@jbrowse/plugin-alignments 2.2.0 → 2.2.2

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -4,15 +4,16 @@ import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
 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';
-const useStyles = makeStyles()(() => ({
+const useStyles = makeStyles()({
     compact: {
         paddingRight: 0,
         paddingTop: 0,
         paddingBottom: 0,
     },
-}));
+});
 const omit = ['clipPos', 'flags'];
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function AlignmentFlags(props) {
@@ -92,12 +93,12 @@ function SupplementaryAlignments(props) {
             const displayEnd = end.toLocaleString('en-US');
             const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand})`;
             return (React.createElement("li", { key: `${locString}-${index}` },
-                React.createElement(Link, { onClick: event => {
+                React.createElement(Link, { onClick: async (event) => {
                         event.preventDefault();
                         const { view } = model;
                         try {
                             if (view) {
-                                view.navToLocString(locString);
+                                await view.navToLocString(locString);
                             }
                             else {
                                 throw new Error('No view associated with this view anymore');
@@ -113,15 +114,13 @@ function SupplementaryAlignments(props) {
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function PairLink({ locString, model }) {
     const session = getSession(model);
-    return (React.createElement(Link, { onClick: () => {
+    return (React.createElement(Link, { onClick: async () => {
             const { view } = model;
+            if (!view) {
+                throw new Error('No view associated with this feature detail panel anymore');
+            }
             try {
-                if (view) {
-                    view.navToLocString(locString);
-                }
-                else {
-                    session.notify('No view associated with this feature detail panel anymore', 'warning');
-                }
+                await view.navToLocString(locString);
             }
             catch (e) {
                 console.error(e);
@@ -132,14 +131,14 @@ function PairLink({ locString, model }) {
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function AlignmentFeatureDetails(props) {
     const { model } = props;
-    const feat = JSON.parse(JSON.stringify(model.featureData));
+    const feat = clone(model.featureData);
     const SA = (feat.tags && feat.tags.SA) || feat.SA;
     return (React.createElement(Paper, { "data-testid": "alignment-side-drawer" },
         React.createElement(FeatureDetails, { ...props, omit: omit, feature: feat, formatter: (value, key) => {
                 return key === 'next_segment_position' ? (React.createElement(PairLink, { model: model, locString: value })) : (React.createElement(Formatter, { value: value }));
             } }),
         SA ? React.createElement(SupplementaryAlignments, { model: model, tag: SA }) : null,
-        React.createElement(AlignmentFlags, { feature: feat, ...props })));
+        feat.flags !== undefined ? (React.createElement(AlignmentFlags, { feature: feat, ...props })) : null));
 }
 export default observer(AlignmentFeatureDetails);
 //# sourceMappingURL=AlignmentsFeatureDetail.js.map

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map

@@ -1 +1 @@
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package/esm/BamAdapter/BamAdapter.d.ts

@@ -1,7 +1,7 @@
 import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Feature } from '@jbrowse/core/util';
 interface Header {
     idToName: string[];
     nameToId: Record<string, number>;

package/esm/BamAdapter/BamAdapter.js

@@ -4,6 +4,7 @@ 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';
+// locals
 import BamSlightlyLazyFeature from './BamSlightlyLazyFeature';
 export default class BamAdapter extends BaseFeatureDataAdapter {
     // derived classes may not use the same configuration so a custom

package/esm/BamAdapter/BamAdapter.js.map

@@ -1 +1 @@
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package/esm/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,3 +1,4 @@
+// locals
 import { getMismatches } from './MismatchParser';
 export default class BamSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class

package/esm/BamAdapter/BamSlightlyLazyFeature.js.map

@@ -1 +1 @@
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package/esm/BamAdapter/MismatchParser.d.ts

