@jbrowse/plugin-alignments 2.2.1 → 2.2.2

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -8,33 +8,13 @@ const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const operators_1 = require("rxjs/operators");
+const generateCoverageBins_1 = __importDefault(require("./generateCoverageBins"));
 const util_1 = require("../util");
-const MismatchParser_1 = require("../BamAdapter/MismatchParser");
-function mismatchLen(mismatch) {
-    return !isInterbase(mismatch.type) ? mismatch.length : 1;
-}
-function isInterbase(type) {
-    return type === 'softclip' || type === 'hardclip' || type === 'insertion';
-}
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function inc(bin, strand, type, field) {
-    let thisBin = bin[type][field];
-    if (thisBin === undefined) {
-        thisBin = bin[type][field] = {
-            total: 0,
-            '-1': 0,
-            '0': 0,
-            '1': 0,
-        };
-    }
-    thisBin.total++;
-    thisBin[strand]++;
-}
 class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configure() {
         var _a, _b;
         const subadapterConfig = this.getConf('subadapter');
-        const sequenceConf = this.getConf(['subadapter', 'sequenceAdapter']);
+        const sequenceConf = subadapterConfig.sequenceAdapter;
         const dataAdapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, subadapterConfig));
         const sequenceAdapter = sequenceConf
             ? await ((_b = this.getSubAdapter) === null || _b === void 0 ? void 0 : _b.call(this, sequenceConf))
@@ -61,7 +41,7 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 .getFeatures(region, opts)
                 .pipe((0, operators_1.toArray)())
                 .toPromise();
-            const { bins, skipmap } = await this.generateCoverageBins(feats, region, opts);
+            const { bins, skipmap } = await (0, generateCoverageBins_1.default)(feats, region, opts, arg => this.fetchSequence(arg));
             bins.forEach((bin, index) => {
                 const start = region.start + index;
                 observer.next(new simpleFeature_1.default({
@@ -101,165 +81,6 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return subadapter.getRefNames(opts);
     }
     freeResources( /* { region } */) { }
-    async generateCoverageBins(features, region, opts) {
-        var _a;
-        const { colorBy } = opts;
-        const binMax = Math.ceil(region.end - region.start);
-        const skipmap = {};
-        const regionSeq = features.length && (0, util_1.shouldFetchReferenceSequence)((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type)
-            ? await this.fetchSequence(region)
-            : undefined;
-        const bins = [];
-        for (let i = 0; i < features.length; i++) {
-            const feature = features[i];
-            const fstart = feature.get('start');
-            const fend = feature.get('end');
-            const fstrand = feature.get('strand');
-            for (let j = fstart; j < fend + 1; j++) {
-                const i = j - region.start;
-                if (i >= 0 && i < binMax) {
-                    if (bins[i] === undefined) {
-                        bins[i] = {
-                            total: 0,
-                            all: 0,
-                            ref: 0,
-                            '-1': 0,
-                            '0': 0,
-                            '1': 0,
-                            lowqual: {},
-                            cov: {},
-                            delskips: {},
-                            noncov: {},
-                        };
-                    }
-                    if (j !== fend) {
-                        bins[i].total++;
-                        bins[i].all++;
-                        bins[i].ref++;
-                        bins[i][fstrand]++;
-                    }
-                }
-            }
-            if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-                const seq = feature.get('seq');
-                const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
-                const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-                const fend = feature.get('end');
-                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
-                    const mod = `mod_${type}`;
-                    for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
-                        const epos = pos + fstart - region.start;
-                        if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
-                            const bin = bins[epos];
-                            if (bin) {
-                                inc(bin, fstrand, 'cov', mod);
-                            }
-                            else {
-                                console.warn('Undefined position in modifications snpcoverage encountered');
-                            }
-                        }
-                    }
-                });
-            }
-            // methylation based coloring takes into account both reference
-            // sequence CpG detection and reads
-            else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
-                if (!regionSeq) {
-                    throw new Error('no region sequence detected, need sequenceAdapter configuration');
-                }
-                const seq = feature.get('seq');
-                const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
-                const methBins = new Array(region.end - region.start).fill(0);
-                const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
-                    // we are processing methylation
-                    if (type === 'm') {
-                        for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
-                            const epos = pos + fstart - region.start;
-                            if (epos >= 0 && epos < methBins.length) {
-                                methBins[epos] = 1;
-                            }
-                        }
-                    }
-                });
-                for (let j = fstart; j < fend; j++) {
-                    const i = j - region.start;
-                    if (i >= 0 && i < bins.length - 1) {
-                        const l1 = regionSeq[i].toLowerCase();
-                        const l2 = regionSeq[i + 1].toLowerCase();
-                        const bin = bins[i];
-                        const bin1 = bins[i + 1];
-                        // color
-                        if (l1 === 'c' && l2 === 'g') {
-                            if (methBins[i] || methBins[i + 1]) {
-                                inc(bin, fstrand, 'cov', 'meth');
-                                inc(bin1, fstrand, 'cov', 'meth');
-                                bins[i].ref--;
-                                bins[i][fstrand]--;
-                                bins[i + 1].ref--;
-                                bins[i + 1][fstrand]--;
-                            }
-                            else {
-                                inc(bin, fstrand, 'cov', 'unmeth');
-                                inc(bin1, fstrand, 'cov', 'unmeth');
-                                bins[i].ref--;
-                                bins[i][fstrand]--;
-                                bins[i + 1].ref--;
-                                bins[i + 1][fstrand]--;
-                            }
-                        }
-                    }
-                }
-            }
-            // normal SNP based coloring
-            const mismatches = feature.get('mismatches') || [];
-            const colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
-            for (let i = 0; i < mismatches.length; i++) {
-                const mismatch = mismatches[i];
-                const mstart = fstart + mismatch.start;
-                const mlen = mismatchLen(mismatch);
-                const mend = mstart + mlen;
-                for (let j = mstart; j < mstart + mlen; j++) {
-                    const epos = j - region.start;
-                    if (epos >= 0 && epos < bins.length) {
-                        const bin = bins[epos];
-                        const { base, type } = mismatch;
-                        const interbase = isInterbase(type);
-                        if (!interbase) {
-                            bin.ref--;
-                            bin[fstrand]--;
-                        }
-                        else {
-                            inc(bin, fstrand, 'noncov', type);
-                        }
-                        if (type === 'deletion' || type === 'skip') {
-                            inc(bin, fstrand, 'delskips', type);
-                            bin.total--;
-                        }
-                        else if (!interbase && colorSNPs) {
-                            inc(bin, fstrand, 'cov', base);
-                            bin.refbase = mismatch.altbase;
-                        }
-                    }
-                }
-                if (mismatch.type === 'skip') {
-                    const hash = `${mstart}_${mend}_${fstrand}`;
-                    if (skipmap[hash] === undefined) {
-                        skipmap[hash] = {
-                            feature: feature,
-                            start: mstart,
-                            end: mend,
-                            strand: fstrand,
-                            xs: (0, util_1.getTag)(feature, 'XS') || (0, util_1.getTag)(feature, 'TS'),
-                            score: 0,
-                        };
-                    }
-                    skipmap[hash].score++;
-                }
-            }
-        }
-        return { bins, skipmap };
-    }
 }
 exports.default = SNPCoverageAdapter;
 const { capabilities } = SNPCoverageAdapter;

