@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -0,0 +1,259 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { toArray } from 'rxjs/operators';
+import { getTag, getTagAlt, fetchSequence, shouldFetchReferenceSequence, } from '../util';
+import { parseCigar, getNextRefPos, getModificationPositions, } from '../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]++;
+}
+export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
+    async configure() {
+        var _a, _b;
+        const subadapterConfig = this.getConf('subadapter');
+        const sequenceConf = this.getConf(['subadapter', '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))
+            : undefined;
+        if (!dataAdapter) {
+            throw new Error('Failed to get subadapter');
+        }
+        return {
+            subadapter: dataAdapter.dataAdapter,
+            sequenceAdapter: sequenceAdapter === null || sequenceAdapter === void 0 ? void 0 : sequenceAdapter.dataAdapter,
+        };
+    }
+    async fetchSequence(region) {
+        const { sequenceAdapter } = await this.configure();
+        if (!sequenceAdapter) {
+            return undefined;
+        }
+        return fetchSequence(region, sequenceAdapter);
+    }
+    getFeatures(region, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { subadapter } = await this.configure();
+            const feats = await subadapter
+                .getFeatures(region, opts)
+                .pipe(toArray())
+                .toPromise();
+            const { bins, skipmap } = await this.generateCoverageBins(feats, region, opts);
+            bins.forEach((bin, index) => {
+                observer.next(new SimpleFeature({
+                    id: `${this.id}-${region.start + index}`,
+                    data: {
+                        score: bin.total,
+                        snpinfo: bin,
+                        start: region.start + index,
+                        end: region.start + index + 1,
+                        refName: region.refName,
+                    },
+                }));
+            });
+            // make fake features from the coverage
+            Object.entries(skipmap).forEach(([key, skip]) => {
+                observer.next(new SimpleFeature({
+                    id: key,
+                    data: {
+                        type: 'skip',
+                        start: skip.start,
+                        end: skip.end,
+                        strand: skip.strand,
+                        score: skip.score,
+                        xs: skip.xs,
+                    },
+                }));
+            });
+            observer.complete();
+        }, opts.signal);
+    }
+    async estimateRegionsStats(regions, opts) {
+        const { subadapter } = await this.configure();
+        return subadapter.estimateRegionsStats(regions, opts);
+    }
+    async getRefNames(opts = {}) {
+        const { subadapter } = await this.configure();
+        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 && 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 = getTagAlt(feature, 'MM', 'Mm') || '';
+                const ops = parseCigar(feature.get('CIGAR'));
+                const fend = feature.get('end');
+                getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
+                    const mod = `mod_${type}`;
+                    for (const pos of 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 = getTagAlt(feature, 'MM', 'Mm') || '';
+                const methBins = new Array(region.end - region.start).fill(0);
+                const ops = parseCigar(feature.get('CIGAR'));
+                getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
+                    // we are processing methylation
+                    if (type === 'm') {
+                        for (const pos of 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: getTag(feature, 'XS') || getTag(feature, 'TS'),
+                            score: 0,
+                        };
+                    }
+                    skipmap[hash].score++;
+                }
+            }
+        }
+        return { bins, skipmap };
+    }
+}
+const { capabilities } = SNPCoverageAdapter;
+export { capabilities };
+//# sourceMappingURL=SNPCoverageAdapter.js.map

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EACL,MAAM,EACN,SAAS,EACT,aAAa,EACb,4BAA4B,GAC7B,MAAM,SAAS,CAAA;AAChB,OAAO,EACL,UAAU,EACV,aAAa,EACb,wBAAwB,GAEzB,MAAM,8BAA8B,CAAA;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,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,sBAAsB;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,aAAa,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,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,OAAO,EAAE,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,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,MAAM,CAAC,KAAK,GAAG,KAAK,EAAE;oBACxC,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK,EAAE,MAAM,CAAC,KAAK,GAAG,KAAK;wBAC3B,GAAG,EAAE,MAAM,CAAC,KAAK,GAAG,KAAK,GAAG,CAAC;wBAC7B,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,aAAa,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,4BAA4B,CAAC,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,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAY,IAAI,EAAE,CAAA;gBAC3D,MAAM,GAAG,GAAG,UAAU,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;gBAC5C,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;gBAE/B,wBAAwB,CAAC,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,aAAa,CAAC,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,SAAS,CAAC,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,UAAU,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;gBAE5C,wBAAwB,CAAC,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,aAAa,CAAC,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,MAAM,CAAC,OAAO,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,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;AAED,MAAM,EAAE,YAAY,EAAE,GAAG,kBAAkB,CAAA;AAC3C,OAAO,EAAE,YAAY,EAAE,CAAA"}

