,CAAA;QAED,OAAO;YACL,GAAG,IAAI,GAAG,CACR,UAAU;iBACP,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;gBACxB,IAAI,KAAK,iBAAiB;gBAC1B,IAAI,KAAK,WAAW,CACvB;iBACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;iBAClD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAC/B;SACF,CAAA;IACH,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,CAAA;IACjD,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC/B,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;IACvD,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,OAAO,aAAa,CAClB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EACjB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EACd,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EACf,IAAI,CAAC,GAAG,EACR,IAAI,CAAC,OAAO,EAAE,CACf,CAAA;IACH,CAAC;IAED,YAAY;QACV,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;QACrC,OAAO,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;IAC3C,CAAC;CACF"}

package/esm/BamAdapter/index.js

@@ -4,6 +4,7 @@ export default (pluginManager) => {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'BamAdapter',
+            displayName: 'BAM adapter',
             configSchema,
             getAdapterClass: () => import('./BamAdapter').then(r => r.default),
         });

package/esm/BamAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BamAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,YAAY;YAClB,YAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BamAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,YAAY;YAClB,WAAW,EAAE,aAAa;YAC1B,YAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -1,7 +1,6 @@
 import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 import { CramRecord } from '@gmod/cram';
 import CramAdapter from './CramAdapter';
-import { Mismatch } from './util';
 export default class CramSlightlyLazyFeature implements Feature {
     private record;
     private _store;
@@ -17,25 +16,24 @@ export default class CramSlightlyLazyFeature implements Feature {
     _read_group_id(): string | undefined;
     _get_qual(): string;
     qualRaw(): number[] | null | undefined;
-    _get_seq_id(): string | undefined;
     _get_refName(): string | undefined;
     _get_is_paired(): boolean;
     _get_pair_orientation(): string | null | undefined;
     _get_template_length(): number | undefined;
-    _get_next_seq_id(): string | undefined;
-    _get_next_pos(): number | undefined;
+    _get_next_ref(): string | undefined;
     _get_next_segment_position(): string | undefined;
+    _get_next_pos(): number | undefined;
     _get_tags(): Record<string, string>;
     _get_seq(): string | null | undefined;
     _get_CIGAR(): string;
     tags(): string[];
     id(): string;
     get(field: string): any;
-    parent(): undefined | Feature;
-    children(): undefined | Feature[];
+    parent(): undefined;
+    children(): undefined;
     set(): void;
     pairedFeature(): boolean;
     _get_clipPos(): any;
     toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): Mismatch[];
+    _get_mismatches(): import("./util").Mismatch[];
 }

package/esm/CramAdapter/CramSlightlyLazyFeature.js

@@ -41,11 +41,8 @@ export default class CramSlightlyLazyFeature {
     qualRaw() {
         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() {
         return !!this.record.mate;
@@ -56,19 +53,20 @@ export default class CramSlightlyLazyFeature {
     _get_template_length() {
         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
             ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${this.record.mate.alignmentStart}`
             : undefined;
     }
+    _get_next_pos() {
+        var _a;
+        return (_a = this.record.mate) === null || _a === void 0 ? void 0 : _a.alignmentStart;
+    }
     _get_tags() {
         const RG = this._read_group_id();
         const { tags } = this.record;

package/esm/CramAdapter/CramSlightlyLazyFeature.js.map

@@ -1 +1 @@
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+{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":"AASA,OAAO,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,QAAQ,CAAA;AAEtE,MAAM,CAAC,OAAO,OAAO,uBAAuB;IAC1C,wEAAwE;IACxE,iFAAiF;IACjF,YAAoB,MAAkB,EAAU,MAAmB;QAA/C,WAAM,GAAN,MAAM,CAAY;QAAU,WAAM,GAAN,MAAM,CAAa;IAAG,CAAC;IAEvE,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,CAAA;IACvC,CAAC;IAED,QAAQ;;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,MAAA,IAAI,CAAC,MAAM,CAAC,WAAW,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACxE,CAAC;IAED,uBAAuB;QACrB,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IACjC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,CAAA;IACnC,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,cAAc;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAA;QAC3C,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACrD,CAAC;IAED,SAAS;QACP,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACpD,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,aAAa,CAAA;IAClC,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACxD,CAAC;IAED,cAAc;QACZ,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAA;IAC3B,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,oBAAoB;QAClB,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,IAAI,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IAC/D,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC;YACtD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,IACrD,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cACnB,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;;QACX,OAAO,MAAA,IAAI,CAAC,MAAM,CAAC,IAAI,0CAAE,cAAc,CAAA;IACzC,CAAC;IAED,SAAS;QACP,MAAM,EAAE,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAA;QAC5B,4DAA4D;QAC5D,OAAO,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;IAClD,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,kDAAkD;IAClD,UAAU;QACR,OAAO,mBAAmB,CACxB,IAAI,CAAC,MAAM,CAAC,YAAY,EACxB,IAAI,CAAC,MAAM,CAAC,cAAc,EAC1B,IAAI,CAAC,MAAM,CAAC,UAAU,EACtB,IAAI,CAAC,MAAM,CAAC,UAAU,CACvB,CAAA;IACH,CAAC;IAED,IAAI;QACF,OAAO,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,CAAC,SAAS,CAAC;aACjE,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;YACxB,IAAI,KAAK,iBAAiB;YAC1B,IAAI,KAAK,yBAAyB,CACrC;aACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;IACpD,CAAC;IAED,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,GAAG,KAAI,CAAC;IAER,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,YAAY;QACV,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;QACzC,IAAI,UAAU,CAAC,MAAM,EAAE;YACrB,MAAM,MAAM,GACV,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;gBACvB,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC;gBACnC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;YAChC,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,EAAE;gBAC9C,OAAO,OAAO,CAAA;aACf;SACF;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;QAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,EAAE,CAAA;QAC3B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAC/B,OAAO,wBAAwB,CAAC,YAAY,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IAC5D,CAAC;CACF"}