@@ -10,13 +10,13 @@ export interface Mismatch {
     cliplen?: number;
 }
 export declare function parseCigar(cigar?: string): string[];
-export declare function cigarToMismatches(ops: string[], seq: string, ref?: string, qual?: Buffer): Mismatch[];
+export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Buffer): Mismatch[];
 /**
  * parse a SAM MD tag to find mismatching bases of the template versus the reference
  * @returns array of mismatches and their positions
  */
 export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer): Mismatch[];
-export declare function getMismatches(cigar: string, md: string, seq: string, ref?: string, qual?: Buffer): Mismatch[];
+export declare function getMismatches(cigar: string, md?: string, seq?: string, ref?: string, qual?: Buffer): Mismatch[];
 export declare function getNextRefPos(cigarOps: string[], positions: number[]): Generator<number, void, unknown>;
 export declare function getModificationPositions(mm: string, fseq: string, fstrand: number): {
     type: string;

package/esm/BamAdapter/MismatchParser.js

@@ -56,7 +56,7 @@ export function cigarToMismatches(ops, seq, ref, qual) {
             });
         }
         else if (op === 'X') {
-            const r = seq.slice(soffset, soffset + len);
+            const r = (seq === null || seq === void 0 ? void 0 : seq.slice(soffset, soffset + len)) || [];
             const q = (qual === null || qual === void 0 ? void 0 : qual.slice(soffset, soffset + len)) || [];
             for (let j = 0; j < len; j++) {
                 mismatches.push({
@@ -167,10 +167,7 @@ export function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
                 }
                 const s = getTemplateCoordLocal(curr.start);
                 curr.base = seq[s] || 'X';
-                const qualScore = qual === null || qual === void 0 ? void 0 : qual[s];
-                if (qualScore) {
-                    curr.qual = qualScore;
-                }
+                curr.qual = qual === null || qual === void 0 ? void 0 : qual[s];
                 curr.altbase = token;
                 nextRecord();
             }
@@ -186,7 +183,7 @@ export function getMismatches(cigar, md, seq, ref, qual) {
         mismatches = mismatches.concat(cigarToMismatches(ops, seq, ref, qual));
     }
     // now let's look for CRAM or MD mismatches
-    if (md) {
+    if (md && seq) {
         mismatches = mismatches.concat(mdToMismatches(md, ops, mismatches, seq, qual));
     }
     return mismatches;
@@ -282,7 +279,7 @@ export function getModificationTypes(mm) {
         const [basemod] = mod.split(',');
         const matches = basemod.match(modificationRegex);
         if (!matches) {
-            throw new Error('bad format for MM tag');
+            throw new Error(`bad format for MM tag: ${mm}`);
         }
         const [, , , typestr] = matches;
         // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so

package/esm/BamAdapter/MismatchParser.js.map

@@ -1 +1 @@
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package/esm/BamAdapter/configSchema.js

@@ -38,7 +38,7 @@ const configSchema = ConfigurationSchema('BamAdapter', {
      */
     fetchSizeLimit: {
         type: 'number',
-        description: 'used to determine when to display a warning to the user that too much data will be fetched',
+        description: 'size to fetch in bytes over which to display a warning to the user that too much data will be fetched',
         defaultValue: 5000000,
     },
     /**

package/esm/BamAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BamAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,YAAY,EACZ;IACE;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;IAED,KAAK,EAAE,mBAAmB,CAAC,UAAU,EAAE;QACrC;;WAEG;QACH,SAAS,EAAE;YACT,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,qBAAqB;gBAC1B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;IACF;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,uGAAuG;QACzG,YAAY,EAAE,OAAS;KACxB;IACD;;;;OAIG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,8EAA8E;QAChF,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,YAAY,CAAA"}

package/esm/BamAdapter/index.js

@@ -1,10 +1,12 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
 export default (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType({
-        name: 'BamAdapter',
-        configSchema,
-        getAdapterClass: () => import('./BamAdapter').then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'BamAdapter',
+            configSchema,
+            getAdapterClass: () => import('./BamAdapter').then(r => r.default),
+        });
+    });
 };
 //# sourceMappingURL=index.js.map