package/esm/SNPCoverageAdapter/configSchema.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/SNPCoverageAdapter/configSchema.js

@@ -0,0 +1,6 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+export default (pluginManager) => types.late(() => ConfigurationSchema('SNPCoverageAdapter', {
+    subadapter: pluginManager.pluggableConfigSchemaType('adapter'),
+}, { explicitlyTyped: true }));
+//# sourceMappingURL=configSchema.js.map

package/esm/SNPCoverageAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,eAAe,CAAC,aAA4B,EAAE,EAAE,CAC9C,KAAK,CAAC,IAAI,CAAC,GAAG,EAAE,CACd,mBAAmB,CACjB,oBAAoB,EACpB;IACE,UAAU,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;CAC/D,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CACF,CAAA"}

package/esm/SNPCoverageAdapter/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/SNPCoverageAdapter/index.js

@@ -0,0 +1,18 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchemaFactory from './configSchema';
+import { capabilities } from './SNPCoverageAdapter';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'SNPCoverageAdapter',
+        adapterMetadata: {
+            category: null,
+            displayName: null,
+            hiddenFromGUI: true,
+            description: null,
+        },
+        getAdapterClass: () => import('./SNPCoverageAdapter').then(r => r.default),
+        configSchema: configSchemaFactory(pluginManager),
+        adapterCapabilities: capabilities,
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/SNPCoverageAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,mBAAmB,MAAM,gBAAgB,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,sBAAsB,CAAA;AAEnD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,oBAAoB;QAC1B,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,WAAW,EAAE,IAAI;YACjB,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;SAClB;QACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,sBAAsB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;QACrD,YAAY,EAAE,mBAAmB,CAAC,aAAa,CAAC;QAChD,mBAAmB,EAAE,YAAY;KAClC,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts

@@ -0,0 +1,20 @@
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
+export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
+    bpPerPx: number;
+    height: number;
+    highResolutionScaling: number;
+    scaleOpts: ScaleOpts;
+}
+export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+    ticks: {
+        values: number[];
+    };
+    displayCrossHatches: boolean;
+    modificationTagMap?: Record<string, string>;
+}
+export default class SNPCoverageRenderer extends WiggleBaseRenderer {
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;
+}