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":";;;;;;AAAA,yEAGgD;AAEhD,qFAAyE;AACzE,kDAA0D;AAC1D,8CAAwC;AACxC,kCAKgB;AAChB,iEAKqC;AAErC,SAAS,WAAW,CAAC,QAAkB;IACrC,OAAO,CAAC,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;AAC1D,CAAC;AAED,SAAS,WAAW,CAAC,IAAY;IAC/B,OAAO,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,WAAW,CAAA;AAC3E,CAAC;AAED,8DAA8D;AAC9D,SAAS,GAAG,CAAC,GAAQ,EAAE,MAAc,EAAE,IAAY,EAAE,KAAa;IAChE,IAAI,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAA;IAC9B,IAAI,OAAO,KAAK,SAAS,EAAE;QACzB,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,GAAG;YAC3B,KAAK,EAAE,CAAC;YACR,IAAI,EAAE,CAAC;YACP,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;SACP,CAAA;KACF;IACD,OAAO,CAAC,KAAK,EAAE,CAAA;IACf,OAAO,CAAC,MAAM,CAAC,EAAE,CAAA;AACnB,CAAC;AAED,MAAqB,kBAAmB,SAAQ,oCAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,YAAY,EAAE,iBAAiB,CAAC,CAAC,CAAA;QACpE,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,IAAA,oBAAa,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,UAAU;iBAC3B,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC;iBACzB,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC;iBACf,SAAS,EAAE,CAAA;YAEd,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,oBAAoB,CACvD,KAAK,EACL,MAAM,EACN,IAAI,CACL,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;gBAClC,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE;oBACzB,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK;wBACL,GAAG,EAAE,KAAK,GAAG,CAAC;wBACd,OAAO,EAAE,MAAM,CAAC,OAAO;qBACxB;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,uCAAuC;YACvC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE;gBAC9C,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG;oBACP,IAAI,EAAE;wBACJ,IAAI,EAAE,MAAM;wBACZ,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,GAAG,EAAE,IAAI,CAAC,GAAG;wBACb,MAAM,EAAE,IAAI,CAAC,MAAM;wBACnB,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,EAAE,EAAE,IAAI,CAAC,EAAE;qBACZ;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,OAAiB,EAAE,IAAkB;QAC9D,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,oBAAoB,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QACtC,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;IAExC,KAAK,CAAC,oBAAoB,CACxB,QAAmB,EACnB,MAAc,EACd,IAAoE;;QAEpE,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;QACxB,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;QAEnD,MAAM,OAAO,GAAG,EASf,CAAA;QAQD,MAAM,SAAS,GACb,QAAQ,CAAC,MAAM,IAAI,IAAA,mCAA4B,EAAC,MAAA,IAAI,CAAC,OAAO,0CAAE,IAAI,CAAC;YACjE,CAAC,CAAC,MAAM,IAAI,CAAC,aAAa,CAAC,MAAM,CAAC;YAClC,CAAC,CAAC,SAAS,CAAA;QAEf,MAAM,IAAI,GAAG,EAYV,CAAA;QAEH,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACnC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAC/B,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAe,CAAA;YAEnD,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;gBACtC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;gBAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,MAAM,EAAE;oBACxB,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;wBACzB,IAAI,CAAC,CAAC,CAAC,GAAG;4BACR,KAAK,EAAE,CAAC;4BACR,GAAG,EAAE,CAAC;4BACN,GAAG,EAAE,CAAC;4BACN,IAAI,EAAE,CAAC;4BACP,GAAG,EAAE,CAAC;4BACN,GAAG,EAAE,CAAC;4BACN,OAAO,EAAE,EAAa;4BACtB,GAAG,EAAE,EAAa;4BAClB,QAAQ,EAAE,EAAa;4BACvB,MAAM,EAAE,EAAa;yBACtB,CAAA;qBACF;oBACD,IAAI,CAAC,KAAK,IAAI,EAAE;wBACd,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,EAAE,CAAA;wBACf,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;wBACb,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;wBACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;qBACnB;iBACF;aACF;YAED,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,EAAE;gBACrC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAW,CAAA;gBACxC,MAAM,EAAE,GAAI,IAAA,gBAAS,EAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAY,IAAI,EAAE,CAAA;gBAC3D,MAAM,GAAG,GAAG,IAAA,2BAAU,EAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;gBAC5C,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;gBAE/B,IAAA,yCAAwB,EAAC,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC,OAAO,CAChD,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,EAAE,EAAE;oBACtB,MAAM,GAAG,GAAG,OAAO,IAAI,EAAE,CAAA;oBACzB,KAAK,MAAM,GAAG,IAAI,IAAA,8BAAa,EAAC,GAAG,EAAE,SAAS,CAAC,EAAE;wBAC/C,MAAM,IAAI,GAAG,GAAG,GAAG,MAAM,GAAG,MAAM,CAAC,KAAK,CAAA;wBACxC,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,IAAI,CAAC,MAAM,IAAI,GAAG,GAAG,MAAM,GAAG,IAAI,EAAE;4BAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;4BACtB,IAAI,GAAG,EAAE;gCACP,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;6BAC9B;iCAAM;gCACL,OAAO,CAAC,IAAI,CACV,6DAA6D,CAC9D,CAAA;6BACF;yBACF;qBACF;gBACH,CAAC,CACF,CAAA;aACF;YAED,+DAA+D;YAC/D,mCAAmC;iBAC9B,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,EAAE;gBACxC,IAAI,CAAC,SAAS,EAAE;oBACd,MAAM,IAAI,KAAK,CACb,iEAAiE,CAClE,CAAA;iBACF;gBACD,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;gBAC9B,MAAM,EAAE,GAAG,IAAA,gBAAS,EAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAA;gBAC/C,MAAM,QAAQ,GAAG,IAAI,KAAK,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBAC7D,MAAM,GAAG,GAAG,IAAA,2BAAU,EAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;gBAE5C,IAAA,yCAAwB,EAAC,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC,OAAO,CAChD,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,EAAE,EAAE;oBACtB,gCAAgC;oBAChC,IAAI,IAAI,KAAK,GAAG,EAAE;wBAChB,KAAK,MAAM,GAAG,IAAI,IAAA,8BAAa,EAAC,GAAG,EAAE,SAAS,CAAC,EAAE;4BAC/C,MAAM,IAAI,GAAG,GAAG,GAAG,MAAM,GAAG,MAAM,CAAC,KAAK,CAAA;4BACxC,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,QAAQ,CAAC,MAAM,EAAE;gCACvC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;6BACnB;yBACF;qBACF;gBACH,CAAC,CACF,CAAA;gBAED,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;oBAClC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;oBAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE;wBACjC,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;wBACrC,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;wBACzC,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;wBACnB,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;wBAExB,QAAQ;wBACR,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;4BAC5B,IAAI,QAAQ,CAAC,CAAC,CAAC,IAAI,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE;gCAClC,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;gCAChC,GAAG,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;gCACjC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gCACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;gCAClB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gCACjB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;6BACvB;iCAAM;gCACL,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,QAAQ,CAAC,CAAA;gCAClC,GAAG,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,QAAQ,CAAC,CAAA;gCACnC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gCACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;gCAClB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gCACjB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;6BACvB;yBACF;qBACF;iBACF;aACF;YAED,4BAA4B;YAC5B,MAAM,UAAU,GAAI,OAAO,CAAC,GAAG,CAAC,YAAY,CAAgB,IAAI,EAAE,CAAA;YAClE,MAAM,SAAS,GACb,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,CAAA;YAEtE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBAC1C,MAAM,QAAQ,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;gBAC9B,MAAM,MAAM,GAAG,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAA;gBACtC,MAAM,IAAI,GAAG,WAAW,CAAC,QAAQ,CAAC,CAAA;gBAClC,MAAM,IAAI,GAAG,MAAM,GAAG,IAAI,CAAA;gBAC1B,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,MAAM,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;oBAC3C,MAAM,IAAI,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;oBAC7B,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,IAAI,CAAC,MAAM,EAAE;wBACnC,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;wBACtB,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,QAAQ,CAAA;wBAC/B,MAAM,SAAS,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;wBACnC,IAAI,CAAC,SAAS,EAAE;4BACd,GAAG,CAAC,GAAG,EAAE,CAAA;4BACT,GAAG,CAAC,OAAO,CAAC,EAAE,CAAA;yBACf;6BAAM;4BACL,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAA;yBAClC;wBAED,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,MAAM,EAAE;4BAC1C,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,UAAU,EAAE,IAAI,CAAC,CAAA;4BACnC,GAAG,CAAC,KAAK,EAAE,CAAA;yBACZ;6BAAM,IAAI,CAAC,SAAS,IAAI,SAAS,EAAE;4BAClC,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;4BAC9B,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,OAAO,CAAA;yBAC/B;qBACF;iBACF;gBAED,IAAI,QAAQ,CAAC,IAAI,KAAK,MAAM,EAAE;oBAC5B,MAAM,IAAI,GAAG,GAAG,MAAM,IAAI,IAAI,IAAI,OAAO,EAAE,CAAA;oBAC3C,IAAI,OAAO,CAAC,IAAI,CAAC,KAAK,SAAS,EAAE;wBAC/B,OAAO,CAAC,IAAI,CAAC,GAAG;4BACd,OAAO,EAAE,OAAO;4BAChB,KAAK,EAAE,MAAM;4BACb,GAAG,EAAE,IAAI;4BACT,MAAM,EAAE,OAAO;4BACf,EAAE,EAAE,IAAA,aAAM,EAAC,OAAO,EAAE,IAAI,CAAC,IAAI,IAAA,aAAM,EAAC,OAAO,EAAE,IAAI,CAAC;4BAClD,KAAK,EAAE,CAAC;yBACT,CAAA;qBACF;oBACD,OAAO,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,CAAA;iBACtB;aACF;SACF;QAED,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,CAAA;IAC1B,CAAC;CACF;AAjTD,qCAiTC;AAED,MAAM,EAAE,YAAY,EAAE,GAAG,kBAAkB,CAAA;AAClC,oCAAY"}
+{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":";;;;;;AAAA,yEAGgD;AAEhD,qFAAyE;AACzE,kDAA0D;AAC1D,8CAAwC;AACxC,kFAAyD;AACzD,kCAAuC;AAEvC,MAAqB,kBAAmB,SAAQ,oCAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,gBAAgB,CAAC,eAAe,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,IAAA,oBAAa,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,UAAU;iBAC3B,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC;iBACzB,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC;iBACf,SAAS,EAAE,CAAA;YAEd,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,IAAA,8BAAoB,EAClD,KAAK,EACL,MAAM,EACN,IAAI,EACJ,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAC/B,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;gBAClC,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE;oBACzB,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK;wBACL,GAAG,EAAE,KAAK,GAAG,CAAC;wBACd,OAAO,EAAE,MAAM,CAAC,OAAO;qBACxB;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,uCAAuC;YACvC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE;gBAC9C,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG;oBACP,IAAI,EAAE;wBACJ,IAAI,EAAE,MAAM;wBACZ,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,GAAG,EAAE,IAAI,CAAC,GAAG;wBACb,MAAM,EAAE,IAAI,CAAC,MAAM;wBACnB,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,EAAE,EAAE,IAAI,CAAC,EAAE;qBACZ;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,OAAiB,EAAE,IAAkB;QAC9D,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,oBAAoB,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QACtC,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AA9FD,qCA8FC;AAED,MAAM,EAAE,YAAY,EAAE,GAAG,kBAAkB,CAAA;AAClC,oCAAY"}

