@jbrowse/plugin-alignments 2.2.0 → 2.2.2

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;
@@ -69,7 +69,8 @@ class SequenceAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     end,
                 }));
                 observer.complete();
-            });
+            })
+                .catch(e => observer.error(e));
             return { unsubscribe: () => { } };
         });
     }

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;iBACD,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;YAChC,OAAO,EAAE,WAAW,EAAE,GAAG,EAAE,GAAE,CAAC,EAAE,CAAA;QAClC,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAjDD,0CAiDC"}

package/dist/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/components/ColorByModifications.d.ts

@@ -2,7 +2,9 @@
 import { ObservableMap } from 'mobx';
 declare function ColorByTagDlg(props: {
     model: {
-        setColorScheme: Function;
+        setColorScheme: (arg: {
+            type: string;
+        }) => void;
         modificationTagMap: ObservableMap<string, string>;
         colorBy?: {
             type: string;

package/dist/LinearPileupDisplay/components/ColorByModifications.js

@@ -6,15 +6,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
+const ui_1 = require("@jbrowse/core/ui");
 const mui_1 = require("tss-react/mui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
     table: {
         border: '1px solid #888',
         margin: theme.spacing(4),
@@ -35,15 +29,10 @@ function ModificationTable({ modifications, }) {
                 } })))))));
 }
 function ColorByTagDlg(props) {
-    const { classes } = useStyles();
     const { model, handleClose } = props;
     const { colorBy, modificationTagMap } = model;
     const modifications = [...modificationTagMap.entries()];
-    return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
-        react_1.default.createElement(material_1.DialogTitle, null,
-            "Color by modifications",
-            react_1.default.createElement(material_1.IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
-                react_1.default.createElement(Close_1.default, null))),
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by modifications" },
         react_1.default.createElement(material_1.DialogContent, null,
             react_1.default.createElement(material_1.Typography, null, "You can choose to color the modifications in the BAM/CRAM MM/ML specification using this dialog. Choosing modifications colors the modified positions and can color multiple modification types. Choosing the methylation setting colors methylated and unmethylated CpG."),
             react_1.default.createElement(material_1.Typography, null, "Note: you can revisit this dialog to see the current mapping of colors to modification type for the modification coloring mode"),
@@ -58,19 +47,15 @@ function ColorByTagDlg(props) {
                         ['unmethylated', 'blue'],
                     ] })) : null),
             react_1.default.createElement(material_1.DialogActions, null,
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", style: { margin: 5 }, onClick: () => {
-                        model.setColorScheme({
-                            type: 'modifications',
-                        });
+                react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
+                        model.setColorScheme({ type: 'modifications' });
                         handleClose();
                     } }, "Modifications"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", style: { margin: 5 }, onClick: () => {
-                        model.setColorScheme({
-                            type: 'methylation',
-                        });
+                react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
+                        model.setColorScheme({ type: 'methylation' });
                         handleClose();
                     } }, "Methylation"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", style: { margin: 5 }, onClick: () => handleClose() }, "Cancel")))));
+                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 exports.default = (0, mobx_react_1.observer)(ColorByTagDlg);
 //# sourceMappingURL=ColorByModifications.js.map

package/dist/LinearPileupDisplay/components/ColorByModifications.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ColorByModifications.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByModifications.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AAErC,4CAMsB;AACtB,yCAAyC;AACzC,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,MAAM,EAAE,gBAAgB;QACxB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACxB,MAAM,EAAE;YACN,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;SAC1B;KACF;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EACzB,aAAa,GAGd;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,yCAAO,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,6CACG,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CACnC,sCAAI,GAAG,EAAE,GAAG;YACV,0CAAK,GAAG,CAAM;YACd,0CAAK,KAAK,CAAM;YAChB,sCACE,KAAK,EAAE;oBACL,KAAK,EAAE,KAAK;oBACZ,UAAU,EAAE,KAAK;iBAClB,GACD,CACC,CACN,CAAC,CACI,CACF,CACT,CAAA;AACH,CAAC;AAED,SAAS,aAAa,CAAC,KAOtB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAE7C,MAAM,aAAa,GAAG,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,CAAA;IAEvD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,wBAAwB;QAC/D,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,oRAKE;YACb,8BAAC,qBAAU,yIAGE;YACb,uCAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE;gBACvB,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,CAAC,CAAC,CAAC,CACnC,2CACG,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,CACtB;;oBAEE,8BAAC,iBAAiB,IAChB,aAAa,EAAE,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,GAChD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;oBACE,8BAAC,qBAAU,4FAGE;oBACb,8BAAC,2BAAgB,IAAC,IAAI,EAAE,EAAE,GAAI,CAC1B,CACP,CACG,CACP,CAAC,CAAC,CAAC,IAAI;gBACP,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,CAAC,CAAC,CAAC,CACjC,8BAAC,iBAAiB,IAChB,aAAa,EAAE;wBACb,CAAC,YAAY,EAAE,KAAK,CAAC;wBACrB,CAAC,cAAc,EAAE,MAAM,CAAC;qBACzB,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACJ;YACN,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,eAAe,EAAE,CAAC,CAAA;wBAC/C,WAAW,EAAE,CAAA;oBACf,CAAC,oBAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,CAAC,CAAA;wBAC7C,WAAW,EAAE,CAAA;oBACf,CAAC,kBAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,aAAa,CAAC,CAAA"}

package/dist/LinearPileupDisplay/components/ColorByTag.js

@@ -22,36 +22,16 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    root: {
-        width: 300,
-    },
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
+const ui_1 = require("@jbrowse/core/ui");
 function ColorByTagDlg(props) {
-    const { classes } = useStyles();
     const { model, handleClose } = props;
     const [tag, setTag] = (0, react_1.useState)('');
     const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
-    return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
-        react_1.default.createElement(material_1.DialogTitle, null,
-            "Color by tag",
-            react_1.default.createElement(material_1.IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
-                react_1.default.createElement(Close_1.default, null))),
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by tag" },
         react_1.default.createElement(material_1.DialogContent, { style: { overflowX: 'hidden' } },
             react_1.default.createElement(material_1.Typography, null, "Enter tag to color by: "),
             react_1.default.createElement(material_1.Typography, { color: "textSecondary" }, "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc."),

package/dist/LinearPileupDisplay/components/ColorByTag.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ColorByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AAEzC,SAAS,aAAa,CAAC,KAGtB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,cAAc;QACrD,8BAAC,wBAAa,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE;YAC3C,8BAAC,qBAAU,kCAAqC;YAChD,8BAAC,qBAAU,IAAC,KAAK,EAAC,eAAe,+IAGpB;YAEb,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;oBACV,SAAS,EAAE,CAAC;oBACZ,aAAa,EAAE,sBAAsB;iBACtC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,EAClE,YAAY,EAAC,KAAK,iBACN,gBAAgB,GAC5B;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC;4BACnB,IAAI,EAAE,KAAK;4BACX,GAAG;yBACJ,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,EACD,QAAQ,EAAE,CAAC,QAAQ,aAGZ;gBACT,8BAAC,iBAAM,IAAC,OAAO,EAAC,WAAW,EAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAE,WAAW,aAEzD,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,aAAa,CAAC,CAAA"}