@jbrowse/plugin-alignments 2.5.0 → 2.6.1

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,5 +1,6 @@
+import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 declare const _default: (props: {
     model: IAnyStateTreeNode;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts

@@ -1,5 +1,6 @@
+import React from 'react';
 export default function AlignmentFlags(props: {
     feature: {
         flags: number;
     };
-}): JSX.Element;
+}): React.JSX.Element;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js

@@ -7,6 +7,7 @@ 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 SimpleField_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField"));
 const useStyles = (0, mui_1.makeStyles)()({
     compact: {
         paddingRight: 0,
@@ -33,7 +34,7 @@ function AlignmentFlags(props) {
     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(SimpleField_1.default, { 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}`;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AlignmentsFeatureFlags.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAqE;AACrE,uCAA0C;AAC1C,yFAA4E;AAC5E,gHAAuF;AAEvF,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,qBAAW,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

@@ -1,5 +1,6 @@
+import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 export default function SupplementaryAlignments(props: {
     tag: string;
     model: IAnyStateTreeNode;
-}): JSX.Element;
+}): React.JSX.Element;

package/dist/BamAdapter/BamAdapter.d.ts

@@ -21,7 +21,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         bam: BamFile;
         sequenceAdapter?: BaseFeatureDataAdapter | undefined;
     }>;
-    getHeader(opts?: BaseOptions): Promise<any>;
+    getHeader(opts?: BaseOptions): Promise<string | undefined>;
     private setupPre;
     setup(opts?: BaseOptions): Promise<Header>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;

package/dist/BamAdapter/BamAdapter.js

@@ -9,9 +9,9 @@ const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const operators_1 = require("rxjs/operators");
+const rxjs_2 = require("rxjs");
 // locals
 const BamSlightlyLazyFeature_1 = __importDefault(require("./BamSlightlyLazyFeature"));
-const rxjs_2 = require("rxjs");
 class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     // derived classes may not use the same configuration so a custom
     // configure method allows derived classes to override this behavior
@@ -28,8 +28,6 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             // chunkSizeLimit and fetchSizeLimit are more troublesome than
             // helpful, and have given overly large values on the ultra long
             // nanopore reads even with 500MB limits, so disabled with infinity
-            chunkSizeLimit: Infinity,
-            fetchSizeLimit: Infinity,
             yieldThreadTime: Infinity,
         });
         const adapterConfig = this.getConf('sequenceAdapter');
@@ -66,9 +64,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             // mapping between ref ref ID numbers and names
             const idToName = [];
             const nameToId = {};
-            samHeader
-                .filter(l => l.tag === 'SQ')
-                .forEach((sqLine, refId) => {
+            samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
                 sqLine.data.forEach(item => {
                     if (item.tag === 'SN') {
                         // this is the ref name
@@ -134,38 +130,37 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { bam } = await this.configure();
             await this.setup(opts);
-            statusCallback('Downloading alignments');
-            const records = await bam.getRecordsForRange(refName, start, end, opts);
-            const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
-            for (const record of records) {
-                let ref;
-                if (!record.get('MD')) {
-                    ref = await this.seqFetch(originalRefName || refName, record.get('start'), record.get('end'));
-                }
-                const flags = record.flags;
-                if (!((flags & flagInclude) === flagInclude && !(flags & flagExclude))) {
-                    continue;
-                }
-                if (tagFilter) {
-                    const val = record.get(tagFilter.tag);
-                    if (!(val === '*' ? val !== undefined : val === tagFilter.value)) {
+            const records = await (0, util_1.updateStatus)('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end, opts));
+            await (0, util_1.updateStatus)('Processing alignments', statusCallback, async () => {
+                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
+                for (const record of records) {
+                    let ref;
+                    if (!record.get('MD')) {
+                        ref = await this.seqFetch(originalRefName || refName, record.get('start'), record.get('end'));
+                    }
+                    const flags = record.flags;
+                    if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
                         continue;
                     }
+                    if (tagFilter) {
+                        const v = record.get(tagFilter.tag);
+                        if (!(v === '*' ? v !== undefined : `${v}` === tagFilter.value)) {
+                            continue;
+                        }
+                    }
+                    if (readName && record.get('name') !== readName) {
+                        continue;
+                    }
+                    observer.next(new BamSlightlyLazyFeature_1.default(record, this, ref));
                 }
-                if (readName && record.get('name') !== readName) {
-                    continue;
-                }
-                observer.next(new BamSlightlyLazyFeature_1.default(record, this, ref));
-            }
-            statusCallback('');
-            observer.complete();
+                observer.complete();
+            });
         }, signal);
     }
     async getMultiRegionFeatureDensityStats(regions, opts) {
         const { bam } = await this.configure();
         // this is a method to avoid calling on htsget adapters
-        // @ts-expect-error
-        if (bam.index.filehandle !== '?') {
+        if (bam.index) {
             const bytes = await (0, util_1.bytesForRegions)(regions, bam);
             const fetchSizeLimit = this.getConf('fetchSizeLimit');
             return { bytes, fetchSizeLimit };