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -0,0 +1,185 @@
+import { createJBrowseTheme } from '@jbrowse/core/ui';
+import { featureSpanPx, bpSpanPx } from '@jbrowse/core/util';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { getOrigin, getScale, WiggleBaseRenderer, YSCALEBAR_LABEL_OFFSET, } from '@jbrowse/plugin-wiggle';
+export default class SNPCoverageRenderer extends WiggleBaseRenderer {
+    // note: the snps are drawn on linear scale even if the data is drawn in log
+    // scape hence the two different scales being used
+    async draw(ctx, props) {
+        const { features, regions, bpPerPx, displayCrossHatches, modificationTagMap = {}, scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, } = props;
+        const theme = createJBrowseTheme(configTheme);
+        const [region] = regions;
+        const width = (region.end - region.start) / bpPerPx;
+        // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
+        // wiggle display, and makes the height of the actual drawn area add
+        // "padding" to the top and bottom of the display
+        const offset = YSCALEBAR_LABEL_OFFSET;
+        const height = unadjustedHeight - offset * 2;
+        const { domain } = scaleOpts;
+        if (!domain) {
+            return;
+        }
+        const opts = { ...scaleOpts, range: [0, height] };
+        const viewScale = getScale(opts);
+        // clipping and insertion indicators, uses a smaller height/2 scale
+        const indicatorViewScale = getScale({
+            ...opts,
+            range: [0, height / 2],
+            scaleType: 'linear',
+        });
+        const originY = getOrigin(scaleOpts.scaleType);
+        const indicatorThreshold = readConfObject(cfg, 'indicatorThreshold');
+        const drawInterbaseCounts = readConfObject(cfg, 'drawInterbaseCounts');
+        const drawArcs = readConfObject(cfg, 'drawArcs');
+        const drawIndicators = readConfObject(cfg, 'drawIndicators');
+        // get the y coordinate that we are plotting at, this can be log scale
+        const toY = (n) => height - (viewScale(n) || 0) + offset;
+        const toHeight = (n) => toY(originY) - toY(n);
+        const indicatorToY = (n) => height - (indicatorViewScale(n) || 0) + offset;
+        const indicatorToHeight = (n) => indicatorToY(getOrigin('linear')) - indicatorToY(n);
+        // @ts-ignore
+        const { bases } = theme.palette;
+        const colorForBase = {
+            A: bases.A.main,
+            C: bases.C.main,
+            G: bases.G.main,
+            T: bases.T.main,
+            total: 'lightgrey',
+            insertion: 'purple',
+            softclip: 'blue',
+            hardclip: 'red',
+            meth: 'red',
+            unmeth: 'blue',
+            ref: 'lightgrey',
+        };
+        const feats = [...features.values()];
+        const coverage = feats.filter(f => f.get('type') !== 'skip');
+        const skips = feats.filter(f => f.get('type') === 'skip');
+        // Use two pass rendering, which helps in visualizing the SNPs at higher
+        // bpPerPx First pass: draw the gray background
+        ctx.fillStyle = colorForBase.total;
+        for (let i = 0; i < coverage.length; i++) {
+            const feature = coverage[i];
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            const w = rightPx - leftPx + 0.3;
+            const score = feature.get('score');
+            ctx.fillRect(leftPx, toY(score), w, toHeight(score));
+        }
+        // Keep track of previous total which we will use it to draw the interbase
+        // indicator (if there is a sudden clip, there will be no read coverage but
+        // there will be "clip" coverage) at that position beyond the read. if the
+        // clip is right at a block boundary then prevTotal will not be available,
+        // so this is a best attempt to plot interbase indicator at the "cliffs"
+        let prevTotal = 0;
+        // extraHorizontallyFlippedOffset is used to draw interbase items, which
+        // are located to the left when forward and right when reversed
+        const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0;
+        // Second pass: draw the SNP data, and add a minimum feature width of 1px
+        // which can be wider than the actual bpPerPx This reduces overdrawing of
+        // the grey background over the SNPs
+        for (let i = 0; i < coverage.length; i++) {
+            const feature = coverage[i];
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            const score = feature.get('score');
+            const snpinfo = feature.get('snpinfo');
+            const w = Math.max(rightPx - leftPx + 0.3, 1);
+            const totalScore = snpinfo.total;
+            const keys = Object.keys(snpinfo.cov).sort();
+            let curr = 0;
+            for (let i = 0; i < keys.length; i++) {
+                const base = keys[i];
+                const { total } = snpinfo.cov[base];
+                ctx.fillStyle =
+                    colorForBase[base] ||
+                        modificationTagMap[base.replace('mod_', '')] ||
+                        '#888';
+                const height = toHeight(score);
+                const bottom = toY(score) + height;
+                ctx.fillRect(leftPx, bottom - ((total + curr) / score) * height, w, (total / score) * height);
+                curr += total;
+            }
+            const interbaseEvents = Object.keys(snpinfo.noncov);
+            const indicatorHeight = 4.5;
+            if (drawInterbaseCounts) {
+                let curr = 0;
+                for (let i = 0; i < interbaseEvents.length; i++) {
+                    const base = interbaseEvents[i];
+                    const { total } = snpinfo.noncov[base];
+                    ctx.fillStyle = colorForBase[base];
+                    ctx.fillRect(leftPx - 0.6 + extraHorizontallyFlippedOffset, indicatorHeight + indicatorToHeight(curr), 1.2, indicatorToHeight(total));
+                    curr += total;
+                }
+            }
+            if (drawIndicators) {
+                let accum = 0;
+                let max = 0;
+                let maxBase = '';
+                for (let i = 0; i < interbaseEvents.length; i++) {
+                    const base = interbaseEvents[i];
+                    const { total } = snpinfo.noncov[base];
+                    accum += total;
+                    if (total > max) {
+                        max = total;
+                        maxBase = base;
+                    }
+                }
+                // avoid drawing a bunch of indicators if coverage is very low e.g.
+                // less than 7, uses the prev total in the case of the "cliff"
+                const indicatorComparatorScore = Math.max(totalScore, prevTotal);
+                if (accum > indicatorComparatorScore * indicatorThreshold &&
+                    indicatorComparatorScore > 7) {
+                    ctx.fillStyle = colorForBase[maxBase];
+                    ctx.beginPath();
+                    const l = leftPx + extraHorizontallyFlippedOffset;
+                    ctx.moveTo(l - 3.5, 0);
+                    ctx.lineTo(l + 3.5, 0);
+                    ctx.lineTo(l, indicatorHeight);
+                    ctx.fill();
+                }
+            }
+            prevTotal = totalScore;
+        }
+        if (drawArcs) {
+            for (let i = 0; i < skips.length; i++) {
+                const f = skips[i];
+                const [left, right] = bpSpanPx(f.get('start'), f.get('end'), region, bpPerPx);
+                ctx.beginPath();
+                const str = f.get('strand');
+                const xs = f.get('xs');
+                const pos = 'rgba(255,200,200,0.7)';
+                const neg = 'rgba(200,200,255,0.7)';
+                const neutral = 'rgba(200,200,200,0.7)';
+                if (xs === '+') {
+                    ctx.strokeStyle = pos;
+                }
+                else if (xs === '-') {
+                    ctx.strokeStyle = neg;
+                }
+                else if (str === 1) {
+                    ctx.strokeStyle = pos;
+                }
+                else if (str === -1) {
+                    ctx.strokeStyle = neg;
+                }
+                else {
+                    ctx.strokeStyle = neutral;
+                }
+                ctx.lineWidth = Math.log(f.get('score') + 1);
+                ctx.moveTo(left, height - offset * 2);
+                ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2);
+                ctx.stroke();
+            }
+        }
+        if (displayCrossHatches) {
+            ctx.lineWidth = 1;
+            ctx.strokeStyle = 'rgba(140,140,140,0.8)';
+            ticks.values.forEach(tick => {
+                ctx.beginPath();
+                ctx.moveTo(0, Math.round(toY(tick)));
+                ctx.lineTo(width, Math.round(toY(tick)));
+                ctx.stroke();
+            });
+        }
+    }
+}
+//# sourceMappingURL=SNPCoverageRenderer.js.map

