@jbrowse/plugin-alignments 3.5.1 → 3.6.0

package/dist/ModificationParser/consts.d.ts

@@ -0,0 +1 @@
+export declare const modificationRegex: RegExp;

package/dist/ModificationParser/consts.js

@@ -0,0 +1,4 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.modificationRegex = void 0;
+exports.modificationRegex = new RegExp(/([A-Z])([-+])([a-z]+|[0-9]+)([.?]?)/);

package/dist/ModificationParser/getMethBins.d.ts

@@ -0,0 +1,7 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function getMethBins(feature: Feature, cigarOps: string[]): {
+    methBins: number[];
+    hydroxyMethBins: number[];
+    methProbs: number[];
+    hydroxyMethProbs: number[];
+};

package/dist/ModificationParser/getMethBins.js

@@ -0,0 +1,49 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getMethBins = getMethBins;
+const MismatchParser_1 = require("../MismatchParser");
+const getModPositions_1 = require("./getModPositions");
+const getModProbabilities_1 = require("./getModProbabilities");
+const util_1 = require("../util");
+function getMethBins(feature, cigarOps) {
+    const fstart = feature.get('start');
+    const fend = feature.get('end');
+    const fstrand = feature.get('strand');
+    const flen = fend - fstart;
+    const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
+    const methBins = [];
+    const hydroxyMethBins = [];
+    const methProbs = [];
+    const hydroxyMethProbs = [];
+    const seq = feature.get('seq');
+    if (seq) {
+        const probabilities = (0, getModProbabilities_1.getModProbabilities)(feature);
+        const modifications = (0, getModPositions_1.getModPositions)(mm, seq, fstrand);
+        let probIndex = 0;
+        for (const { type, positions } of modifications) {
+            for (const { ref, idx } of (0, MismatchParser_1.getNextRefPos)(cigarOps, positions)) {
+                if (ref < 0 || ref >= flen) {
+                    continue;
+                }
+                const isReverseStrand = fstrand === -1;
+                const idx2 = probIndex + (isReverseStrand ? positions.length - 1 - idx : idx);
+                const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[idx2]) || 0;
+                if (type === 'm') {
+                    methBins[ref] = 1;
+                    methProbs[ref] = prob;
+                }
+                else if (type === 'h') {
+                    hydroxyMethBins[ref] = 1;
+                    hydroxyMethProbs[ref] = prob;
+                }
+            }
+            probIndex += positions.length;
+        }
+    }
+    return {
+        methBins,
+        hydroxyMethBins,
+        methProbs,
+        hydroxyMethProbs,
+    };
+}

package/dist/ModificationParser/getModPositions.d.ts

@@ -0,0 +1,6 @@
+export declare function getModPositions(mm: string, fseq: string, fstrand: number): {
+    type: string;
+    positions: number[];
+    base: string;
+    strand: string;
+}[];

package/dist/ModificationParser/getModPositions.js

@@ -0,0 +1,64 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getModPositions = getModPositions;
+const util_1 = require("@jbrowse/core/util");
+const consts_1 = require("./consts");
+function getModPositions(mm, fseq, fstrand) {
+    const seq = fstrand === -1 ? (0, util_1.revcom)(fseq) : fseq;
+    const mods = mm.split(';');
+    const result = [];
+    for (const mod of mods) {
+        if (mod === '') {
+            continue;
+        }
+        const split = mod.split(',');
+        const basemod = split[0];
+        const matches = consts_1.modificationRegex.exec(basemod);
+        if (!matches) {
+            throw new Error(`bad format for MM tag: "${mod}"`);
+        }
+        const [, base, strand, typestr] = matches;
+        const types = typestr.split(/(\d+|.)/);
+        if (strand === '-') {
+            console.warn('unsupported negative strand modifications');
+            result.push({
+                type: 'unsupported',
+                positions: [],
+                base: base,
+                strand: strand,
+            });
+        }
+        for (const type of types) {
+            if (type === '') {
+                continue;
+            }
+            let currPos = 0;
+            const positions = [];
+            for (let i = 1, l = split.length; i < l; i++) {
+                let delta = +split[i];
+                do {
+                    if (base === 'N' || base === seq[currPos]) {
+                        delta--;
+                    }
+                    currPos++;
+                } while (delta >= 0 && currPos < seq.length);
+                if (fstrand === -1) {
+                    const pos = seq.length - currPos;
+                    if (pos >= 0) {
+                        positions.unshift(pos);
+                    }
+                }
+                else {
+                    positions.push(currPos - 1);
+                }
+            }
+            result.push({
+                type,
+                base: base,
+                strand: strand,
+                positions,
+            });
+        }
+    }
+    return result;
+}