package/esm/CramAdapter/CramTestAdapters.js

@@ -61,7 +61,8 @@ export class SequenceAdapter extends BaseFeatureDataAdapter {
                     end,
                 }));
                 observer.complete();
-            });
+            })
+                .catch(e => observer.error(e));
             return { unsubscribe: () => { } };
         });
     }

package/esm/CramAdapter/CramTestAdapters.js.map

@@ -1 +1 @@
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+{"version":3,"file":"CramTestAdapters.js","sourceRoot":"","sources":["../../src/CramAdapter/CramTestAdapters.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AACjC,OAAO,aAAa,MAAM,kCAAkC,CAAA;AAC5D,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAE,mBAAmB,EAAE,MAAM,iDAAiD,CAAA;AAErF,iCAAiC;AACjC,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;QAC5D,MAAM,CAAC,EAAE,EAAE,GAAG,gBAAgB,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QACpD,MAAM,WAAW,GAAG,gBAAgB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC9C,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QACrD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAA;IACtC,CAAC,CAAC,CAAA;AACN,CAAC;AAID,MAAM,OAAO,mBAAmB;IAG9B,YAAY,UAAsB;QAChC,IAAI,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE;YAC9C,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACpC,OAAO,eAAe,CAAC,IAAI,CAAC,CAAA;QAC9B,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,EAAU,EAAE,KAAa,EAAE,GAAW;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,MAAM,KAAK,GAAG,IAAI,CAAC,EAAE,CAAC,CAAA;QACtB,MAAM,MAAM,GAAG,GAAG,GAAG,KAAK,GAAG,CAAC,CAAA;QAC9B,IAAI,CAAC,KAAK,EAAE;YACV,MAAM,IAAI,KAAK,CAAC,uBAAuB,EAAE,SAAS,CAAC,CAAA;SACpD;QACD,OAAO,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,GAAG,MAAM,CAAC,CAAA;IACpD,CAAC;IAED,KAAK,CAAC,eAAe;QACnB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,OAAO,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;IACpC,CAAC;CACF;AAED,MAAM,OAAO,eAAgB,SAAQ,sBAAsB;IAKzD,YAAY,UAAsB;QAChC,KAAK,CAAC,mBAAmB,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAA;QAHlD,aAAQ,GAAa,EAAE,CAAA;QAIrB,IAAI,CAAC,KAAK,GAAG,IAAI,mBAAmB,CAAC,UAAU,CAAC,CAAA;IAClD,CAAC;IAED,KAAK,CAAC,WAAW;QACf,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED,WAAW,CAAC,EACV,OAAO,EACP,KAAK,EACL,GAAG,GAKJ;QACC,OAAO,IAAI,UAAU,CAAC,QAAQ,CAAC,EAAE;YAC/B,IAAI,CAAC,KAAK;iBACP,eAAe,EAAE;iBACjB,IAAI,CAAC,QAAQ,CAAC,EAAE;gBACf,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;YAC1B,CAAC,CAAC;iBACD,IAAI,CAAC,GAAG,EAAE,CACT,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,KAAK,EAAE,GAAG,CAAC,CAC7D;iBACA,IAAI,CAAC,GAAG,CAAC,EAAE;gBACV,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,QAAQ,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,GAAG,EAAE;oBACtC,GAAG,EAAE,GAAG;oBACR,KAAK;oBACL,GAAG;iBACJ,CAAC,CACH,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;YACrB,CAAC,CAAC;iBACD,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;YAChC,OAAO,EAAE,WAAW,EAAE,GAAG,EAAE,GAAE,CAAC,EAAE,CAAA;QAClC,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC"}

package/esm/CramAdapter/index.js

@@ -5,6 +5,7 @@ export default (pluginManager) => {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'CramAdapter',
+            displayName: 'CRAM adapter',
             configSchema,
             getAdapterClass: () => import('./CramAdapter').then(r => r.default),
         });

package/esm/CramAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,aAAa;YACnB,YAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACpE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,aAAa;YACnB,WAAW,EAAE,cAAc;YAC3B,YAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACpE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/GuessAlignmentsTypes/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;