package/dist/BamAdapter/BamAdapter.js.map

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package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -12,7 +12,7 @@ export default class BamSlightlyLazyFeature implements Feature {
     _get_score(): number;
     _get_flags(): string;
     _get_strand(): number;
-    _get_pair_orientation(): string | null | undefined;
+    _get_pair_orientation(): string | undefined;
     _get_next_ref(): string | undefined;
     _get_next_pos(): number | undefined;
     _get_next_segment_position(): string | undefined;

package/dist/CramAdapter/CramAdapter.js

@@ -92,33 +92,33 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async setupPre(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const conf = await this.configure();
-        statusCallback('Downloading index');
-        const { cram } = conf;
-        const samHeader = await cram.cram.getSamHeader();
-        // use the @SQ lines in the header to figure out the
-        // mapping between ref ID numbers and names
-        const idToName = [];
-        const nameToId = {};
-        samHeader
-            .filter(l => l.tag === 'SQ')
-            .forEach((sqLine, refId) => {
-            sqLine.data.forEach(item => {
-                if (item.tag === 'SN') {
-                    // this is the ref name
-                    const refName = item.value;
-                    nameToId[refName] = refId;
-                    idToName[refId] = refName;
-                }
+        return (0, util_1.updateStatus)('Downloading index', statusCallback, async () => {
+            const conf = await this.configure();
+            const { cram } = conf;
+            const samHeader = await cram.cram.getSamHeader();
+            // use the @SQ lines in the header to figure out the
+            // mapping between ref ID numbers and names
+            const idToName = [];
+            const nameToId = {};
+            samHeader
+                .filter(l => l.tag === 'SQ')
+                .forEach((sqLine, refId) => {
+                sqLine.data.forEach(item => {
+                    if (item.tag === 'SN') {
+                        // this is the ref name
+                        const refName = item.value;
+                        nameToId[refName] = refId;
+                        idToName[refId] = refName;
+                    }
+                });
             });
+            const readGroups = samHeader
+                .filter(l => l.tag === 'RG')
+                .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
+            const data = { idToName, nameToId, readGroups };
+            this.samHeader = data;
+            return { samHeader: data, ...conf };
         });
-        const readGroups = samHeader
-            .filter(l => l.tag === 'RG')
-            .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
-        const data = { idToName, nameToId, readGroups };
-        statusCallback('');
-        this.samHeader = data;
-        return { samHeader: data, ...conf };
     }
     async setup(opts) {
         if (!this.setupP) {
@@ -170,29 +170,31 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             if (originalRefName) {
                 this.seqIdToOriginalRefName[refId] = originalRefName;
             }
-            statusCallback('Downloading alignments');
-            const records = await cram.getRecordsForRange(refId, start, end);
+            const records = await (0, util_1.updateStatus)('Downloading alignments', statusCallback, () => cram.getRecordsForRange(refId, start, end));
             (0, util_1.checkAbortSignal)(signal);
-            const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
-            let filtered = records.filter(record => {
-                const flags = record.flags;
-                return (flags & flagInclude) === flagInclude && !(flags & flagExclude);
-            });
-            if (tagFilter) {
-                filtered = filtered.filter(record => {
-                    // @ts-expect-error
-                    const val = record[tagFilter.tag];
-                    return val === '*' ? val !== undefined : val === tagFilter.value;
-                });
-            }
-            if (readName) {
-                filtered = filtered.filter(record => record.readName === readName);
-            }
-            filtered.forEach(record => {
-                observer.next(this.cramRecordToFeature(record));
+            await (0, util_1.updateStatus)('Processing alignments', statusCallback, () => {
+                var _a;
+                const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
+                for (const record of records) {
+                    const flags = record.flags;
+                    if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
+                        continue;
+                    }
+                    if (tagFilter) {
+                        const v = tagFilter.tag === 'RG'
+                            ? (_a = this.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
+                            : record.tags[tagFilter.tag];
+                        if (!(v === '*' ? v !== undefined : `${v}` === tagFilter.value)) {
+                            continue;
+                        }
+                    }
+                    if (readName && record.readName !== readName) {
+                        continue;
+                    }
+                    observer.next(this.cramRecordToFeature(record));
+                }
+                observer.complete();
             });
-            statusCallback('');
-            observer.complete();
         }, signal);
     }
     freeResources( /* { region } */) { }