package/dist/SNPCoverageAdapter/generateCoverageBins.d.ts

@@ -0,0 +1,53 @@
+import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export default function generateCoverageBins(features: Feature[], region: Region, opts: {
+    bpPerPx?: number;
+    colorBy?: {
+        type: string;
+        tag?: string;
+    };
+}, fetchSequence: (arg: Region) => Promise<string>): Promise<{
+    bins: {
+        refbase?: string | undefined;
+        total: number;
+        all: number;
+        ref: number;
+        '-1': 0;
+        '0': 0;
+        '1': 0;
+        lowqual: {
+            total: number;
+            strands: {
+                [key: string]: number;
+            };
+        };
+        cov: {
+            total: number;
+            strands: {
+                [key: string]: number;
+            };
+        };
+        delskips: {
+            total: number;
+            strands: {
+                [key: string]: number;
+            };
+        };
+        noncov: {
+            total: number;
+            strands: {
+                [key: string]: number;
+            };
+        };
+    }[];
+    skipmap: {
+        [key: string]: {
+            score: number;
+            feature: unknown;
+            start: number;
+            end: number;
+            strand: number;
+            xs: string;
+        };
+    };
+}>;

package/dist/SNPCoverageAdapter/generateCoverageBins.js

@@ -0,0 +1,185 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const util_1 = require("../util");
+const MismatchParser_1 = require("../BamAdapter/MismatchParser");
+function mismatchLen(mismatch) {
+    return !isInterbase(mismatch.type) ? mismatch.length : 1;
+}
+function isInterbase(type) {
+    return type === 'softclip' || type === 'hardclip' || type === 'insertion';
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function inc(bin, strand, type, field) {
+    let thisBin = bin[type][field];
+    if (thisBin === undefined) {
+        thisBin = bin[type][field] = {
+            total: 0,
+            '-1': 0,
+            '0': 0,
+            '1': 0,
+        };
+    }
+    thisBin.total++;
+    thisBin[strand]++;
+}
+async function generateCoverageBins(features, region, opts, fetchSequence) {
+    var _a;
+    const { colorBy } = opts;
+    const binMax = Math.ceil(region.end - region.start);
+    const skipmap = {};
+    const regionSeq = features.length && (0, util_1.shouldFetchReferenceSequence)((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type)
+        ? await fetchSequence(region)
+        : undefined;
+    const bins = [];
+    for (let i = 0; i < features.length; i++) {
+        const feature = features[i];
+        const fstart = feature.get('start');
+        const fend = feature.get('end');
+        const fstrand = feature.get('strand');
+        for (let j = fstart; j < fend + 1; j++) {
+            const i = j - region.start;
+            if (i >= 0 && i < binMax) {
+                if (bins[i] === undefined) {
+                    bins[i] = {
+                        total: 0,
+                        all: 0,
+                        ref: 0,
+                        '-1': 0,
+                        '0': 0,
+                        '1': 0,
+                        lowqual: {},
+                        cov: {},
+                        delskips: {},
+                        noncov: {},
+                    };
+                }
+                if (j !== fend) {
+                    bins[i].total++;
+                    bins[i].all++;
+                    bins[i].ref++;
+                    bins[i][fstrand]++;
+                }
+            }
+        }
+        if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
+            const seq = feature.get('seq');
+            const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
+            const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
+            const fend = feature.get('end');
+            (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
+                const mod = `mod_${type}`;
+                for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
+                    const epos = pos + fstart - region.start;
+                    if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
+                        const bin = bins[epos];
+                        if (bin) {
+                            inc(bin, fstrand, 'cov', mod);
+                        }
+                        else {
+                            console.warn('Undefined position in modifications snpcoverage encountered');
+                        }
+                    }
+                }
+            });
+        }
+        // methylation based coloring takes into account both reference
+        // sequence CpG detection and reads
+        else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
+            if (!regionSeq) {
+                throw new Error('no region sequence detected, need sequenceAdapter configuration');
+            }
+            const seq = feature.get('seq');
+            const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
+            const methBins = new Array(region.end - region.start).fill(0);
+            const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
+            (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
+                // we are processing methylation
+                if (type === 'm') {
+                    for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
+                        const epos = pos + fstart - region.start;
+                        if (epos >= 0 && epos < methBins.length) {
+                            methBins[epos] = 1;
+                        }
+                    }
+                }
+            });
+            for (let j = fstart; j < fend; j++) {
+                const i = j - region.start;
+                if (i >= 0 && i < bins.length - 1) {
+                    const l1 = regionSeq[i].toLowerCase();
+                    const l2 = regionSeq[i + 1].toLowerCase();
+                    const bin = bins[i];
+                    const bin1 = bins[i + 1];
+                    // color
+                    if (l1 === 'c' && l2 === 'g') {
+                        if (methBins[i] || methBins[i + 1]) {
+                            inc(bin, fstrand, 'cov', 'meth');
+                            inc(bin1, fstrand, 'cov', 'meth');
+                            bins[i].ref--;
+                            bins[i][fstrand]--;
+                            bins[i + 1].ref--;
+                            bins[i + 1][fstrand]--;
+                        }
+                        else {
+                            inc(bin, fstrand, 'cov', 'unmeth');
+                            inc(bin1, fstrand, 'cov', 'unmeth');
+                            bins[i].ref--;
+                            bins[i][fstrand]--;
+                            bins[i + 1].ref--;
+                            bins[i + 1][fstrand]--;
+                        }
+                    }
+                }
+            }
+        }
+        // normal SNP based coloring
+        const mismatches = feature.get('mismatches') || [];
+        const colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
+        for (let i = 0; i < mismatches.length; i++) {
+            const mismatch = mismatches[i];
+            const mstart = fstart + mismatch.start;
+            const mlen = mismatchLen(mismatch);
+            const mend = mstart + mlen;
+            for (let j = mstart; j < mstart + mlen; j++) {
+                const epos = j - region.start;
+                if (epos >= 0 && epos < bins.length) {
+                    const bin = bins[epos];
+                    const { base, type } = mismatch;
+                    const interbase = isInterbase(type);
+                    if (!interbase) {
+                        bin.ref--;
+                        bin[fstrand]--;
+                    }
+                    else {
+                        inc(bin, fstrand, 'noncov', type);
+                    }
+                    if (type === 'deletion' || type === 'skip') {
+                        inc(bin, fstrand, 'delskips', type);
+                        bin.total--;
+                    }
+                    else if (!interbase && colorSNPs) {
+                        inc(bin, fstrand, 'cov', base);
+                        bin.refbase = mismatch.altbase;
+                    }
+                }
+            }
+            if (mismatch.type === 'skip') {
+                const hash = `${mstart}_${mend}_${fstrand}`;
+                if (skipmap[hash] === undefined) {
+                    skipmap[hash] = {
+                        feature: feature,
+                        start: mstart,
+                        end: mend,
+                        strand: fstrand,
+                        xs: (0, util_1.getTag)(feature, 'XS') || (0, util_1.getTag)(feature, 'TS'),
+                        score: 0,
+                    };
+                }
+                skipmap[hash].score++;
+            }
+        }
+    }
+    return { bins, skipmap };
+}
+exports.default = generateCoverageBins;
+//# sourceMappingURL=generateCoverageBins.js.map