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SNPCoverageRenderer.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/SNPCoverageRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAA;AAE5D,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAE5D,OAAO,EACL,SAAS,EACT,QAAQ,EAER,kBAAkB,EAClB,sBAAsB,GACvB,MAAM,wBAAwB,CAAA;AA2B/B,MAAM,CAAC,OAAO,OAAO,mBAAoB,SAAQ,kBAAkB;IACjE,4EAA4E;IAC5E,kDAAkD;IAClD,KAAK,CAAC,IAAI,CACR,GAA6B,EAC7B,KAAyC;QAEzC,MAAM,EACJ,QAAQ,EACR,OAAO,EACP,OAAO,EACP,mBAAmB,EACnB,kBAAkB,GAAG,EAAE,EACvB,SAAS,EACT,MAAM,EAAE,gBAAgB,EACxB,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,GAAG,EACX,KAAK,GACN,GAAG,KAAK,CAAA;QACT,MAAM,KAAK,GAAG,kBAAkB,CAAC,WAAW,CAAC,CAAA;QAC7C,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;QACxB,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QAEnD,yEAAyE;QACzE,oEAAoE;QACpE,iDAAiD;QACjD,MAAM,MAAM,GAAG,sBAAsB,CAAA;QACrC,MAAM,MAAM,GAAG,gBAAgB,GAAG,MAAM,GAAG,CAAC,CAAA;QAE5C,MAAM,EAAE,MAAM,EAAE,GAAG,SAAS,CAAA;QAC5B,IAAI,CAAC,MAAM,EAAE;YACX,OAAM;SACP;QACD,MAAM,IAAI,GAAG,EAAE,GAAG,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,CAAC,EAAE,CAAA;QACjD,MAAM,SAAS,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;QAEhC,mEAAmE;QACnE,MAAM,kBAAkB,GAAG,QAAQ,CAAC;YAClC,GAAG,IAAI;YACP,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,GAAG,CAAC,CAAC;YACtB,SAAS,EAAE,QAAQ;SACpB,CAAC,CAAA;QACF,MAAM,OAAO,GAAG,SAAS,CAAC,SAAS,CAAC,SAAS,CAAC,CAAA;QAE9C,MAAM,kBAAkB,GAAG,cAAc,CAAC,GAAG,EAAE,oBAAoB,CAAC,CAAA;QACpE,MAAM,mBAAmB,GAAG,cAAc,CAAC,GAAG,EAAE,qBAAqB,CAAC,CAAA;QACtE,MAAM,QAAQ,GAAG,cAAc,CAAC,GAAG,EAAE,UAAU,CAAC,CAAA;QAChD,MAAM,cAAc,GAAG,cAAc,CAAC,GAAG,EAAE,gBAAgB,CAAC,CAAA;QAE5D,sEAAsE;QACtE,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAChE,MAAM,QAAQ,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QAErD,MAAM,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CACjC,MAAM,GAAG,CAAC,kBAAkB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAChD,MAAM,iBAAiB,GAAG,CAAC,CAAS,EAAE,EAAE,CACtC,YAAY,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAC,GAAG,YAAY,CAAC,CAAC,CAAC,CAAA;QAErD,aAAa;QACb,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,OAAO,CAAA;QAC/B,MAAM,YAAY,GAA8B;YAC9C,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,KAAK,EAAE,WAAW;YAClB,SAAS,EAAE,QAAQ;YACnB,QAAQ,EAAE,MAAM;YAChB,QAAQ,EAAE,KAAK;YACf,IAAI,EAAE,KAAK;YACX,MAAM,EAAE,MAAM;YACd,GAAG,EAAE,WAAW;SACjB,CAAA;QAED,MAAM,KAAK,GAAG,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;QACpC,MAAM,QAAQ,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAC5D,MAAM,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAEzD,wEAAwE;QACxE,+CAA+C;QAC/C,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,KAAK,CAAA;QAClC,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,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YACjE,MAAM,CAAC,GAAG,OAAO,GAAG,MAAM,GAAG,GAAG,CAAA;YAChC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAA;SACrD;QAED,0EAA0E;QAC1E,2EAA2E;QAC3E,0EAA0E;QAC1E,0EAA0E;QAC1E,wEAAwE;QACxE,IAAI,SAAS,GAAG,CAAC,CAAA;QAEjB,wEAAwE;QACxE,+DAA+D;QAC/D,MAAM,8BAA8B,GAAG,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAExE,yEAAyE;QACzE,yEAAyE;QACzE,oCAAoC;QAEpC,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,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YAEjE,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAY,CAAA;YACjD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,GAAG,MAAM,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;YAC7C,MAAM,UAAU,GAAG,OAAO,CAAC,KAAK,CAAA;YAChC,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAA;YAE5C,IAAI,IAAI,GAAG,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACpC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;gBACpB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