@jbrowse/plugin-alignments 2.5.0 → 2.6.0

package/dist/util.js

@@ -1,19 +1,22 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.shouldFetchReferenceSequence = exports.fetchSequence = exports.getColorWGBS = exports.orientationTypes = exports.getTagAlt = exports.getTag = void 0;
+exports.randomColor = exports.createAutorun = exports.modificationColors = exports.shouldFetchReferenceSequence = exports.fetchSequence = exports.getColorWGBS = exports.pairMap = exports.orientationTypes = exports.getTagAlt = exports.getTag = void 0;
 const operators_1 = require("rxjs/operators");
 const rxjs_1 = require("rxjs");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mobx_1 = require("mobx");
 // get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
 // BAM does not
 function getTag(feature, tag) {
     const tags = feature.get('tags');
-    return tags ? tags[tag] : feature.get(tag);
+    return tags !== undefined ? tags[tag] : feature.get(tag);
 }
 exports.getTag = getTag;
 // use fallback alt tag, used in situations where upper case/lower case tags
 // exist e.g. Mm/MM for base modifications
 function getTagAlt(feature, tag, alt) {
-    return getTag(feature, tag) || getTag(feature, alt);
+    var _a;
+    return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
 }
 exports.getTagAlt = getTagAlt;
 // orientation definitions from igv.js, see also
@@ -50,6 +53,12 @@ exports.orientationTypes = {
         F1F2: 'RL',
     },
 };
+exports.pairMap = {
+    LR: 'color_pair_lr',
+    LL: 'color_pair_ll',
+    RR: 'color_pair_rr',
+    RL: 'color_pair_rl',
+};
 function getColorWGBS(strand, base) {
     if (strand === 1) {
         if (base === 'C') {
@@ -70,14 +79,17 @@ function getColorWGBS(strand, base) {
     return '#888';
 }
 exports.getColorWGBS = getColorWGBS;
+// fetches region sequence augmenting by +/- 1bp for CpG on either side of
+// requested region
 async function fetchSequence(region, adapter) {
     var _a;
-    const { end, originalRefName, refName } = region;
+    const { start, end, originalRefName, refName } = region;
     const feats = await (0, rxjs_1.firstValueFrom)(adapter
         .getFeatures({
         ...region,
         refName: originalRefName || refName,
         end: end + 1,
+        start: Math.max(0, start - 1),
     })
         .pipe((0, operators_1.toArray)()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
@@ -88,4 +100,33 @@ function shouldFetchReferenceSequence(type) {
     return type === 'methylation';
 }
 exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
+// adapted from IGV
+// https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27
+exports.modificationColors = {
+    m: 'rgb(255,0,0)',
+    h: 'rgb(11, 132, 165)',
+    o: 'rgb(111, 78, 129)',
+    f: 'rgb(246, 200, 95)',
+    c: 'rgb(157, 216, 102)',