package/dist/SNPCoverageAdapter/generateCoverageBins.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"generateCoverageBins.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/generateCoverageBins.ts"],"names":[],"mappings":";;AAEA,kCAAyE;AACzE,iEAKqC;AAErC,SAAS,WAAW,CAAC,QAAkB;IACrC,OAAO,CAAC,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;AAC1D,CAAC;AAED,SAAS,WAAW,CAAC,IAAY;IAC/B,OAAO,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,WAAW,CAAA;AAC3E,CAAC;AAED,8DAA8D;AAC9D,SAAS,GAAG,CAAC,GAAQ,EAAE,MAAc,EAAE,IAAY,EAAE,KAAa;IAChE,IAAI,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAA;IAC9B,IAAI,OAAO,KAAK,SAAS,EAAE;QACzB,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,GAAG;YAC3B,KAAK,EAAE,CAAC;YACR,IAAI,EAAE,CAAC;YACP,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;SACP,CAAA;KACF;IACD,OAAO,CAAC,KAAK,EAAE,CAAA;IACf,OAAO,CAAC,MAAM,CAAC,EAAE,CAAA;AACnB,CAAC;AAEc,KAAK,UAAU,oBAAoB,CAChD,QAAmB,EACnB,MAAc,EACd,IAAoE,EACpE,aAA+C;;IAE/C,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;IACxB,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAEnD,MAAM,OAAO,GAAG,EASf,CAAA;IAQD,MAAM,SAAS,GACb,QAAQ,CAAC,MAAM,IAAI,IAAA,mCAA4B,EAAC,MAAA,IAAI,CAAC,OAAO,0CAAE,IAAI,CAAC;QACjE,CAAC,CAAC,MAAM,aAAa,CAAC,MAAM,CAAC;QAC7B,CAAC,CAAC,SAAS,CAAA;IAEf,MAAM,IAAI,GAAG,EAYV,CAAA;IAEH,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;QAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QACnC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAe,CAAA;QAEnD,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACtC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;YAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,MAAM,EAAE;gBACxB,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;oBACzB,IAAI,CAAC,CAAC,CAAC,GAAG;wBACR,KAAK,EAAE,CAAC;wBACR,GAAG,EAAE,CAAC;wBACN,GAAG,EAAE,CAAC;wBACN,IAAI,EAAE,CAAC;wBACP,GAAG,EAAE,CAAC;wBACN,GAAG,EAAE,CAAC;wBACN,OAAO,EAAE,EAAa;wBACtB,GAAG,EAAE,EAAa;wBAClB,QAAQ,EAAE,EAAa;wBACvB,MAAM,EAAE,EAAa;qBACtB,CAAA;iBACF;gBACD,IAAI,CAAC,KAAK,IAAI,EAAE;oBACd,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,EAAE,CAAA;oBACf,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;oBACb,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;oBACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;iBACnB;aACF;SACF;QAED,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,EAAE;YACrC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAW,CAAA;YACxC,MAAM,EAAE,GAAI,IAAA,gBAAS,EAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAY,IAAI,EAAE,CAAA;YAC3D,MAAM,GAAG,GAAG,IAAA,2BAAU,EAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;YAC5C,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAE/B,IAAA,yCAAwB,EAAC,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC,OAAO,CAChD,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,OAAO,IAAI,EAAE,CAAA;gBACzB,KAAK,MAAM,GAAG,IAAI,IAAA,8BAAa,EAAC,GAAG,EAAE,SAAS,CAAC,EAAE;oBAC/C,MAAM,IAAI,GAAG,GAAG,GAAG,MAAM,GAAG,MAAM,CAAC,KAAK,CAAA;oBACxC,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,IAAI,CAAC,MAAM,IAAI,GAAG,GAAG,MAAM,GAAG,IAAI,EAAE;wBAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;wBACtB,IAAI,GAAG,EAAE;4BACP,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;yBAC9B;6BAAM;4BACL,OAAO,CAAC,IAAI,CACV,6DAA6D,CAC9D,CAAA;yBACF;qBACF;iBACF;YACH,CAAC,CACF,CAAA;SACF;QAED,+DAA+D;QAC/D,mCAAmC;aAC9B,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,EAAE;YACxC,IAAI,CAAC,SAAS,EAAE;gBACd,MAAM,IAAI,KAAK,CACb,iEAAiE,CAClE,CAAA;aACF;YACD,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAC9B,MAAM,EAAE,GAAG,IAAA,gBAAS,EAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAA;YAC/C,MAAM,QAAQ,GAAG,IAAI,KAAK,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YAC7D,MAAM,GAAG,GAAG,IAAA,2BAAU,EAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;YAE5C,IAAA,yCAAwB,EAAC,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC,OAAO,CAChD,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,EAAE,EAAE;gBACtB,gCAAgC;gBAChC,IAAI,IAAI,KAAK,GAAG,EAAE;oBAChB,KAAK,MAAM,GAAG,IAAI,IAAA,8BAAa,EAAC,GAAG,EAAE,SAAS,CAAC,EAAE;wBAC/C,MAAM,IAAI,GAAG,GAAG,GAAG,MAAM,GAAG,MAAM,CAAC,KAAK,CAAA;wBACxC,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,QAAQ,CAAC,MAAM,EAAE;4BACvC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;yBACnB;qBACF;iBACF;YACH,CAAC,CACF,CAAA;YAED,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;gBAClC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;gBAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE;oBACjC,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;oBACrC,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;oBACzC,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;oBACnB,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;oBAExB,QAAQ;oBACR,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;wBAC5B,IAAI,QAAQ,CAAC,CAAC,CAAC,IAAI,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE;4BAClC,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;4BAChC,GAAG,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;4BACjC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;4BACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;4BAClB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;4BACjB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;yBACvB;6BAAM;4BACL,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,QAAQ,CAAC,CAAA;4BAClC,GAAG,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,QAAQ,CAAC,CAAA;4BACnC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;4BACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;4BAClB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;4BACjB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;yBACvB;qBACF;iBACF;aACF;SACF;QAED,4BAA4B;QAC5B,MAAM,UAAU,GAAI,OAAO,CAAC,GAAG,CAAC,YAAY,CAAgB,IAAI,EAAE,CAAA;QAClE,MAAM,SAAS,GACb,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,CAAA;QAEtE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC1C,MAAM,QAAQ,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YAC9B,MAAM,MAAM,GAAG,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAA;YACtC,MAAM,IAAI,GAAG,WAAW,CAAC,QAAQ,CAAC,CAAA;YAClC,MAAM,IAAI,GAAG,MAAM,GAAG,IAAI,CAAA;YAC1B,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,MAAM,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;gBAC3C,MAAM,IAAI,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;gBAC7B,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,IAAI,CAAC,MAAM,EAAE;oBACnC,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;oBACtB,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,QAAQ,CAAA;oBAC/B,MAAM,SAAS,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;oBACnC,IAAI,CAAC,SAAS,EAAE;wBACd,GAAG,CAAC,GAAG,EAAE,CAAA;wBACT,GAAG,CAAC,OAAO,CAAC,EAAE,CAAA;qBACf;yBAAM;wBACL,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAA;qBAClC;oBAED,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,MAAM,EAAE;wBAC1C,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,UAAU,EAAE,IAAI,CAAC,CAAA;wBACnC,GAAG,CAAC,KAAK,EAAE,CAAA;qBACZ;yBAAM,IAAI,CAAC,SAAS,IAAI,SAAS,EAAE;wBAClC,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;wBAC9B,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,OAAO,CAAA;qBAC/B;iBACF;aACF;YAED,IAAI,QAAQ,CAAC,IAAI,KAAK,MAAM,EAAE;gBAC5B,MAAM,IAAI,GAAG,GAAG,MAAM,IAAI,IAAI,IAAI,OAAO,EAAE,CAAA;gBAC3C,IAAI,OAAO,CAAC,IAAI,CAAC,KAAK,SAAS,EAAE;oBAC/B,OAAO,CAAC,IAAI,CAAC,GAAG;wBACd,OAAO,EAAE,OAAO;wBAChB,KAAK,EAAE,MAAM;wBACb,GAAG,EAAE,IAAI;wBACT,MAAM,EAAE,OAAO;wBACf,EAAE,EAAE,IAAA,aAAM,EAAC,OAAO,EAAE,IAAI,CAAC,IAAI,IAAA,aAAM,EAAC,OAAO,EAAE,IAAI,CAAC;wBAClD,KAAK,EAAE,CAAC;qBACT,CAAA;iBACF;gBACD,OAAO,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,CAAA;aACtB;SACF;KACF;IAED,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,CAAA;AAC1B,CAAC;AAnND,uCAmNC"}

