@jbrowse/plugin-alignments 2.2.0 → 2.2.1

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

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

package/esm/CramAdapter/CramTestAdapters.d.ts

@@ -7,7 +7,7 @@ export declare function parseSmallFasta(text: string): {
     description: string;
     sequence: string;
 }[];
-declare type FileHandle = GenericFilehandle;
+type FileHandle = GenericFilehandle;
 export declare class FetchableSmallFasta {
     data: Promise<ReturnType<typeof parseSmallFasta>>;
     constructor(filehandle: FileHandle);

package/esm/CramAdapter/CramTestAdapters.js

@@ -29,7 +29,7 @@ export class FetchableSmallFasta {
         if (!entry) {
             throw new Error(`no sequence with id ${id} exists`);
         }
-        return entry.sequence.substr(start - 1, length);
+        return entry.sequence.slice(start, start + length);
     }
     async getSequenceList() {
         const data = await this.data;

package/esm/CramAdapter/CramTestAdapters.js.map

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

@@ -10,7 +10,7 @@ const configSchema = ConfigurationSchema('CramAdapter', {
      */
     fetchSizeLimit: {
         type: 'number',
-        description: 'used to determine when to display a warning to the user that too much data will be fetched',
+        description: 'size in bytes over which to display a warning to the user that too much data will be fetched',
         defaultValue: 3000000,
     },
     /**
@@ -40,7 +40,7 @@ const configSchema = ConfigurationSchema('CramAdapter', {
      */
     sequenceAdapter: {
         type: 'frozen',
-        description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
+        description: 'sequence data adapter',
         defaultValue: null,
     },
 }, { explicitlyTyped: true });

package/esm/CramAdapter/configSchema.js.map

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

@@ -2,10 +2,12 @@ import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 // locals
 import configSchema from './configSchema';
 export default (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType({
-        name: 'CramAdapter',
-        configSchema,
-        getAdapterClass: () => import('./CramAdapter').then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'CramAdapter',
+            configSchema,
+            getAdapterClass: () => import('./CramAdapter').then(r => r.default),
+        });
+    });
 };
 //# sourceMappingURL=index.js.map

package/esm/CramAdapter/index.js.map

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

package/esm/CramAdapter/util.d.ts

@@ -0,0 +1,18 @@
+import { CramRecord } from '@gmod/cram';
+type ReadFeatures = CramRecord['readFeatures'];
+export interface Mismatch {
+    qual?: number;
+    start: number;
+    length: number;
+    type: string;
+    base: string | undefined;
+    altbase?: string;
+    seq?: string;
+    cliplen?: number;
+}
+export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
+export declare function readFeaturesToCIGAR(readFeatures: ReadFeatures, alignmentStart: number, readLen: number, refRegion?: {
+    seq: string;
+    start: number;
+}): string;
+export {};