package/dist/ModificationParser/getModProbabilities.d.ts

@@ -0,0 +1,2 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function getModProbabilities(feature: Feature): number[] | undefined;

package/dist/ModificationParser/getModProbabilities.js

@@ -0,0 +1,34 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getModProbabilities = getModProbabilities;
+const util_1 = require("../util");
+function getModProbabilities(feature) {
+    const m = (0, util_1.getTagAlt)(feature, 'ML', 'Ml') || [];
+    if (m) {
+        const result = [];
+        if (typeof m === 'string') {
+            const parts = m.split(',');
+            for (let i = 0, l = parts.length; i < l; i++) {
+                result.push(+parts[i] / 255);
+            }
+        }
+        else {
+            for (let i = 0, l = m.length; i < l; i++) {
+                result.push(m[i] / 255);
+            }
+        }
+        return result;
+    }
+    else {
+        const mp = (0, util_1.getTagAlt)(feature, 'MP', 'Mp');
+        if (mp) {
+            const result = [];
+            for (let i = 0, l = mp.length; i < l; i++) {
+                const phred = mp.charCodeAt(i) - 33;
+                result.push(Math.min(1, phred / 50));
+            }
+            return result;
+        }
+        return undefined;
+    }
+}

package/dist/ModificationParser/getModTypes.d.ts

@@ -0,0 +1,5 @@
+export declare function getModTypes(mm: string): {
+    type: string;
+    base: string;
+    strand: string;
+}[];

package/dist/ModificationParser/getModTypes.js

@@ -0,0 +1,35 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getModTypes = getModTypes;
+const consts_1 = require("./consts");
+function getModTypes(mm) {
+    const result = [];
+    const mods = mm.split(';');
+    for (let i = 0, modsLen = mods.length; i < modsLen; i++) {
+        const mod = mods[i];
+        if (mod === '') {
+            continue;
+        }
+        const basemod = mod.split(',')[0];
+        const matches = consts_1.modificationRegex.exec(basemod);
+        if (!matches) {
+            throw new Error(`bad format for MM tag: "${mod}"`);
+        }
+        const base = matches[1];
+        const strand = matches[2];
+        const typestr = matches[3];
+        const types = typestr.split(/(\d+|.)/);
+        for (let j = 0, typesLen = types.length; j < typesLen; j++) {
+            const type = types[j];
+            if (type === '') {
+                continue;
+            }
+            result.push({
+                type,
+                base,
+                strand,
+            });
+        }
+    }
+    return result;
+}

package/dist/PileupRPC/methods/GetVisibleModifications.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const rxjs_1 = require("rxjs");
 const operators_1 = require("rxjs/operators");
-const ModificationParser_1 = require("../../ModificationParser");
+const getModTypes_1 = require("../../ModificationParser/getModTypes");
 const util_1 = require("../../util");
 const base_1 = __importDefault(require("../base"));
 class PileupGetVisibleModifications extends base_1.default {
@@ -23,7 +23,8 @@ class PileupGetVisibleModifications extends base_1.default {
             .pipe((0, operators_1.toArray)()));
         const uniqueModifications = new Map();
         for (const feat of featuresArray) {
-            for (const mod of (0, ModificationParser_1.getModTypes)((0, util_1.getTagAlt)(feat, 'MM', 'Mm') || '')) {
+            const mmTag = (0, util_1.getTagAlt)(feat, 'MM', 'Mm');
+            for (const mod of (0, getModTypes_1.getModTypes)(typeof mmTag === 'string' ? mmTag : '')) {
                 if (!uniqueModifications.has(mod.type)) {
                     uniqueModifications.set(mod.type, mod);
                 }