package/dist/CramAdapter/CramAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"CramAdapter.js","sourceRoot":"","sources":["../../src/CramAdapter/CramAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qCAAmE;AACnE,yEAIgD;AAChD,6CAK2B;AAC3B,8CAAoD;AACpD,kDAA0D;AAC1D,8CAAwC;AACxC,+BAAqC;AACrC,wFAA+D;AAe/D,MAAqB,WAAY,SAAQ,oCAAsB;IAA/D;;QACE,cAAS,GAAW,EAAE,CAAA;QAgBtB,gFAAgF;QACxE,2BAAsB,GAAa,EAAE,CAAA;IAiR/C,CAAC;IA/QQ,KAAK,CAAC,YAAY;QACvB,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,MAAM,IAAI,GAAG,IAAI,sBAAe,CAAC;YAC/B,cAAc,EAAE,IAAA,iBAAY,EAAC,YAAY,EAAE,EAAE,CAAC;YAC9C,KAAK,EAAE,IAAI,gBAAS,CAAC,EAAE,UAAU,EAAE,IAAA,iBAAY,EAAC,YAAY,EAAE,EAAE,CAAC,EAAE,CAAC;YACpE,QAAQ,EAAE,CAAC,GAAG,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,IAAI,CAAC;YAC7C,gBAAgB,EAAE,KAAK;YACvB,cAAc,EAAE,SAAW,EAAE,kDAAkD;SAChF,CAAC,CAAA;QAEF,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QAC/C,MAAM,UAAU,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;QAEpD,OAAO;YACL,IAAI;YACJ,eAAe,EAAE,UAAU,CAAC,WAAkC;SAC/D,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACvC,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;IAClC,CAAC;IAEO,KAAK,CAAC,QAAQ,CACpB,KAAa,EACb,KAAa,EACb,GAAW;QAEX,KAAK,IAAI,CAAC,CAAA,CAAC,2CAA2C;QAEtD,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,MAAM,OAAO,GAAG,IAAI,CAAC,mBAAmB,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;QAC1E,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;SAC3B;QAED,MAAM,SAAS,GAAG,MAAM,IAAA,qBAAc,EACpC,eAAe;aACZ,WAAW,CAAC;YACX,OAAO;YACP,KAAK;YACL,GAAG;YACH,YAAY,EAAE,EAAE;SACjB,CAAC;aACD,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACnB,CAAA;QAED,MAAM,QAAQ,GAAG,SAAS;aACvB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;aAC/C,GAAG,CAAC,KAAK,CAAC,EAAE;YACX,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,UAAU,EAAE,CAAC,CAAC,CAAA;YACjD,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,UAAU,EAAE,QAAQ,GAAG,UAAU,CAAC,CAAA;YACjE,MAAM,UAAU,GAAG,OAAO,GAAG,SAAS,CAAA;YACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;YAC1D,OAAO,QAAQ,CAAC,KAAK,CAAC,SAAS,EAAE,SAAS,GAAG,UAAU,CAAC,CAAA;QAC1D,CAAC,CAAC;aACD,IAAI,CAAC,EAAE,CAAC,CAAA;QAEX,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,GAAG,KAAK,EAAE;YACnC,MAAM,IAAI,KAAK,CACb,mCAAmC,OAAO,IAAI,CAC5C,KAAK,GAAG,CAAC,CACV,CAAC,cAAc,EAAE,IAAI,GAAG,CAAC,cAAc,EAAE,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CACzH,GAAG,GAAG,KAAK,CACZ,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;SACF;QACD,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,OAAO,IAAA,mBAAY,EAAC,mBAAmB,EAAE,cAAc,EAAE,KAAK,IAAI,EAAE;YAClE,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