@jbrowse/plugin-alignments 2.2.0 → 2.2.1

package/dist/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/dist/CramAdapter/CramTestAdapters.js

@@ -36,7 +36,7 @@ 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/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,yFAAqF;AAErF,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,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QACrD,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,yCAAmB,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,CAAA;YACJ,OAAO,EAAE,WAAW,EAAE,GAAG,EAAE,GAAE,CAAC,EAAE,CAAA;QAClC,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAhDD,0CAgDC"}

package/dist/CramAdapter/configSchema.js

@@ -12,7 +12,7 @@ const configSchema = (0, configuration_1.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,
     },
     /**
@@ -42,7 +42,7 @@ const configSchema = (0, configuration_1.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/dist/CramAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/CramAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,aAAa,EACb;IACE;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,4FAA4F;QAC9F,YAAY,EAAE,OAAS;KACxB;IAED;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,kBAAkB;YACvB,YAAY,EAAE,aAAa;SAC5B;KACF;IAED;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,uBAAuB;YAC5B,YAAY,EAAE,aAAa;SAC5B;KACF;IAED;;;;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;AACD,kBAAe,YAAY,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/CramAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,aAAa,EACb;IACE;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,8FAA8F;QAChG,YAAY,EAAE,OAAS;KACxB;IAED;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,kBAAkB;YACvB,YAAY,EAAE,aAAa;SAC5B;KACF;IAED;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,uBAAuB;YAC5B,YAAY,EAAE,aAAa;SAC5B;KACF;IAED;;;;OAIG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,uBAAuB;QACpC,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,kBAAe,YAAY,CAAA"}

package/dist/CramAdapter/index.js

@@ -30,10 +30,12 @@ const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
 // locals
 const configSchema_1 = __importDefault(require("./configSchema"));
 exports.default = (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'CramAdapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType_1.default({
+            name: 'CramAdapter',
+            configSchema: configSchema_1.default,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
+        });
+    });
 };
 //# sourceMappingURL=index.js.map

package/dist/CramAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,SAAS;AACT,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,eAAe,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,SAAS;AACT,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,aAAa;YACnB,YAAY,EAAZ,sBAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,eAAe,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACpE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/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/dist/CramAdapter/util.js

@@ -0,0 +1,241 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.readFeaturesToCIGAR = exports.readFeaturesToMismatches = void 0;
+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: `${insLen}`,
+            length: 0,
+        };
+        insLen = 0;
+    }
+    return mismatches.slice(0, j);
+}
+exports.readFeaturesToMismatches = readFeaturesToMismatches;
+function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
+    let seq = '';
+    let cigar = '';
+    let op = 'M';
+    let oplen = 0;
+    if (!refRegion) {
+        return '';
+    }
+    // not sure I should access these, but...
+    const ref = refRegion.seq;
+    const refStart = refRegion.start;
+    let lastPos = alignmentStart;
+    let sublen = 0;
+    let insLen = 0;
+    if (readFeatures !== undefined) {
+        for (let i = 0; i < readFeatures.length; i++) {
+            const { code, refPos, sub, data } = readFeatures[i];
+            sublen = refPos - lastPos;
+            seq += ref.substring(lastPos - refStart, refPos - refStart);
+            lastPos = refPos;
+            if (insLen > 0 && sublen) {
+                cigar += `${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;
+}
+exports.readFeaturesToCIGAR = readFeaturesToCIGAR;
+//# sourceMappingURL=util.js.map

package/dist/CramAdapter/util.js.map

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

@@ -5,9 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
-const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(() => ({
     resizeHandle: {
         height: 2,

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

@@ -1 +1 @@
-{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,+DAAqD;AACrD,yCAA+C;AAC/C,uCAA0C;AAG1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,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,sDACe,WAAW,IAAA,uBAAO,EAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE9B,YAAY,CAAC,CAAC,CAAC,CACd;YACE,sDAAiB,sBAAsB;gBACrC,8BAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;YACN,8BAAC,iBAAY,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,sDACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,YAAY,CAAC,CAAC,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;aAClD;YAED,8BAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,iBAAiB,CAAC,CAAA"}
+{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,uCAA0C;AAC1C,+DAAqD;AACrD,yCAA+C;AAK/C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,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,sDACe,WAAW,IAAA,uBAAO,EAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE9B,YAAY,CAAC,CAAC,CAAC,CACd;YACE,sDAAiB,sBAAsB;gBACrC,8BAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;YACN,8BAAC,iBAAY,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,sDACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,YAAY,CAAC,CAAC,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;aAClD;YAED,8BAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,iBAAiB,CAAC,CAAA"}

package/dist/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;

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

@@ -141,15 +141,15 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #action
      */
-    setSNPCoverageDisplay(displayConfig: AnyConfigurationModel): void;
+    setSNPCoverageDisplay(configuration: AnyConfigurationModel): void;
     /**
      * #action
      */
-    setUserFeatureScreenDensity(limit: number): void;
+    updateStatsLimit(stats: unknown): void;
     /**
      * #action
      */
-    setPileupDisplay(displayConfig: AnyConfigurationModel): void;
+    setPileupDisplay(configuration: AnyConfigurationModel): void;
     /**
      * #action
      */
@@ -168,5 +168,5 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     }): Promise<JSX.Element>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;
-export declare type AlignmentsDisplayStateModel = ReturnType<typeof stateModelFactory>;
-export declare type AlignmentsDisplayModel = Instance<AlignmentsDisplayStateModel>;
+export type AlignmentsDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type AlignmentsDisplayModel = Instance<AlignmentsDisplayStateModel>;