package/esm/CramAdapter/CramTestAdapters.js

@@ -61,7 +61,8 @@ export class SequenceAdapter extends BaseFeatureDataAdapter {
                     end,
                 }));
                 observer.complete();
-            });
+            })
+                .catch(e => observer.error(e));
             return { unsubscribe: () => { } };
         });
     }

package/esm/CramAdapter/CramTestAdapters.js.map

@@ -1 +1 @@
-{"version":3,"file":"CramTestAdapters.js","sourceRoot":"","sources":["../../src/CramAdapter/CramTestAdapters.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AACjC,OAAO,aAAa,MAAM,kCAAkC,CAAA;AAC5D,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAE,mBAAmB,EAAE,MAAM,iDAAiD,CAAA;AAErF,iCAAiC;AACjC,MAAM,UAAU,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;AAID,MAAM,OAAO,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;AAED,MAAM,OAAO,eAAgB,SAAQ,sBAAsB;IAKzD,YAAY,UAAsB;QAChC,KAAK,CAAC,mBAAmB,CAAC,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,UAAU,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,aAAa,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"}
+{"version":3,"file":"CramTestAdapters.js","sourceRoot":"","sources":["../../src/CramAdapter/CramTestAdapters.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AACjC,OAAO,aAAa,MAAM,kCAAkC,CAAA;AAC5D,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAE,mBAAmB,EAAE,MAAM,iDAAiD,CAAA;AAErF,iCAAiC;AACjC,MAAM,UAAU,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;AAID,MAAM,OAAO,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;AAED,MAAM,OAAO,eAAgB,SAAQ,sBAAsB;IAKzD,YAAY,UAAsB;QAChC,KAAK,CAAC,mBAAmB,CAAC,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,UAAU,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,aAAa,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"}

package/esm/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/esm/LinearPileupDisplay/components/ColorByModifications.js

