@jbrowse/plugin-alignments 2.0.0 → 2.1.2

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -1,93 +1,15 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
-var __values = (this && this.__values) || function(o) {
-    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
-    if (m) return m.call(o);
-    if (o && typeof o.length === "number") return {
-        next: function () {
-            if (o && i >= o.length) o = void 0;
-            return { value: o && o[i++], done: !o };
-        }
-    };
-    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.capabilities = void 0;
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-var rxjs_1 = require("@jbrowse/core/util/rxjs");
-var operators_1 = require("rxjs/operators");
-var util_1 = require("../util");
-var MismatchParser_1 = require("../BamAdapter/MismatchParser");
+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 util_1 = require("../util");
+const MismatchParser_1 = require("../BamAdapter/MismatchParser");
 function mismatchLen(mismatch) {
     return !isInterbase(mismatch.type) ? mismatch.length : 1;
 }
@@ -96,7 +18,7 @@ function isInterbase(type) {
 }
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function inc(bin, strand, type, field) {
-    var thisBin = bin[type][field];
+    let thisBin = bin[type][field];
     if (thisBin === undefined) {
         thisBin = bin[type][field] = {
             total: 0,
@@ -108,345 +30,238 @@ function inc(bin, strand, type, field) {
     thisBin.total++;
     thisBin[strand]++;
 }
-var SNPCoverageAdapter = /** @class */ (function (_super) {
-    __extends(SNPCoverageAdapter, _super);
-    function SNPCoverageAdapter() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    SNPCoverageAdapter.prototype.configure = function () {
+class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
+    async configure() {
         var _a, _b;
-        return __awaiter(this, void 0, void 0, function () {
-            var subadapterConfig, sequenceConf, dataAdapter, sequenceAdapter, _c;
-            return __generator(this, function (_d) {
-                switch (_d.label) {
-                    case 0:
-                        subadapterConfig = this.getConf('subadapter');
-                        sequenceConf = this.getConf(['subadapter', 'sequenceAdapter']);
-                        return [4 /*yield*/, ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, subadapterConfig))];
-                    case 1:
-                        dataAdapter = _d.sent();
-                        if (!sequenceConf) return [3 /*break*/, 3];
-                        return [4 /*yield*/, ((_b = this.getSubAdapter) === null || _b === void 0 ? void 0 : _b.call(this, sequenceConf))];
-                    case 2:
-                        _c = _d.sent();
-                        return [3 /*break*/, 4];
-                    case 3:
-                        _c = undefined;
-                        _d.label = 4;
-                    case 4:
-                        sequenceAdapter = _c;
-                        if (!dataAdapter) {
-                            throw new Error('Failed to get subadapter');
-                        }
-                        return [2 /*return*/, {
-                                subadapter: dataAdapter.dataAdapter,
-                                sequenceAdapter: sequenceAdapter === null || sequenceAdapter === void 0 ? void 0 : sequenceAdapter.dataAdapter,
-                            }];
-                }
-            });
-        });
-    };
-    SNPCoverageAdapter.prototype.fetchSequence = function (region) {
-        return __awaiter(this, void 0, void 0, function () {
-            var sequenceAdapter;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        sequenceAdapter = (_a.sent()).sequenceAdapter;
-                        if (!sequenceAdapter) {
-                            return [2 /*return*/, undefined];
-                        }
-                        return [2 /*return*/, (0, util_1.fetchSequence)(region, sequenceAdapter)];
-                }
-            });
-        });
-    };
-    SNPCoverageAdapter.prototype.getFeatures = function (region, opts) {
-        var _this = this;
-        if (opts === void 0) { opts = {}; }
-        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
-            var subadapter, feats, _a, bins, skipmap;
-            var _this = this;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        subadapter = (_b.sent()).subadapter;
-                        return [4 /*yield*/, subadapter
-                                .getFeatures(region, opts)
-                                .pipe((0, operators_1.toArray)())
-                                .toPromise()];
-                    case 2:
-                        feats = _b.sent();
-                        return [4 /*yield*/, this.generateCoverageBins(feats, region, opts)];
-                    case 3:
-                        _a = _b.sent(), bins = _a.bins, skipmap = _a.skipmap;
-                        bins.forEach(function (bin, index) {
-                            observer.next(new simpleFeature_1.default({
-                                id: "".concat(_this.id, "-").concat(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(function (_a) {
-                            var _b = __read(_a, 2), key = _b[0], skip = _b[1];
-                            observer.next(new simpleFeature_1.default({
-                                id: key,
-                                data: {
-                                    type: 'skip',
-                                    start: skip.start,
-                                    end: skip.end,
-                                    strand: skip.strand,
-                                    score: skip.score,
-                                    xs: skip.xs,
-                                },
-                            }));
-                        });
-                        observer.complete();
-                        return [2 /*return*/];
-                }
-            });
-        }); }, opts.signal);
-    };
-    SNPCoverageAdapter.prototype.estimateRegionsStats = function (regions, opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var subadapter;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        subadapter = (_a.sent()).subadapter;
-                        return [2 /*return*/, subadapter.estimateRegionsStats(regions, opts)];
-                }
+        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 (0, util_1.fetchSequence)(region, sequenceAdapter);
+    }