package/esm/CramAdapter/util.js

@@ -0,0 +1,236 @@
+export function readFeaturesToMismatches(readFeatures, start, qual) {
+    if (!readFeatures) {
+        return [];
+    }
+    const mismatches = new Array(readFeatures.length);
+    let j = 0;
+    let insLen = 0;
+    let refPos = 0;
+    let sublen = 0;
+    let lastPos = start;
+    for (let i = 0; i < readFeatures.length; i++) {
+        const f = readFeatures[i];
+        const { code, pos, data, sub, ref } = f;
+        sublen = refPos - lastPos;
+        lastPos = refPos;
+        if (sublen && insLen > 0) {
+            mismatches[j++] = {
+                start: refPos,
+                type: 'insertion',
+                base: `${insLen}`,
+                length: 0,
+            };
+            insLen = 0;
+        }
+        refPos = f.refPos - 1 - start;
+        if (code === 'X') {
+            // substitution
+            mismatches[j++] = {
+                start: refPos,
+                length: 1,
+                base: sub,
+                qual: qual === null || qual === void 0 ? void 0 : qual[pos - 1],
+                altbase: ref === null || ref === void 0 ? void 0 : ref.toUpperCase(),
+                type: 'mismatch',
+            };
+        }
+        else if (code === 'I') {
+            // insertion
+            mismatches[j++] = {
+                start: refPos,
+                type: 'insertion',
+                base: `${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, we collect these if there are multiple in a row
+            // into a single insertion entry
+            insLen++;
+        }
+        else if (code === 'Q') {
+            // single quality value
+        }
+    }
+    if (sublen && insLen > 0) {
+        mismatches[j++] = {
+            start: refPos,
+            type: 'insertion',
+            base: `${insLen}`,
+            length: 0,
+        };
+        insLen = 0;
+    }
+    return mismatches.slice(0, j);
+}
+export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
+    let seq = '';
+    let cigar = '';
+    let op = 'M';
+    let oplen = 0;
+    if (!refRegion) {
+        return '';
+    }
+    // not sure I should access these, but...
+    const ref = refRegion.seq;
+    const refStart = refRegion.start;
+    let lastPos = alignmentStart;
+    let sublen = 0;
+    let insLen = 0;
+    if (readFeatures !== undefined) {
+        for (let i = 0; i < readFeatures.length; i++) {
+            const { code, refPos, sub, data } = readFeatures[i];
+            sublen = refPos - lastPos;
+            seq += ref.substring(lastPos - refStart, refPos - refStart);
+            lastPos = refPos;
+            if (insLen > 0 && sublen) {
+                cigar += `${insLen}I`;
+                insLen = 0;
+            }
+            if (oplen && op !== 'M') {
+                cigar += oplen + op;
+                oplen = 0;
+            }
+            if (sublen) {
+                op = 'M';
+                oplen += sublen;
+            }
+            if (code === 'b') {
+                // An array of bases stored verbatim
+                const ret = data.split(',');
+                const added = String.fromCharCode(...ret);
+                seq += added;
+                lastPos += added.length;
+                oplen += added.length;
+            }
+            else if (code === 'B') {
+                // Single base (+ qual score)
+                seq += sub;
+                lastPos++;
+                oplen++;
+            }
+            else if (code === 'X') {
+                // Substitution
+                seq += sub;
+                lastPos++;
+                oplen++;
+            }
+            else if (code === 'D' || code === 'N') {
+                // Deletion or Ref Skip
+                lastPos += 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++;
+                seq += data;
+                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 = readLen - seq.length;
+    }
+    if (seq.length !== readLen) {
+        sublen = readLen - seq.length;
+        seq += ref.substring(lastPos - refStart, lastPos - refStart + sublen);
+        if (oplen && op !== 'M') {
+            cigar += oplen + op;
+            oplen = 0;
+        }
+        op = 'M';
+        oplen += sublen;
+    }
+    if (sublen && insLen > 0) {
+        cigar += `${insLen}I`;
+    }
+    if (oplen) {
+        cigar += oplen + op;
+    }
+    return cigar;
+}
+//# sourceMappingURL=util.js.map

package/esm/CramAdapter/util.js.map

@@ -0,0 +1 @@
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package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -1,8 +1,8 @@
 import React from 'react';
 import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
 import { getConf } from '@jbrowse/core/configuration';
 import { ResizeHandle } from '@jbrowse/core/ui';
-import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(() => ({
     resizeHandle: {
         height: 2,

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

@@ -1 +1 @@
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+{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAK/C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,GAAG,EAAE,CAAC,CAAC;IACpC,YAAY,EAAE;QACZ,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAAqC;IACrE,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,UAAU,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IAC7E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,kBAAkB,CAAC,MAAM,CAAA;IACrC,OAAO,CACL,4CACe,WAAW,OAAO,CAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE9B,YAAY,CAAC,CAAC,CAAC,CACd;YACE,4CAAiB,sBAAsB;gBACrC,oBAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;YACN,oBAAC,YAAY,IACX,MAAM,EAAE,KAAK,CAAC,EAAE;oBACd,kBAAkB,CAAC,SAAS,CAAC,kBAAkB,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;oBAC/D,OAAO,KAAK,CAAA;gBACd,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE;oBACL,GAAG;iBACJ,GACD,CACD,CACJ,CAAC,CAAC,CAAC,IAAI;QAEP,UAAU,CAAC,CAAC,CAAC,CACZ,4CACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,YAAY,CAAC,CAAC,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;aAClD;YAED,oBAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,iBAAiB,CAAC,CAAA"}

package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts

@@ -1,4 +1,4 @@
 import PluginManager from '@jbrowse/core/PluginManager';
 declare const configModelFactory: (pm: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare type AlignmentsConfigModel = ReturnType<typeof configModelFactory>;
+export type AlignmentsConfigModel = ReturnType<typeof configModelFactory>;
 export default configModelFactory;