;gBACnC,GAAG,CAAC,SAAS;oBACX,YAAY,CAAC,IAAI,CAAC;wBAClB,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;wBAC5C,MAAM,CAAA;gBAER,MAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;gBAC9B,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,MAAM,CAAA;gBAClC,GAAG,CAAC,QAAQ,CACV,MAAM,EACN,MAAM,GAAG,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,KAAK,CAAC,GAAG,MAAM,EAC1C,CAAC,EACD,CAAC,KAAK,GAAG,KAAK,CAAC,GAAG,MAAM,CACzB,CAAA;gBACD,IAAI,IAAI,KAAK,CAAA;aACd;YAED,MAAM,eAAe,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YACnD,MAAM,eAAe,GAAG,GAAG,CAAA;YAC3B,IAAI,mBAAmB,EAAE;gBACvB,IAAI,IAAI,GAAG,CAAC,CAAA;gBACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/C,MAAM,IAAI,GAAG,eAAe,CAAC,CAAC,CAAC,CAAA;oBAC/B,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;oBACtC,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;oBAClC,GAAG,CAAC,QAAQ,CACV,MAAM,GAAG,GAAG,GAAG,8BAA8B,EAC7C,eAAe,GAAG,iBAAiB,CAAC,IAAI,CAAC,EACzC,GAAG,EACH,iBAAiB,CAAC,KAAK,CAAC,CACzB,CAAA;oBACD,IAAI,IAAI,KAAK,CAAA;iBACd;aACF;YAED,IAAI,cAAc,EAAE;gBAClB,IAAI,KAAK,GAAG,CAAC,CAAA;gBACb,IAAI,GAAG,GAAG,CAAC,CAAA;gBACX,IAAI,OAAO,GAAG,EAAE,CAAA;gBAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/C,MAAM,IAAI,GAAG,eAAe,CAAC,CAAC,CAAC,CAAA;oBAC/B,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;oBACtC,KAAK,IAAI,KAAK,CAAA;oBACd,IAAI,KAAK,GAAG,GAAG,EAAE;wBACf,GAAG,GAAG,KAAK,CAAA;wBACX,OAAO,GAAG,IAAI,CAAA;qBACf;iBACF;gBAED,mEAAmE;gBACnE,8DAA8D;gBAC9D,MAAM,wBAAwB,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,EAAE,SAAS,CAAC,CAAA;gBAChE,IACE,KAAK,GAAG,wBAAwB,GAAG,kBAAkB;oBACrD,wBAAwB,GAAG,CAAC,EAC5B;oBACA,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;oBACrC,GAAG,CAAC,SAAS,EAAE,CAAA;oBACf,MAAM,CAAC,GAAG,MAAM,GAAG,8BAA8B,CAAA;oBACjD,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;oBACtB,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;oBACtB,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,eAAe,CAAC,CAAA;oBAC9B,GAAG,CAAC,IAAI,EAAE,CAAA;iBACX;aACF;YACD,SAAS,GAAG,UAAU,CAAA;SACvB;QAED,IAAI,QAAQ,EAAE;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACrC,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBAClB,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,GAAG,QAAQ,CAC5B,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EACd,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EACZ,MAAM,EACN,OAAO,CACR,CAAA;gBAED,GAAG,CAAC,SAAS,EAAE,CAAA;gBACf,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAW,CAAA;gBACrC,MAAM,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,IAAI,CAAW,CAAA;gBAChC,MAAM,GAAG,GAAG,uBAAuB,CAAA;gBACnC,MAAM,GAAG,GAAG,uBAAuB,CAAA;gBACnC,MAAM,OAAO,GAAG,uBAAuB,CAAA;gBAEvC,IAAI,EAAE,KAAK,GAAG,EAAE;oBACd,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,EAAE,KAAK,GAAG,EAAE;oBACrB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,GAAG,KAAK,CAAC,EAAE;oBACpB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,GAAG,KAAK,CAAC,CAAC,EAAE;oBACrB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM;oBACL,GAAG,CAAC,WAAW,GAAG,OAAO,CAAA;iBAC1B;gBAED,GAAG,CAAC,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAA;gBAC5C,GAAG,CAAC,MAAM,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAC,CAAA;gBACrC,GAAG,CAAC,aAAa,CAAC,IAAI,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAC,CAAA;gBAChE,GAAG,CAAC,MAAM,EAAE,CAAA;aACb;SACF;QAED,IAAI,mBAAmB,EAAE;YACvB,GAAG,CAAC,SAAS,GAAG,CAAC,CAAA;YACjB,GAAG,CAAC,WAAW,GAAG,uBAAuB,CAAA;YACzC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;gBAC1B,GAAG,CAAC,SAAS,EAAE,CAAA;gBACf,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACpC,GAAG,CAAC,MAAM,CAAC,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACxC,GAAG,CAAC,MAAM,EAAE,CAAA;YACd,CAAC,CAAC,CAAA;SACH;IACH,CAAC;CACF"}