+    getFeatures(region, opts = {}) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const { subadapter } = await this.configure();
+            const feats = await subadapter
+                .getFeatures(region, opts)
+                .pipe((0, operators_1.toArray)())
+                .toPromise();
+            const { bins, skipmap } = await this.generateCoverageBins(feats, region, opts);
+            bins.forEach((bin, index) => {
+                const start = region.start + index;
+                observer.next(new simpleFeature_1.default({
+                    id: `${this.id}-${start}`,
+                    data: {
+                        score: bin.total,
+                        snpinfo: bin,
+                        start,
+                        end: start + 1,
+                        refName: region.refName,
+                    },
+                }));
             });
-        });
-    };
-    SNPCoverageAdapter.prototype.getRefNames = function (opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var subadapter;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        subadapter = (_a.sent()).subadapter;
-                        return [2 /*return*/, subadapter.getRefNames(opts)];
-                }
+            // make fake features from the coverage
+            Object.entries(skipmap).forEach(([key, skip]) => {
+                observer.next(new simpleFeature_1.default({
+                    id: key,
+                    data: {
+                        type: 'skip',
+                        start: skip.start,
+                        end: skip.end,
+                        strand: skip.strand,
+                        score: skip.score,
+                        xs: skip.xs,
+                    },
+                }));
             });
-        });
-    };
-    SNPCoverageAdapter.prototype.freeResources = function ( /* { region } */) { };
-    SNPCoverageAdapter.prototype.generateCoverageBins = function (features, region, opts) {
+            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;
-        return __awaiter(this, void 0, void 0, function () {
-            var colorBy, binMax, skipmap, regionSeq, _b, bins, _loop_1, i;
-            return __generator(this, function (_c) {
-                switch (_c.label) {
-                    case 0:
-                        colorBy = opts.colorBy;
-                        binMax = Math.ceil(region.end - region.start);
-                        skipmap = {};
-                        if (!(features.length && (0, util_1.shouldFetchReferenceSequence)((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type))) return [3 /*break*/, 2];
-                        return [4 /*yield*/, this.fetchSequence(region)];
-                    case 1:
-                        _b = _c.sent();
-                        return [3 /*break*/, 3];
-                    case 2:
-                        _b = undefined;
-                        _c.label = 3;
-                    case 3:
-                        regionSeq = _b;
-                        bins = [];
-                        _loop_1 = function (i) {
-                            var feature = features[i];
-                            var fstart = feature.get('start');
-                            var fend = feature.get('end');
-                            var fstrand = feature.get('strand');
-                            for (var j = fstart; j < fend + 1; j++) {
-                                var i_1 = j - region.start;
-                                if (i_1 >= 0 && i_1 < binMax) {
-                                    if (bins[i_1] === undefined) {
-                                        bins[i_1] = {
-                                            total: 0,
-                                            all: 0,
-                                            ref: 0,
-                                            '-1': 0,
-                                            '0': 0,
-                                            '1': 0,
-                                            lowqual: {},
-                                            cov: {},
-                                            delskips: {},
-                                            noncov: {},
-                                        };
-                                    }
-                                    if (j !== fend) {
-                                        bins[i_1].total++;
-                                        bins[i_1].all++;
-                                        bins[i_1].ref++;
-                                        bins[i_1][fstrand]++;
-                                    }
-                                }
+        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);
                             }
-                            if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-                                var seq = feature.get('seq');
-                                var mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
-                                var ops_1 = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-                                var fend_1 = feature.get('end');
-                                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(function (_a) {
-                                    var e_1, _b;
-                                    var type = _a.type, positions = _a.positions;
-                                    var mod = "mod_".concat(type);
-                                    try {
-                                        for (var _c = (e_1 = void 0, __values((0, MismatchParser_1.getNextRefPos)(ops_1, positions))), _d = _c.next(); !_d.done; _d = _c.next()) {
-                                            var pos = _d.value;
-                                            var epos = pos + fstart - region.start;
-                                            if (epos >= 0 && epos < bins.length && pos + fstart < fend_1) {
-                                                var bin = bins[epos];
-                                                if (bin) {
-                                                    inc(bin, fstrand, 'cov', mod);
-                                                }
-                                                else {
-                                                    console.warn('Undefined position in modifications snpcoverage encountered');
-                                                }
-                                            }
-                                        }
-                                    }