package/dist/PileupRenderer/renderMethylation.js

@@ -4,7 +4,7 @@ exports.renderMethylation = renderMethylation;
 const util_1 = require("@jbrowse/core/util");
 const colord_1 = require("@jbrowse/core/util/colord");
 const util_2 = require("./util");
-const ModificationParser_1 = require("../ModificationParser");
+const getMethBins_1 = require("../ModificationParser/getMethBins");
 function renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
     const { regionSequence } = renderArgs;
     const { feature, topPx, heightPx } = feat;
@@ -17,7 +17,7 @@ function renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth
     }
     const fstart = feature.get('start');
     const fend = feature.get('end');
-    const { methBins, methProbs, hydroxyMethBins, hydroxyMethProbs } = (0, ModificationParser_1.getMethBins)(feature, cigarOps);
+    const { methBins, methProbs, hydroxyMethBins, hydroxyMethProbs } = (0, getMethBins_1.getMethBins)(feature, cigarOps);
     function getCol(k) {
         if (methBins[k]) {
             const p = methProbs[k] || 0;

package/dist/SNPCoverageAdapter/processReferenceCpGs.js

@@ -3,8 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.processReferenceCpGs = processReferenceCpGs;
 const util_1 = require("@jbrowse/core/util");
 const MismatchParser_1 = require("../MismatchParser");
-const ModificationParser_1 = require("../ModificationParser");
 const util_2 = require("./util");
+const getMethBins_1 = require("../ModificationParser/getMethBins");
 function processReferenceCpGs({ feature, region, bins, regionSequence, }) {
     var _a;
     const fstart = feature.get('start');
@@ -15,7 +15,7 @@ function processReferenceCpGs({ feature, region, bins, regionSequence, }) {
     const r = regionSequence.toLowerCase();
     if (seq) {
         const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-        const { methBins, methProbs } = (0, ModificationParser_1.getMethBins)(feature, cigarOps);
+        const { methBins, methProbs } = (0, getMethBins_1.getMethBins)(feature, cigarOps);
         const dels = mismatches.filter(f => f.type === 'deletion');
         for (let i = 0; i < fend - fstart; i++) {
             const j = i + fstart;

package/dist/shared/getMaximumModificationAtEachPosition.js

@@ -2,7 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getMaxProbModAtEachPosition = getMaxProbModAtEachPosition;
 const MismatchParser_1 = require("../MismatchParser");
-const ModificationParser_1 = require("../ModificationParser");
+const getModPositions_1 = require("../ModificationParser/getModPositions");
+const getModProbabilities_1 = require("../ModificationParser/getModProbabilities");
 const util_1 = require("../util");
 function getMaxProbModAtEachPosition(feature, cigarOps) {
     const fstrand = feature.get('strand');
@@ -10,8 +11,8 @@ function getMaxProbModAtEachPosition(feature, cigarOps) {
     const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
     const ops = cigarOps || (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
     if (seq) {
-        const modifications = (0, ModificationParser_1.getModPositions)(mm, seq, fstrand);
-        const probabilities = (0, ModificationParser_1.getModProbabilities)(feature);
+        const modifications = (0, getModPositions_1.getModPositions)(mm, seq, fstrand);
+        const probabilities = (0, getModProbabilities_1.getModProbabilities)(feature);
         const maxProbModForPosition = [];
         let probIndex = 0;
         for (const { type, positions } of modifications) {

package/esm/ModificationParser/consts.d.ts

@@ -0,0 +1 @@
+export declare const modificationRegex: RegExp;