package/esm/SNPCoverageRenderer/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/SNPCoverageRenderer/configSchema.js

@@ -0,0 +1,29 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('SNPCoverageRenderer', {
+    clipColor: {
+        type: 'color',
+        description: 'the color of the clipping marker',
+        defaultValue: 'red',
+    },
+    indicatorThreshold: {
+        type: 'number',
+        description: 'the proportion of reads containing a insertion/clip indicator',
+        defaultValue: 0.4,
+    },
+    drawArcs: {
+        type: 'boolean',
+        description: 'Draw sashimi-style arcs for intron features',
+        defaultValue: true,
+    },
+    drawInterbaseCounts: {
+        type: 'boolean',
+        description: 'draw count "upsidedown histogram" of the interbase events that don\'t contribute to the coverage count so are not drawn in the normal histogram',
+        defaultValue: true,
+    },
+    drawIndicators: {
+        type: 'boolean',
+        description: 'draw a triangular indicator where an event has been detected',
+        defaultValue: true,
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/SNPCoverageRenderer/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/configSchema.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,qBAAqB,EACrB;IACE,SAAS,EAAE;QACT,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,kCAAkC;QAC/C,YAAY,EAAE,KAAK;KACpB;IACD,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,+DAA+D;QACjE,YAAY,EAAE,GAAG;KAClB;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,6CAA6C;QAC1D,YAAY,EAAE,IAAI;KACnB;IACD,mBAAmB,EAAE;QACnB,IAAI,EAAE,SAAS;QACf,WAAW,EACT,iJAAiJ;QACnJ,YAAY,EAAE,IAAI;KACnB;IACD,cAAc,EAAE;QACd,IAAI,EAAE,SAAS;QACf,WAAW,EACT,8DAA8D;QAChE,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/SNPCoverageRenderer/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function register(pluginManager: PluginManager): void;