YACnC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;YACrB,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,CAAA;YAEhD,oDAAoD;YACpD,2CAA2C;YAC3C,MAAM,QAAQ,GAAa,EAAE,CAAA;YAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;YAC3C,SAAS;iBACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;iBAC3B,OAAO,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;gBACzB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;oBACzB,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;wBACrB,uBAAuB;wBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;wBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;wBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;qBAC1B;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YAEJ,MAAM,UAAU,GAAG,SAAS;iBACzB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;iBAC3B,GAAG,CAAC,MAAM,CAAC,EAAE,WAAC,OAAA,MAAA,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,GAAG,KAAK,IAAI,CAAC,0CAAE,KAAK,CAAA,EAAA,CAAC,CAAA;YAEpE,MAAM,IAAI,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAA;YAC/C,IAAI,CAAC,SAAS,GAAG,IAAI,CAAA;YACrB,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,GAAG,IAAI,EAAE,CAAA;QACrC,CAAC,CAAC,CAAA;IACJ,CAAC;IAEO,KAAK,CAAC,KAAK,CAAC,IAAkB;QACpC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,SAAS,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC5C,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,OAAO,SAAS,CAAC,QAAQ,CAAA;IAC3B,CAAC;IAED,mEAAmE;IACnE,gEAAgE;IAChE,WAAW,CAAC,OAAe;QACzB,IAAI,IAAI,CAAC,SAAS,CAAC,QAA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package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -34,8 +34,8 @@ class CramSlightlyLazyFeature {
         return this.record.isReverseComplemented() ? -1 : 1;
     }
     _read_group_id() {
-        const rg = this._store.samHeader.readGroups;
-        return rg ? rg[this.record.readGroupId] : undefined;
+        var _a;
+        return (_a = this._store.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[this.record.readGroupId];
     }
     _get_qual() {
         return (this.record.qualityScores || []).join(' ');
@@ -114,9 +114,7 @@ class CramSlightlyLazyFeature {
     _get_clipPos() {
         const mismatches = this.get('mismatches');
         if (mismatches.length) {
-            const record = this.get('strand') === -1
-                ? mismatches[mismatches.length - 1]
-                : mismatches[0];
+            const record = this.get('strand') === -1 ? mismatches.at(-1) : mismatches[0];
             const { type, cliplen } = record;
             if (type === 'softclip' || type === 'hardclip') {
                 return cliplen;