package/esm/ModificationParser/consts.js

@@ -0,0 +1 @@
+export const modificationRegex = new RegExp(/([A-Z])([-+])([a-z]+|[0-9]+)([.?]?)/);

package/esm/ModificationParser/getMethBins.d.ts

@@ -0,0 +1,7 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function getMethBins(feature: Feature, cigarOps: string[]): {
+    methBins: number[];
+    hydroxyMethBins: number[];
+    methProbs: number[];
+    hydroxyMethProbs: number[];
+};

package/esm/ModificationParser/getMethBins.js

@@ -0,0 +1,46 @@
+import { getNextRefPos } from '../MismatchParser';
+import { getModPositions } from './getModPositions';
+import { getModProbabilities } from './getModProbabilities';
+import { getTagAlt } from '../util';
+export function getMethBins(feature, cigarOps) {
+    const fstart = feature.get('start');
+    const fend = feature.get('end');
+    const fstrand = feature.get('strand');
+    const flen = fend - fstart;
+    const mm = getTagAlt(feature, 'MM', 'Mm') || '';
+    const methBins = [];
+    const hydroxyMethBins = [];
+    const methProbs = [];
+    const hydroxyMethProbs = [];
+    const seq = feature.get('seq');
+    if (seq) {
+        const probabilities = getModProbabilities(feature);
+        const modifications = getModPositions(mm, seq, fstrand);
+        let probIndex = 0;
+        for (const { type, positions } of modifications) {
+            for (const { ref, idx } of getNextRefPos(cigarOps, positions)) {
+                if (ref < 0 || ref >= flen) {
+                    continue;
+                }
+                const isReverseStrand = fstrand === -1;
+                const idx2 = probIndex + (isReverseStrand ? positions.length - 1 - idx : idx);
+                const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[idx2]) || 0;
+                if (type === 'm') {
+                    methBins[ref] = 1;
+                    methProbs[ref] = prob;
+                }
+                else if (type === 'h') {
+                    hydroxyMethBins[ref] = 1;
+                    hydroxyMethProbs[ref] = prob;
+                }
+            }
+            probIndex += positions.length;
+        }
+    }
+    return {
+        methBins,
+        hydroxyMethBins,
+        methProbs,
+        hydroxyMethProbs,
+    };
+}

package/esm/ModificationParser/getModPositions.d.ts

@@ -0,0 +1,6 @@
+export declare function getModPositions(mm: string, fseq: string, fstrand: number): {
+    type: string;
+    positions: number[];
+    base: string;
+    strand: string;
+}[];

package/esm/ModificationParser/getModPositions.js

@@ -0,0 +1,61 @@
+import { revcom } from '@jbrowse/core/util';
+import { modificationRegex } from './consts';
+export function getModPositions(mm, fseq, fstrand) {
+    const seq = fstrand === -1 ? revcom(fseq) : fseq;
+    const mods = mm.split(';');
+    const result = [];
+    for (const mod of mods) {
+        if (mod === '') {
+            continue;
+        }
+        const split = mod.split(',');
+        const basemod = split[0];
+        const matches = modificationRegex.exec(basemod);
+        if (!matches) {
+            throw new Error(`bad format for MM tag: "${mod}"`);
+        }
+        const [, base, strand, typestr] = matches;
+        const types = typestr.split(/(\d+|.)/);
+        if (strand === '-') {
+            console.warn('unsupported negative strand modifications');
+            result.push({
+                type: 'unsupported',
+                positions: [],
+                base: base,
+                strand: strand,
+            });
+        }
+        for (const type of types) {
+            if (type === '') {
+                continue;
+            }
+            let currPos = 0;
+            const positions = [];
+            for (let i = 1, l = split.length; i < l; i++) {
+                let delta = +split[i];
+                do {
+                    if (base === 'N' || base === seq[currPos]) {
+                        delta--;
+                    }
+                    currPos++;
+                } while (delta >= 0 && currPos < seq.length);
+                if (fstrand === -1) {
+                    const pos = seq.length - currPos;
+                    if (pos >= 0) {
+                        positions.unshift(pos);
+                    }
+                }
+                else {
+                    positions.push(currPos - 1);
+                }
+            }
+            result.push({
+                type,
+                base: base,
+                strand: strand,
+                positions,
+            });
+        }
+    }
+    return result;
+}