package/esm/SNPCoverageRenderer/index.js

@@ -0,0 +1,14 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import ConfigSchema from './configSchema';
+import SNPCoverageRenderer from './SNPCoverageRenderer';
+import { WiggleRendering } from '@jbrowse/plugin-wiggle';
+export const configSchema = ConfigurationSchema('SNPCoverageRenderer', {}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+export default function register(pluginManager) {
+    pluginManager.addRendererType(() => new SNPCoverageRenderer({
+        name: 'SNPCoverageRenderer',
+        ReactComponent: WiggleRendering,
+        configSchema,
+        pluginManager,
+    }));
+}
+//# sourceMappingURL=index.js.map

package/esm/SNPCoverageRenderer/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AAEvD,OAAO,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAA;AAExD,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAC7C,qBAAqB,EACrB,EAAE,EACF,EAAE,iBAAiB,EAAE,YAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA;AAED,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,mBAAmB,CAAC;QACtB,IAAI,EAAE,qBAAqB;QAC3B,cAAc,EAAE,eAAe;QAC/B,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC"}

package/esm/index.d.ts

@@ -0,0 +1,10 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+import * as MismatchParser from './BamAdapter/MismatchParser';
+import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
+export { MismatchParser };
+export type { LinearPileupDisplayModel };
+export default class AlignmentsPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}