package/dist/LinearAlignmentsDisplay/models/model.js

@@ -182,27 +182,27 @@ function stateModelFactory(pluginManager, configSchema) {
         /**
          * #action
          */
-        setSNPCoverageDisplay(displayConfig) {
+        setSNPCoverageDisplay(configuration) {
             self.SNPCoverageDisplay = {
                 type: 'LinearSNPCoverageDisplay',
-                configuration: displayConfig,
+                configuration,
                 height: self.snpCovHeight,
             };
         },
         /**
          * #action
          */
-        setUserFeatureScreenDensity(limit) {
-            self.PileupDisplay.setUserFeatureScreenDensity(limit);
-            self.SNPCoverageDisplay.setUserFeatureScreenDensity(limit);
+        updateStatsLimit(stats) {
+            self.PileupDisplay.updateStatsLimit(stats);
+            self.SNPCoverageDisplay.updateStatsLimit(stats);
         },
         /**
          * #action
          */
-        setPileupDisplay(displayConfig) {
+        setPileupDisplay(configuration) {
             self.PileupDisplay = {
                 type: 'LinearPileupDisplay',
-                configuration: displayConfig,
+                configuration,
             };
         },
         /**

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

@@ -1 +1 @@
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package/dist/LinearPileupDisplay/configSchema.d.ts

@@ -1,6 +1,6 @@
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
-declare function PileupConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare type LinearPileupDisplayConfigModel = ReturnType<typeof PileupConfigFactory>;
-export declare type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
-export default PileupConfigFactory;
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export type LinearPileupDisplayConfigModel = ReturnType<typeof configSchemaF>;
+export type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
+export default configSchemaF;

package/dist/LinearPileupDisplay/configSchema.js

@@ -7,7 +7,7 @@ const mobx_state_tree_1 = require("mobx-state-tree");
  * #config LinearPileupDisplay
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-function PileupConfigFactory(pluginManager) {
+function configSchemaF(pluginManager) {
     // modify config schema to take in a sub coverage display
     return (0, configuration_1.ConfigurationSchema)('LinearPileupDisplay', {
         /**
@@ -56,5 +56,5 @@ function PileupConfigFactory(pluginManager) {
         explicitlyTyped: true,
     });
 }
-exports.default = PileupConfigFactory;
+exports.default = configSchemaF;
 //# sourceMappingURL=configSchema.js.map

package/dist/LinearPileupDisplay/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAA0F;AAC1F,qDAAiD;AAGjD;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,aAAa,CAAC,aAA4B;IACjD,yDAAyD;IACzD,OAAO,IAAA,mCAAmB,EACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,IAAA,mCAAmB,EAAC,wBAAwB,EAAE;YACvD,cAAc,EACZ,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY;SAC/D,CAAC;QACF;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAID,kBAAe,aAAa,CAAA"}

package/dist/LinearPileupDisplay/index.d.ts

@@ -1,2 +1,5 @@
+import configSchemaFactory from './configSchema';
+import modelFactory from './model';
 import PluginManager from '@jbrowse/core/PluginManager';
 export default function register(pluginManager: PluginManager): void;
+export { modelFactory as linearPileupDisplayStateModelFactory, configSchemaFactory as linearPileupDisplayConfigSchemaFactory, };

package/dist/LinearPileupDisplay/index.js

@@ -3,8 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.linearPileupDisplayConfigSchemaFactory = exports.linearPileupDisplayStateModelFactory = void 0;
 const configSchema_1 = __importDefault(require("./configSchema"));
+exports.linearPileupDisplayConfigSchemaFactory = configSchema_1.default;
 const model_1 = __importDefault(require("./model"));
+exports.linearPileupDisplayStateModelFactory = model_1.default;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 function register(pluginManager) {

package/dist/LinearPileupDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":";;;;;AAAA,kEAAgD;AAChD,oDAAkC;AAClC,kGAAyE;AAEzE,kFAA+E;AAE/E,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,YAAY,CAAC;YACtC,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAZD,2BAYC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":";;;;;;AAAA,kEAAgD;AAsBvB,iDAtBlB,sBAAmB,CAsBqC;AArB/D,oDAAkC;AAoBhB,+CApBX,eAAY,CAoBmC;AAnBtD,kGAAyE;AAEzE,kFAA+E;AAE/E,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,YAAY,CAAC;YACtC,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAZD,2BAYC"}

package/dist/LinearPileupDisplay/model.d.ts

@@ -6,6 +6,7 @@ import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
 import { LinearPileupDisplayConfigModel } from './configSchema';
 /**
  * #stateModel LinearPileupDisplay
+ * extends `BaseLinearDisplay`
  */
 declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -29,10 +30,14 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        renderInProgress: AbortController | undefined; /**
+         * #property
+         */
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
-        features: Map<string, Feature> | undefined;
+        features: Map<string, Feature> | undefined; /**
+         * #property
+         */
         layout: any;
         status: string;
         error: unknown;
@@ -43,7 +48,9 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
         }) => any;
         renderProps: any;
     } & {
-        doReload(): void;
+        doReload(): void; /**
+         * #property
+         */
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
@@ -104,9 +111,7 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
-             * #action
-             */
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
@@ -221,12 +226,17 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
     colorTagMap: import("mobx").ObservableMap<string, string>;
     modificationTagMap: import("mobx").ObservableMap<string, string>;
     featureUnderMouseVolatile: Feature | undefined;
+    currSortBpPerPx: number;
     ready: boolean;
 } & {
     /**
      * #action
      */
     setReady(flag: boolean): void;
+    /**
+     * #action
+     */
+    setCurrSortBpPerPx(n: number): void;
     /**
      * #action
      */
@@ -409,12 +419,12 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
     })[];
 }, import("mobx-state-tree")._NotCustomized, {
     type: string;
-    id: string;
     height: number;
+    id: string;
     rpcDriverName: string | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;
-export declare type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
-export declare type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
+export type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
 export default stateModelFactory;