package/esm/ModificationParser/getModProbabilities.d.ts

@@ -0,0 +1,2 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function getModProbabilities(feature: Feature): number[] | undefined;

package/esm/ModificationParser/getModProbabilities.js

@@ -0,0 +1,31 @@
+import { getTagAlt } from '../util';
+export function getModProbabilities(feature) {
+    const m = getTagAlt(feature, 'ML', 'Ml') || [];
+    if (m) {
+        const result = [];
+        if (typeof m === 'string') {
+            const parts = m.split(',');
+            for (let i = 0, l = parts.length; i < l; i++) {
+                result.push(+parts[i] / 255);
+            }
+        }
+        else {
+            for (let i = 0, l = m.length; i < l; i++) {
+                result.push(m[i] / 255);
+            }
+        }
+        return result;
+    }
+    else {
+        const mp = getTagAlt(feature, 'MP', 'Mp');
+        if (mp) {
+            const result = [];
+            for (let i = 0, l = mp.length; i < l; i++) {
+                const phred = mp.charCodeAt(i) - 33;
+                result.push(Math.min(1, phred / 50));
+            }
+            return result;
+        }
+        return undefined;
+    }
+}

package/esm/ModificationParser/getModTypes.d.ts

@@ -0,0 +1,5 @@
+export declare function getModTypes(mm: string): {
+    type: string;
+    base: string;
+    strand: string;
+}[];

package/esm/ModificationParser/getModTypes.js

@@ -0,0 +1,32 @@
+import { modificationRegex } from './consts';
+export function getModTypes(mm) {
+    const result = [];
+    const mods = mm.split(';');
+    for (let i = 0, modsLen = mods.length; i < modsLen; i++) {
+        const mod = mods[i];
+        if (mod === '') {
+            continue;
+        }
+        const basemod = mod.split(',')[0];
+        const matches = modificationRegex.exec(basemod);
+        if (!matches) {
+            throw new Error(`bad format for MM tag: "${mod}"`);
+        }
+        const base = matches[1];
+        const strand = matches[2];
+        const typestr = matches[3];
+        const types = typestr.split(/(\d+|.)/);
+        for (let j = 0, typesLen = types.length; j < typesLen; j++) {
+            const type = types[j];
+            if (type === '') {
+                continue;
+            }
+            result.push({
+                type,
+                base,
+                strand,
+            });
+        }
+    }
+    return result;
+}

package/esm/PileupRPC/methods/GetVisibleModifications.js

@@ -1,7 +1,7 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
-import { getModTypes } from '../../ModificationParser';
+import { getModTypes } from '../../ModificationParser/getModTypes';
 import { getTagAlt } from '../../util';
 import PileupBaseRPC from '../base';
 export default class PileupGetVisibleModifications extends PileupBaseRPC {
@@ -18,7 +18,8 @@ export default class PileupGetVisibleModifications extends PileupBaseRPC {
             .pipe(toArray()));
         const uniqueModifications = new Map();
         for (const feat of featuresArray) {
-            for (const mod of getModTypes(getTagAlt(feat, 'MM', 'Mm') || '')) {
+            const mmTag = getTagAlt(feat, 'MM', 'Mm');
+            for (const mod of getModTypes(typeof mmTag === 'string' ? mmTag : '')) {
                 if (!uniqueModifications.has(mod.type)) {
                     uniqueModifications.set(mod.type, mod);
                 }

package/esm/PileupRenderer/renderMethylation.js

@@ -1,7 +1,7 @@
 import { bpSpanPx } from '@jbrowse/core/util';
 import { colord } from '@jbrowse/core/util/colord';
 import { fillRect } from './util';
-import { getMethBins } from '../ModificationParser';
+import { getMethBins } from '../ModificationParser/getMethBins';
 export function renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
     const { regionSequence } = renderArgs;
     const { feature, topPx, heightPx } = feat;