+    g: 'rgb(255, 160, 86)',
+    e: 'rgb(141, 221, 208)',
+    b: 'rgb(202, 71, 47)',
+};
+function createAutorun(self, cb, opts) {
+    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
+        try {
+            await cb();
+        }
+        catch (e) {
+            if ((0, mobx_state_tree_1.isAlive)(self)) {
+                self.setError(e);
+            }
+        }
+    }, opts));
+}
+exports.createAutorun = createAutorun;
+function randomColor() {
+    return `hsl(${Math.random() * 200}, 50%, 50%)`;
+}
+exports.randomColor = randomColor;
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;AAEA,8CAAwC;AACxC,+BAAqC;AACrC,qDAAyE;AACzE,+BAA+C;AAE/C,4EAA4E;AAC5E,eAAe;AACf,SAAgB,MAAM,CAAC,OAAgB,EAAE,GAAW;IAClD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC1D,CAAC;AAHD,wBAGC;AAED,4EAA4E;AAC5E,0CAA0C;AAC1C,SAAgB,SAAS,CAAC,OAAgB,EAAE,GAAW,EAAE,GAAW;;IAClE,OAAO,MAAA,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,mCAAI,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;AACrD,CAAC;AAFD,8BAEC;AAED,gDAAgD;AAChD,kFAAkF;AACrE,QAAA,gBAAgB,GAAG;IAC9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;CAC/B,CAAA;AAEY,QAAA,OAAO,GAAG;IACrB,EAAE,EAAE,eAAe;IACnB,EAAE,EAAE,eAAe;IACnB,EAAE,EAAE,eAAe;IACnB,EAAE,EAAE,eAAe;CACX,CAAA;AAEV,SAAgB,YAAY,CAAC,MAAc,EAAE,IAAY;IACvD,IAAI,MAAM,KAAK,CAAC,EAAE;QAChB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;SAAM,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE;QACxB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAjBD,oCAiBC;AAED,0EAA0E;AAC1E,mBAAmB;AACZ,KAAK,UAAU,aAAa,CACjC,MAAuB,EACvB,OAA+B;;IAE/B,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;IAEvD,MAAM,KAAK,GAAG,MAAM,IAAA,qBAAc,EAChC,OAAO;SACJ,WAAW,CAAC;QACX,GAAG,MAAM;QACT,OAAO,EAAE,eAAe,IAAI,OAAO;QACnC,GAAG,EAAE,GAAG,GAAG,CAAC;QACZ,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,CAAC,CAAC;KAC9B,CAAC;SACD,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACnB,CAAA;IACD,OAAO,MAAA,KAAK,CAAC,CAAC,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,CAAA;AAC7B,CAAC;AAjBD,sCAiBC;AAED,kEAAkE;AAClE,SAAgB,4BAA4B,CAAC,IAAa;IACxD,OAAO,IAAI,KAAK,aAAa,CAAA;AAC/B,CAAC;AAFD,oEAEC;AAED,mBAAmB;AACnB,oJAAoJ;AACvI,QAAA,kBAAkB,GAAG;IAChC,CAAC,EAAE,cAAc;IACjB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,oBAAoB;IACvB,CAAC,EAAE,mBAAmB;IACtB,CAAC,EAAE,oBAAoB;IACvB,CAAC,EAAE,kBAAkB;CACgB,CAAA;AAIvC,SAAgB,aAAa,CAC3B,IAAkB,EAClB,EAAuB,EACvB,IAAsB;IAEtB,IAAA,6BAAW,EACT,IAAI,EACJ,IAAA,cAAO,EAAC,KAAK,IAAI,EAAE;QACjB,IAAI;YACF,MAAM,EAAE,EAAE,CAAA;SACX;QAAC,OAAO,CAAC,EAAE;YACV,IAAI,IAAA,yBAAO,EAAC,IAAI,CAAC,EAAE;gBACjB,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;aACjB;SACF;IACH,CAAC,EAAE,IAAI,CAAC,CACT,CAAA;AACH,CAAC;AAjBD,sCAiBC;AACD,SAAgB,WAAW;IACzB,OAAO,OAAO,IAAI,CAAC,MAAM,EAAE,GAAG,GAAG,aAAa,CAAA;AAChD,CAAC;AAFD,kCAEC"}