@@ -1,15 +1,9 @@
 import React from 'react';
 import { observer } from 'mobx-react';
-import { Button, CircularProgress, Dialog, DialogActions, DialogContent, DialogTitle, IconButton, Typography, } from '@mui/material';
+import { Button, CircularProgress, DialogActions, DialogContent, Typography, } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
 import { makeStyles } from 'tss-react/mui';
-import CloseIcon from '@mui/icons-material/Close';
 const useStyles = 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),
@@ -30,15 +24,10 @@ function ModificationTable({ modifications, }) {
                 } })))))));
 }
 function ColorByTagDlg(props) {
-    const { classes } = useStyles();
     const { model, handleClose } = props;
     const { colorBy, modificationTagMap } = model;
     const modifications = [...modificationTagMap.entries()];
-    return (React.createElement(Dialog, { open: true, onClose: handleClose },
-        React.createElement(DialogTitle, null,
-            "Color by modifications",
-            React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
-                React.createElement(CloseIcon, null))),
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Color by modifications" },
         React.createElement(DialogContent, null,
             React.createElement(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.createElement(Typography, null, "Note: you can revisit this dialog to see the current mapping of colors to modification type for the modification coloring mode"),
@@ -53,19 +42,15 @@ function ColorByTagDlg(props) {
                         ['unmethylated', 'blue'],
                     ] })) : null),
             React.createElement(DialogActions, null,
-                React.createElement(Button, { variant: "contained", color: "primary", style: { margin: 5 }, onClick: () => {
-                        model.setColorScheme({
-                            type: 'modifications',
-                        });
+                React.createElement(Button, { variant: "contained", onClick: () => {
+                        model.setColorScheme({ type: 'modifications' });
                         handleClose();
                     } }, "Modifications"),
-                React.createElement(Button, { variant: "contained", color: "primary", style: { margin: 5 }, onClick: () => {
-                        model.setColorScheme({
-                            type: 'methylation',
-                        });
+                React.createElement(Button, { variant: "contained", onClick: () => {
+                        model.setColorScheme({ type: 'methylation' });
                         handleClose();
                     } }, "Methylation"),
-                React.createElement(Button, { variant: "contained", color: "secondary", style: { margin: 5 }, onClick: () => handleClose() }, "Cancel")))));
+                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel")))));
 }
 export default observer(ColorByTagDlg);
 //# sourceMappingURL=ColorByModifications.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"ColorByModifications.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByModifications.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EACL,MAAM,EACN,gBAAgB,EAChB,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,UAAU,EACV,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAEjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;IACD,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,+BAAO,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,mCACG,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CACnC,4BAAI,GAAG,EAAE,GAAG;YACV,gCAAK,GAAG,CAAM;YACd,gCAAK,KAAK,CAAM;YAChB,4BACE,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,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,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,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,oBAAC,WAAW;;YAEV,oBAAC,UAAU,kBACE,OAAO,EAClB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,WAAW;gBAEpB,oBAAC,SAAS,OAAG,CACF,CACD;QACd,oBAAC,aAAa;YACZ,oBAAC,UAAU,oRAKE;YACb,oBAAC,UAAU,yIAGE;YACb,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE;gBACvB,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,CAAC,CAAC,CAAC,CACnC,iCACG,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,CACtB;;oBAEE,oBAAC,iBAAiB,IAChB,aAAa,EAAE,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,GAChD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;oBACE,oBAAC,UAAU,4FAGE;oBACb,oBAAC,gBAAgB,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,oBAAC,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,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,EACpB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC;4BACnB,IAAI,EAAE,eAAe;yBACtB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,oBAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,EACpB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC;4BACnB,IAAI,EAAE,aAAa;yBACpB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,kBAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,EACpB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,aAAa,CAAC,CAAA"}
+{"version":3,"file":"ColorByModifications.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByModifications.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EACL,MAAM,EACN,gBAAgB,EAChB,aAAa,EACb,aAAa,EACb,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,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,+BAAO,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,mCACG,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CACnC,4BAAI,GAAG,EAAE,GAAG;YACV,gCAAK,GAAG,CAAM;YACd,gCAAK,KAAK,CAAM;YAChB,4BACE,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,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,wBAAwB;QAC/D,oBAAC,aAAa;YACZ,oBAAC,UAAU,oRAKE;YACb,oBAAC,UAAU,yIAGE;YACb,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE;gBACvB,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,CAAC,CAAC,CAAC,CACnC,iCACG,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,CACtB;;oBAEE,oBAAC,iBAAiB,IAChB,aAAa,EAAE,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,GAChD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;oBACE,oBAAC,UAAU,4FAGE;oBACb,oBAAC,gBAAgB,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,oBAAC,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,oBAAC,aAAa;gBACZ,oBAAC,MAAM,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,oBAAC,MAAM,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,oBAAC,MAAM,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,eAAe,QAAQ,CAAC,aAAa,CAAC,CAAA"}

package/esm/LinearPileupDisplay/components/ColorByTag.js

@@ -1,29 +1,12 @@
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
-import { Button, Dialog, DialogContent, DialogActions, DialogTitle, IconButton, TextField, Typography, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-import CloseIcon from '@mui/icons-material/Close';
-const useStyles = makeStyles()(theme => ({
-    root: {
-        width: 300,
-    },
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
+import { Button, DialogContent, DialogActions, TextField, Typography, } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
 function ColorByTagDlg(props) {
-    const { classes } = useStyles();
     const { model, handleClose } = props;
     const [tag, setTag] = useState('');
     const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose },
-        React.createElement(DialogTitle, null,
-            "Color by tag",
-            React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
-                React.createElement(CloseIcon, null))),
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Color by tag" },
         React.createElement(DialogContent, { style: { overflowX: 'hidden' } },
             React.createElement(Typography, null, "Enter tag to color by: "),
             React.createElement(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."),