package/dist/CramAdapter/CramSlightlyLazyFeature.js.map

@@ -1 +1 @@
-{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":";;AASA,iCAAsE;AAEtE,MAAqB,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,IAAA,0BAAmB,EACxB,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,mBAAmB;QACnB,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,mBAAmB;YACnB,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,IAAA,+BAAwB,EAAC,YAAY,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IAC5D,CAAC;CACF;AAhLD,0CAgLC"}
+{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":";;AASA,iCAAsE;AAEtE,MAAqB,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,OAAO,MAAA,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,UAAU,0CAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;IACpE,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,IAAA,0BAAmB,EACxB,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,mBAAmB;QACnB,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,mBAAmB;YACnB,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,CAAC,CAAC,CAAC,UAAU,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YAC/D,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,IAAA,+BAAwB,EAAC,YAAY,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IAC5D,CAAC;CACF;AA7KD,0CA6KC"}

package/dist/CramAdapter/CramTestAdapters.js

@@ -17,7 +17,7 @@ function parseSmallFasta(text) {
         const [defLine, ...seqLines] = entryText.split(/\n|\r\n|\r/);
         const [id, ...descriptionLines] = defLine.split(' ');
         const description = descriptionLines.join(' ');
-        const sequence = seqLines.join('').replace(/\s/g, '');
+        const sequence = seqLines.join('').replaceAll(/\s/g, '');
         return { id, description, sequence };
     });
 }

package/dist/CramAdapter/CramTestAdapters.js.map

@@ -1 +1 @@
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+{"version":3,"file":"CramTestAdapters.js","sourceRoot":"","sources":["../../src/CramAdapter/CramTestAdapters.ts"],"names":[],"mappings":";;;;;;AACA,+BAAiC;AACjC,qFAA4D;AAC5D,yEAAgF;AAChF,+DAAiE;AAEjE,iCAAiC;AACjC,SAAgB,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,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QACxD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAA;IACtC,CAAC,CAAC,CAAA;AACN,CAAC;AAXD,0CAWC;AAID,MAAa,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;AAxBD,kDAwBC;AAED,MAAa,eAAgB,SAAQ,oCAAsB;IAKzD,YAAY,UAAsB;QAChC,KAAK,CAAC,IAAA,mCAAmB,EAAC,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,iBAAU,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,uBAAa,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;AAjDD,0CAiDC"}

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -1,6 +1,7 @@
+import React from 'react';
 import { AlignmentsDisplayModel } from '../models/model';
 declare function AlignmentsDisplay({ model }: {
     model: AlignmentsDisplayModel;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof AlignmentsDisplay;
 export default _default;

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

@@ -24,6 +24,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 }, {
     rendererTypeName: string;
     error: unknown;
+    message: string | undefined;
 } & {
     readonly RenderingComponent: React.FC<{
         model: {
@@ -33,6 +34,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         } & IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -40,6 +42,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
@@ -52,6 +55,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined; /**
+             * #property
+             * refers to LinearPileupDisplay sub-display model
+             */
         } & IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -59,19 +66,22 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
-    readonly adapterConfig: any;
+    readonly adapterConfig: any; /**
+     * #stateModel LinearAlignmentsDisplay
+     * extends `BaseDisplay`
+     */
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: React.FC<any> | undefined;
     trackMenuItems(): MenuItem[];
-    readonly viewMenuActions: MenuItem[]; /**
-     * #action
-     */
-    regionCannotBeRendered(): undefined;
+    readonly viewMenuActions: MenuItem[];
+    regionCannotBeRendered(): null;
 } & {
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -153,7 +163,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
      */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
-    }): Promise<JSX.Element>;
+    }): Promise<React.JSX.Element>;
 } & {
     /**
      * #method

package/dist/LinearAlignmentsDisplay/models/model.js

@@ -258,7 +258,8 @@ function stateModelFactory(pluginManager, configSchema) {
          */
         async renderSvg(opts) {
             const pileupHeight = self.height - self.SNPCoverageDisplay.height;
-            await (0, mobx_1.when)(() => self.PileupDisplay.ready);
+            await (0, mobx_1.when)(() => !self.PileupDisplay.renderProps().notReady &&
+                !self.SNPCoverageDisplay.renderProps().notReady);
             return (react_1.default.createElement(react_1.default.Fragment, null,
                 react_1.default.createElement("g", null, await self.SNPCoverageDisplay.renderSvg(opts)),
                 react_1.default.createElement("g", { transform: `translate(0 ${self.SNPCoverageDisplay.height})` }, await self.PileupDisplay.renderSvg({