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,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,YAAY;QAClB,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACnE,CAAC,CACL,CAAA;AACH,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,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

@@ -1,16 +1,7 @@
 import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 import { CramRecord } from '@gmod/cram';
 import CramAdapter from './CramAdapter';
-export interface Mismatch {
-    qual?: number;
-    start: number;
-    length: number;
-    type: string;
-    base: string;
-    altbase?: string;
-    seq?: string;
-    cliplen?: number;
-}
+import { Mismatch } from './util';
 export default class CramSlightlyLazyFeature implements Feature {
     private record;
     private _store;

package/esm/CramAdapter/CramSlightlyLazyFeature.js

@@ -1,3 +1,4 @@
+import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util';
 export default class CramSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class
     // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
@@ -79,123 +80,10 @@ export default class CramSlightlyLazyFeature {
     }
     // generate a CIGAR, based on code from jkbonfield
     _get_CIGAR() {
-        let seq = '';
-        let cigar = '';
-        let op = 'M';
-        let oplen = 0;
-        if (!this.record._refRegion) {
-            return '';
-        }
-        // not sure I should access these, but...
-        const ref = this.record._refRegion.seq;
-        const refStart = this.record._refRegion.start;
-        let last_pos = this.record.alignmentStart;
-        let sublen = 0;
-        if (typeof this.record.readFeatures !== 'undefined') {
-            let insLen = 0;
-            // @ts-ignore
-            for (let i = 0; i < this.record.readFeatures.length; i++) {
-                const { code, refPos, sub, data } = this.record.readFeatures[i];
-                sublen = refPos - last_pos;
-                seq += ref.substring(last_pos - refStart, refPos - refStart);
-                last_pos = refPos;
-                if (oplen && op !== 'M') {
-                    cigar += oplen + op;
-                    oplen = 0;
-                }
-                if (sublen) {
-                    op = 'M';
-                    oplen += sublen;
-                }
-                if (insLen > 0 && code !== 'i') {
-                    cigar += `${insLen}I`;
-                    insLen = 0;
-                }
-                if (code === 'b') {
-                    // An array of bases stored verbatim
-                    const ret = data.split(',');
-                    const added = String.fromCharCode(...ret);
-                    seq += added;
-                    last_pos += added.length;
-                    oplen += added.length;
-                }
-                else if (code === 'B') {
-                    // Single base (+ qual score)
-                    seq += sub;
-                    last_pos++;
-                    oplen++;
-                }
-                else if (code === 'X') {
-                    // Substitution
-                    seq += sub;
-                    last_pos++;
-                    oplen++;
-                }
-                else if (code === 'D' || code === 'N') {
-                    // Deletion or Ref Skip
-                    last_pos += data;
-                    if (oplen) {
-                        cigar += oplen + op;
-                    }
-                    cigar += data + code;
-                    oplen = 0;
-                }
-                else if (code === 'I' || code === 'S') {
-                    // Insertion or soft-clip
-                    seq += data;
-                    if (oplen) {
-                        cigar += oplen + op;
-                    }
-                    cigar += data.length + code;
-                    oplen = 0;
-                }
-                else if (code === 'i') {
-                    // Single base insertion
-                    // seq += data
-                    if (oplen) {
-                        cigar += oplen + op;
-                    }
-                    insLen++;
-                    oplen = 0;
-                }
-                else if (code === 'P') {
-                    // Padding
-                    if (oplen) {
-                        cigar += oplen + op;
-                    }
-                    cigar += `${data}P`;
-                }
-                else if (code === 'H') {
-                    // Hard clip
-                    if (oplen) {
-                        cigar += oplen + op;
-                    }
-                    cigar += `${data}H`;
-                    oplen = 0;
-                } // else q or Q
-            }
-        }
-        else {
-            sublen = this.record.readLength - seq.length;
-        }