package/esm/SNPCoverageAdapter/processReferenceCpGs.js

@@ -1,7 +1,7 @@
 import { doesIntersect2 } from '@jbrowse/core/util';
 import { parseCigar } from '../MismatchParser';
-import { getMethBins } from '../ModificationParser';
 import { incWithProbabilities } from './util';
+import { getMethBins } from '../ModificationParser/getMethBins';
 export function processReferenceCpGs({ feature, region, bins, regionSequence, }) {
     var _a;
     const fstart = feature.get('start');

package/esm/shared/getMaximumModificationAtEachPosition.js

@@ -1,5 +1,6 @@
 import { getNextRefPos, parseCigar } from '../MismatchParser';
-import { getModPositions, getModProbabilities } from '../ModificationParser';
+import { getModPositions } from '../ModificationParser/getModPositions';
+import { getModProbabilities } from '../ModificationParser/getModProbabilities';
 import { getTagAlt } from '../util';
 export function getMaxProbModAtEachPosition(feature, cigarOps) {
     const fstrand = feature.get('strand');

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "3.5.1",
+  "version": "3.6.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,10 +38,10 @@
   "dependencies": {
     "@gmod/bam": "^6.0.1",
     "@gmod/cram": "^5.0.4",
-    "@jbrowse/core": "^3.5.1",
-    "@jbrowse/plugin-linear-genome-view": "^3.5.1",
-    "@jbrowse/plugin-wiggle": "^3.5.1",
-    "@jbrowse/sv-core": "^3.5.1",
+    "@jbrowse/core": "^3.6.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.6.0",
+    "@jbrowse/plugin-wiggle": "^3.6.0",
+    "@jbrowse/sv-core": "^3.6.0",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "canvas2svg": "^1.0.16",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "cb8859da9d838ad2594964777c5c54f385d98f5e"
+  "gitHead": "133a68815ab348d156c18d83cffc997356c3cfbb"
 }

package/dist/ModificationParser/index.d.ts

@@ -1,19 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function getModProbabilities(feature: Feature): number[] | undefined;
-export declare function getModPositions(mm: string, fseq: string, fstrand: number): {
-    type: string;
-    positions: number[];
-    base: string;
-    strand: string;
-}[];
-export declare function getModTypes(mm: string): {
-    type: string;
-    base: string;
-    strand: string;
-}[];
-export declare function getMethBins(feature: Feature, cigarOps: string[]): {
-    methBins: number[];
-    hydroxyMethBins: number[];
-    methProbs: number[];
-    hydroxyMethProbs: number[];
-};