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

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/model.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,+BAAoC;AACpC,qDAOwB;AACxB,sEAAuC;AAEvC,UAAU;AACV,+DAKoC;AACpC,uEAAwE;AAKxE,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAE3B,SAAS,qBAAqB,CAAC,aAA4B;IACzD,OAAO,CACL,aAAa;SACV,kBAAkB,EAAE;QACrB,mBAAmB;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,CAAA,MAAA,CAAC,CAAC,UAAU,0CAAE,IAAI,MAAK,yBAAyB,CAAA,EAAA,CAAC;QAC9D,mBAAmB;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,MAAA,CAAC,CAAC,UAAU,0CAAE,UAAU,CAAA,EAAA,CAAC,CACzC,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CACf,EAAK,EACL,EAAK;IAEL,OAAO,IAAA,yBAAS,EACd,EAAE,CAAC,CAAC,CAAC,IAAA,6BAAW,EAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,EAChC,EAAE,CAAC,CAAC,CAAC,IAAA,6BAAW,EAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CACjC,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,IAA4B;IAC5C,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,OAAO,CACL,aAAa;QACb,IAAA,yBAAO,EAAC,aAAa,CAAC;QACtB,kBAAkB;QAClB,IAAA,yBAAO,EAAC,kBAAkB,CAAC,CAC5B,CAAA;AACH,CAAC;AAED,SAAS,gBAAgB,CAAC,IAA4B;IACpD,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,EAAE;QAC7C,OAAM;KACP;IACD,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,OAAO,EAAE,kBAAkB,CAAC,OAAO,CAAC,EAAE;QAChE,kBAAkB,CAAC,UAAU,CAAC,IAAA,6BAAW,EAAC,aAAa,CAAC,OAAO,CAAC,CAAC,CAAA;KAClE;AACH,CAAC;AAED,SAAS,iBAAiB,CAAC,IAA4B;IACrD,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,QAAQ,EAAE;QAC9C,OAAM;KACP;IACD,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,QAAQ,EAAE,kBAAkB,CAAC,QAAQ,CAAC,EAAE;QAClE,kBAAkB,CAAC,WAAW,CAAC,IAAA,6BAAW,EAAC,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAA;KACpE;AACH,CAAC;AAED,SAAS,eAAe,CACtB,aAA4B,EAC5B,YAAwC;IAExC,MAAM,kBAAkB,GAAG,qBAAqB,CAAC,aAAa,CAAC,CAAC,GAAG,CACjE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAClB,CAAA;IAED,OAAO,uBAAK,CAAC,KAAK,CAAC;QACjB;;;WAGG;QACH,aAAa,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,KAAK,CAAC,GAAG,kBAAkB,CAAC,CAAC;QAC9D;;;WAGG;QACH,kBAAkB,EAAE,uBAAK,CAAC,KAAK,CAC7B,aAAa,CAAC,cAAc,CAAC,0BAA0B,CAAC,CAAC,UAAU,CACpE;QACD;;WAEG;QACH,YAAY,EAAE,EAAE;QAChB;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,yBAAyB,CAAC;QAC9C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;QACnD;;WAEG;QACH,eAAe,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;QAC1C;;WAEG;QACH,wBAAwB,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;QACnD;;WAEG;QACH,cAAc,EAAE,qBAAqB;KACtC,CAAC,CAAA;AACJ,CAAC;AAED;;;GAGG;AACH,SAAS,iBAAiB,CACxB,aAA4B,EAC5B,YAAwC;IAExC,OAAO,uBAAK;SACT,OAAO,CACN,yBAAyB,EACzB,oBAAW,EACX,eAAe,CAAC,aAAa,EAAE,YAAY,CAAC,CAC7C;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,SAAS,EAAE,CAAC;KACb,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,YAAY,CAAC,SAAiB;YAC5B,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;QAC5B,CAAC;QAED;;WAEG;QACH,oBAAoB,CAAC,CAAS;YAC5B,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACvB,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,MAAM;;YACR,OAAO,MAAA,IAAI,CAAC,eAAe,mCAAI,IAAA,uBAAO,EAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;QACxD,CAAC;QAED,IAAI,mBAAmB;YACrB,OAAO,CACL,IAAI,CAAC,aAAa,CAAC,mBAAmB;gBACtC,IAAI,CAAC,kBAAkB,CAAC,mBAAmB,CAC5C,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,UAAU;YACZ,MAAM,IAAI,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,eAAe,CAAC,CAAA;YAC3C,OAAO;gBACL,GAAG,IAAI;gBACP,IAAI,EAAE,IAAI,CAAC,cAAc;gBACzB,SAAS,EAAE,GAAG,IAAI,CAAC,aAAa,CAAC,SAAS,IAAI,IAAI,CAAC,cAAc,MAAM,EAAE,yEAAyE;aACnJ,CAAA;QACH,CAAC;QAED;;WAEG;QACH,cAAc,CAAC,QAAgB,EAAE,EAAU;YACzC,OAAO,IAAI,CAAC,aAAa,CAAC,cAAc,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;QACxD,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,EAAU;YAC1B,OAAO,IAAI,CAAC,aAAa,CAAC,iBAAiB,CAAC,EAAE,CAAC,CAAA;QACjD,CAAC;QAED;;WAEG;QACH,IAAI,QAAQ;YACV,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAA;QACpC,CAAC;QAED;;WAEG;QACH,IAAI,YAAY;;YACd,OAAO,MAAA,IAAI,CAAC,aAAa,0CAAE,YAAY,CAAA;QACzC,CAAC;QAED;;WAEG;QACH,IAAI,QAAQ;YACV,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAA;QACpC,CAAC;QAED;;WAEG;QACH,IAAI,YAAY;YACd,MAAM,IAAI,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,oBAAoB,CAAC,CAAA;YAChD,OAAO;gBACL,GAAG,IAAI;gBACP,SAAS,EAAE,GAAG,IAAI,CAAC,aAAa,CAAC,SAAS,kBAAkB,EAAE,yEAAyE;aACxI,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,qBAAqB,CAAC,aAAoC;YACxD,IAAI,CAAC,kBAAkB,GAAG;gBACxB,IAAI,EAAE,0BAA0B;gBAChC,aAAa;gBACb,MAAM,EAAE,IAAI,CAAC,YAAY;aAC1B,CAAA;QACH,CAAC;QACD;;WAEG;QACH,2BAA2B,CAAC,KAA2B;YACrD,IAAI,CAAC,aAAa,CAAC,2BAA2B,CAAC,KAAK,CAAC,CAAA;YACrD,IAAI,CAAC,kBAAkB,CAAC,2BAA2B,CAAC,KAAK,CAAC,CAAA;QAC5D,CAAC;QAED;;WAEG;QACH,gBAAgB,CAAC,aAAoC;YACnD,IAAI,CAAC,aAAa,GAAG;gBACnB,IAAI,EAAE,aAAa,CAAC,IAAI,IAAI,qBAAqB;gBACjD,aAAa;aACd,CAAA;QACH,CAAC;QACD;;WAEG;QACH,SAAS,CAAC,CAAS;YACjB,IAAI,CAAC,eAAe,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,gBAAgB,CAAC,CAAA;YACpD,OAAO,IAAI,CAAC,eAAe,CAAA;QAC7B,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,IAAY;YAC5B,IAAI,CAAC,cAAc,GAAG,IAAI,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,YAAY,CAAC,QAAgB;YAC3B,MAAM,SAAS,GAAG,IAAI,CAAC,MAAM,CAAA;YAC7B,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,MAAM,GAAG,QAAQ,CAAC,CAAA;YACxD,OAAO,SAAS,GAAG,SAAS,CAAA;QAC9B,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YA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package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts

@@ -1,3 +1,4 @@
+import React from 'react';
 import { ObservableMap } from 'mobx';
 declare function ColorByTagDlg(props: {
     model: {
@@ -10,6 +11,6 @@ declare function ColorByTagDlg(props: {
         };
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof ColorByTagDlg;
 export default _default;