-        if (seq.length !== this.record.readLength) {
-            sublen = this.record.readLength - seq.length;
-            seq += ref.substring(last_pos - refStart, last_pos - refStart + sublen);
-            if (oplen && op !== 'M') {
-                cigar += oplen + op;
-                oplen = 0;
-            }
-            op = 'M';
-            oplen += sublen;
-        }
-        if (oplen) {
-            cigar += oplen + op;
-        }
-        return cigar;
+        return readFeaturesToCIGAR(this.record.readFeatures, this.record.alignmentStart, this.record.readLength, this.record._refRegion);
     }
     tags() {
-        const properties = Object.getOwnPropertyNames(CramSlightlyLazyFeature.prototype);
-        return properties
+        return Object.getOwnPropertyNames(CramSlightlyLazyFeature.prototype)
             .filter(prop => prop.startsWith('_get_') &&
             prop !== '_get_mismatches' &&
             prop !== '_get_cram_read_features')
@@ -245,111 +133,10 @@ export default class CramSlightlyLazyFeature {
         };
     }
     _get_mismatches() {
-        const readFeatures = this.get('cram_read_features');
+        const readFeatures = this.record.readFeatures;
         const qual = this.qualRaw();
-        if (!readFeatures) {
-            return [];
-        }
         const start = this.get('start');
-        const mismatches = new Array(readFeatures.length);
-        let j = 0;
-        let insLen = 0;
-        let refPos = 0;
-        for (let i = 0; i < readFeatures.length; i++) {
-            const f = readFeatures[i];
-            const { code, pos, data, sub, ref } = f;
-            if (insLen > 0 && code !== 'i') {
-                mismatches[j++] = {
-                    start: refPos,
-                    type: 'insertion',
-                    base: `${insLen}`,
-                    length: 0,
-                };
-                insLen = 0;
-            }
-            refPos = f.refPos - 1 - start;
-            if (code === 'X') {
-                // substitution
-                mismatches[j++] = {
-                    start: refPos,
-                    length: 1,
-                    base: sub,
-                    qual: qual === null || qual === void 0 ? void 0 : qual[pos],
-                    altbase: ref,
-                    type: 'mismatch',
-                };
-            }
-            else if (code === 'I') {
-                // insertion
-                mismatches[j++] = {
-                    start: refPos,
-                    type: 'insertion',
-                    base: `${data.length}`,
-                    length: 0,
-                };
-            }
-            else if (code === 'N') {
-                // reference skip
-                mismatches[j++] = {
-                    type: 'skip',
-                    length: data,
-                    start: refPos,
-                    base: 'N',
-                };
-            }
-            else if (code === 'S') {
-                // soft clip
-                const len = data.length;
-                mismatches[j++] = {
-                    start: refPos,
-                    type: 'softclip',
-                    base: `S${len}`,
-                    cliplen: len,
-                    length: 1,
-                };
-            }
-            else if (code === 'P') {
-                // padding
-            }
-            else if (code === 'H') {
-                // hard clip
-                const len = data;
-                mismatches[j++] = {
-                    start: refPos,
-                    type: 'hardclip',
-                    base: `H${len}`,
-                    cliplen: len,
-                    length: 1,
-                };
-            }
-            else if (code === 'D') {
-                // deletion
-                mismatches[j++] = {
-                    type: 'deletion',
-                    length: data,
-                    start: refPos,
-                    base: '*',
-                };
-            }
-            else if (code === 'b') {
-                // stretch of bases
-            }
-            else if (code === 'q') {
-                // stretch of qual scores
-            }
-            else if (code === 'B') {
-                // a pair of [base, qual]
-            }
-            else if (code === 'i') {
-                // single-base insertion
-                // insertion
-                insLen++;
-            }
-            else if (code === 'Q') {
-                // single quality value
-            }
-        }
-        return mismatches.slice(0, j);
+        return readFeaturesToMismatches(readFeatures, start, qual);
     }
 }
 //# sourceMappingURL=CramSlightlyLazyFeature.js.map

package/esm/CramAdapter/CramSlightlyLazyFeature.js.map

@@ -1 +1 @@
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