package/esm/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/esm/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/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js

@@ -1,7 +1,8 @@
 import React from 'react';
 import { Checkbox, FormControlLabel, FormGroup } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import { BaseCard, SimpleValue, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import SimpleField from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField';
 const useStyles = makeStyles()({
     compact: {
         paddingRight: 0,
@@ -28,7 +29,7 @@ export default function AlignmentFlags(props) {
     const { feature } = props;
     const { flags } = feature;
     return (React.createElement(BaseCard, { ...props, title: "Flags" },
-        React.createElement(SimpleValue, { name: "Flag", value: flags }),
+        React.createElement(SimpleField, { name: "Flag", value: flags }),
         React.createElement(FormGroup, null, flagNames.map((name, idx) => {
             const val = flags & (1 << idx);
             const key = `${name}_${val}`;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map

@@ -1 +1 @@
-{"version":3,"file":"AlignmentsFeatureFlags.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACrE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EACL,QAAQ,EACR,WAAW,GACZ,MAAM,mDAAmD,CAAA;AAE1D,MAAM,SAAS,GAAG,UAAU,EAAE,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,MAAM,CAAC,OAAO,UAAU,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,oBAAC,QAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,OAAO;QAChC,oBAAC,WAAW,IAAC,IAAI,EAAC,MAAM,EAAC,KAAK,EAAE,KAAK,GAAI;QACzC,oBAAC,SAAS,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,oBAAC,gBAAgB,IACf,GAAG,EAAE,GAAG,EACR,OAAO,EACL,oBAAC,QAAQ,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"}
+{"version":3,"file":"AlignmentsFeatureFlags.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACrE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,mDAAmD,CAAA;AAC5E,OAAO,WAAW,MAAM,+DAA+D,CAAA;AAEvF,MAAM,SAAS,GAAG,UAAU,EAAE,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,MAAM,CAAC,OAAO,UAAU,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,oBAAC,QAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,OAAO;QAChC,oBAAC,WAAW,IAAC,IAAI,EAAC,MAAM,EAAC,KAAK,EAAE,KAAK,GAAI;QACzC,oBAAC,SAAS,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,oBAAC,gBAAgB,IACf,GAAG,EAAE,GAAG,EACR,OAAO,EACL,oBAAC,QAAQ,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"}

package/esm/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/esm/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/esm/BamAdapter/BamAdapter.js

@@ -4,9 +4,9 @@ import { bytesForRegions, updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { toArray } from 'rxjs/operators';
+import { firstValueFrom } from 'rxjs';
 // locals
 import BamSlightlyLazyFeature from './BamSlightlyLazyFeature';
-import { firstValueFrom } from 'rxjs';
 export default class BamAdapter extends BaseFeatureDataAdapter {
     // derived classes may not use the same configuration so a custom
     // configure method allows derived classes to override this behavior
@@ -23,8 +23,6 @@ export default class BamAdapter extends 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');
@@ -61,9 +59,7 @@ export default class BamAdapter extends 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
@@ -129,38 +125,37 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         return 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 updateStatus('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end, opts));
+            await 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(record, this, ref));
                 }
-                if (readName && record.get('name') !== readName) {
-                    continue;
-                }
-                observer.next(new BamSlightlyLazyFeature(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 bytesForRegions(regions, bam);
             const fetchSizeLimit = this.getConf('fetchSizeLimit');
             return { bytes, fetchSizeLimit };

package/esm/BamAdapter/BamAdapter.js.map

@@ -1 +1 @@
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package/esm/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/esm/CramAdapter/CramAdapter.js

@@ -1,6 +1,6 @@
 import { CraiIndex, IndexedCramFile } from '@gmod/cram';
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { checkAbortSignal } from '@jbrowse/core/util';
+import { checkAbortSignal, updateStatus, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { toArray } from 'rxjs/operators';
@@ -87,33 +87,33 @@ export default class CramAdapter extends 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 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) {
@@ -165,29 +165,31 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
             if (originalRefName) {
                 this.seqIdToOriginalRefName[refId] = originalRefName;
             }
-            statusCallback('Downloading alignments');
-            const records = await cram.getRecordsForRange(refId, start, end);
+            const records = await updateStatus('Downloading alignments', statusCallback, () => cram.getRecordsForRange(refId, start, end));
             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 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/esm/CramAdapter/CramAdapter.js.map

@@ -1 +1 @@
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package/esm/CramAdapter/CramSlightlyLazyFeature.js

@@ -32,8 +32,8 @@ export default 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(' ');
@@ -112,9 +112,7 @@ export default 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/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,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,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,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,wBAAwB,CAAC,YAAY,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IAC5D,CAAC;CACF"}

package/esm/CramAdapter/CramTestAdapters.js

@@ -11,7 +11,7 @@ export 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/esm/CramAdapter/CramTestAdapters.js.map

@@ -1 +1 @@
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package/esm/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;