-                                    catch (e_1_1) { e_1 = { error: e_1_1 }; }
-                                    finally {
-                                        try {
-                                            if (_d && !_d.done && (_b = _c.return)) _b.call(_c);
-                                        }
-                                        finally { if (e_1) throw e_1.error; }
-                                    }
-                                });
+                            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');
-                                }
-                                var seq = feature.get('seq');
-                                var mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
-                                var methBins_1 = new Array(region.end - region.start).fill(0);
-                                var ops_2 = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-                                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(function (_a) {
-                                    var e_2, _b;
-                                    var type = _a.type, positions = _a.positions;
-                                    // we are processing methylation
-                                    if (type === 'm') {
-                                        try {
-                                            for (var _c = (e_2 = void 0, __values((0, MismatchParser_1.getNextRefPos)(ops_2, positions))), _d = _c.next(); !_d.done; _d = _c.next()) {
-                                                var pos = _d.value;
-                                                var epos = pos + fstart - region.start;
-                                                if (epos >= 0 && epos < methBins_1.length) {
-                                                    methBins_1[epos] = 1;
-                                                }
-                                            }
-                                        }
-                                        catch (e_2_1) { e_2 = { error: e_2_1 }; }
-                                        finally {
-                                            try {
-                                                if (_d && !_d.done && (_b = _c.return)) _b.call(_c);
-                                            }
-                                            finally { if (e_2) throw e_2.error; }
-                                        }
-                                    }
-                                });
-                                for (var j = fstart; j < fend; j++) {
-                                    var i_2 = j - region.start;
-                                    if (i_2 >= 0 && i_2 < bins.length - 1) {
-                                        var l1 = regionSeq[i_2].toLowerCase();
-                                        var l2 = regionSeq[i_2 + 1].toLowerCase();
-                                        var bin = bins[i_2];
-                                        var bin1 = bins[i_2 + 1];
-                                        // color
-                                        if (l1 === 'c' && l2 === 'g') {
-                                            if (methBins_1[i_2] || methBins_1[i_2 + 1]) {
-                                                inc(bin, fstrand, 'cov', 'meth');
-                                                inc(bin1, fstrand, 'cov', 'meth');
-                                                bins[i_2].ref--;
-                                                bins[i_2][fstrand]--;
-                                                bins[i_2 + 1].ref--;
-                                                bins[i_2 + 1][fstrand]--;
-                                            }
-                                            else {
-                                                inc(bin, fstrand, 'cov', 'unmeth');
-                                                inc(bin1, fstrand, 'cov', 'unmeth');
-                                                bins[i_2].ref--;
-                                                bins[i_2][fstrand]--;
-                                                bins[i_2 + 1].ref--;
-                                                bins[i_2 + 1][fstrand]--;
-                                            }
-                                        }
-                                    }
-                                }
+                        }
+                    }
+                });
+            }
+            // 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]--;
                             }
-                            // normal SNP based coloring
-                            var mismatches = feature.get('mismatches') || [];
-                            var colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
-                            for (var i_3 = 0; i_3 < mismatches.length; i_3++) {
-                                var mismatch = mismatches[i_3];
-                                var mstart = fstart + mismatch.start;
-                                var mlen = mismatchLen(mismatch);
-                                var mend = mstart + mlen;
-                                for (var j = mstart; j < mstart + mlen; j++) {
-                                    var epos = j - region.start;
-                                    if (epos >= 0 && epos < bins.length) {
-                                        var bin = bins[epos];
-                                        var base = mismatch.base, type = mismatch.type;
-                                        var 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') {
-                                    var hash = "".concat(mstart, "_").concat(mend, "_").concat(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++;
-                                }
+                            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]--;
                             }
-                        };
-                        for (i = 0; i < features.length; i++) {
-                            _loop_1(i);
                         }
-                        return [2 /*return*/, { bins: bins, skipmap: skipmap }];
+                    }
                 }
-            });
-        });
-    };
-    return SNPCoverageAdapter;
-}(BaseAdapter_1.BaseFeatureDataAdapter));
+            }
+            // 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;
-var capabilities = SNPCoverageAdapter.capabilities;
+const { capabilities } = SNPCoverageAdapter;
 exports.capabilities = capabilities;
 //# sourceMappingURL=SNPCoverageAdapter.js.map