package/dist/ModificationParser/index.js

@@ -1,127 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getModProbabilities = getModProbabilities;
-exports.getModPositions = getModPositions;
-exports.getModTypes = getModTypes;
-exports.getMethBins = getMethBins;
-const util_1 = require("@jbrowse/core/util");
-const MismatchParser_1 = require("../MismatchParser");
-const util_2 = require("../util");
-const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
-function getModProbabilities(feature) {
-    var _a;
-    const m = (0, util_2.getTagAlt)(feature, 'ML', 'Ml') || [];
-    return m
-        ? (typeof m === 'string' ? m.split(',').map(e => +e) : m).map(e => e / 255)
-        : (_a = (0, util_2.getTagAlt)(feature, 'MP', 'Mp')) === null || _a === void 0 ? void 0 : _a.split('').map(s => s.charCodeAt(0) - 33).map(elt => Math.min(1, elt / 50));
-}
-function getModPositions(mm, fseq, fstrand) {
-    const seq = fstrand === -1 ? (0, util_1.revcom)(fseq) : fseq;
-    const mods = mm.split(';').filter(mod => !!mod);
-    const result = [];
-    for (const mod of mods) {
-        const [basemod, ...skips] = mod.split(',');
-        const matches = modificationRegex.exec(basemod);
-        if (!matches) {
-            throw new Error('bad format for MM tag');
-        }
-        const [, base, strand, typestr] = matches;
-        const types = typestr.split(/(\d+|.)/).filter(f => !!f);
-        if (strand === '-') {
-            console.warn('unsupported negative strand modifications');
-            result.push({
-                type: 'unsupported',
-                positions: [],
-                base: base,
-                strand: strand,
-            });
-        }
-        for (const type of types) {
-            let i = 0;
-            const positions = [];
-            for (const d of skips) {
-                let delta = +d;
-                do {
-                    if (base === 'N' || base === seq[i]) {
-                        delta--;
-                    }
-                    i++;
-                } while (delta >= 0 && i < seq.length);
-                if (fstrand === -1) {
-                    const pos = seq.length - i;
-                    if (pos >= 0) {
-                        positions.unshift(pos);
-                    }
-                }
-                else {
-                    positions.push(i - 1);
-                }
-            }
-            result.push({
-                type,
-                base: base,
-                strand: strand,
-                positions,
-            });
-        }
-    }
-    return result;
-}
-function getModTypes(mm) {
-    return mm
-        .split(';')
-        .filter(mod => !!mod)
-        .flatMap(mod => {
-        const basemod = mod.split(',')[0];
-        const matches = modificationRegex.exec(basemod);
-        if (!matches) {
-            throw new Error('bad format for MM tag');
-        }
-        const [, base, strand, typestr] = matches;
-        return typestr
-            .split(/(\d+|.)/)
-            .filter(f => !!f)
-            .map(type => ({
-            type,
-            base: base,
-            strand: strand,
-        }));
-    });
-}
-function getMethBins(feature, cigarOps) {
-    const fstart = feature.get('start');
-    const fend = feature.get('end');
-    const fstrand = feature.get('strand');
-    const flen = fend - fstart;
-    const mm = (0, util_2.getTagAlt)(feature, 'MM', 'Mm') || '';
-    const methBins = [];
-    const hydroxyMethBins = [];
-    const methProbs = [];
-    const hydroxyMethProbs = [];
-    const seq = feature.get('seq');
-    if (seq) {
-        const probabilities = getModProbabilities(feature);
-        const modifications = getModPositions(mm, seq, fstrand);
-        let probIndex = 0;
-        for (const { type, positions } of modifications) {
-            for (const { ref, idx } of (0, MismatchParser_1.getNextRefPos)(cigarOps, positions)) {
-                const idx2 = probIndex + (fstrand === -1 ? positions.length - 1 - idx : idx);
-                const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[idx2]) || 0;
-                if (type === 'm') {
-                    if (ref >= 0 && ref < flen) {
-                        methBins[ref] = 1;
-                        methProbs[ref] = prob;
-                    }
-                }
-                else if (type === 'h') {
-                    if (ref >= 0 && ref < flen) {
-                        hydroxyMethBins[ref] = 1;
-                        hydroxyMethProbs[ref] = prob;
-                    }
-                }
-            }
-            probIndex += positions.length;
-        }
-    }
-    return { methBins, hydroxyMethBins, methProbs, hydroxyMethProbs };
-}

package/esm/ModificationParser/index.d.ts

@@ -1,19 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function getModProbabilities(feature: Feature): number[] | undefined;
-export declare function getModPositions(mm: string, fseq: string, fstrand: number): {
-    type: string;
-    positions: number[];
-    base: string;
-    strand: string;
-}[];
-export declare function getModTypes(mm: string): {
-    type: string;
-    base: string;
-    strand: string;
-}[];
-export declare function getMethBins(feature: Feature, cigarOps: string[]): {
-    methBins: number[];
-    hydroxyMethBins: number[];
-    methProbs: number[];
-    hydroxyMethProbs: number[];
-};

package/esm/ModificationParser/index.js

@@ -1,121 +0,0 @@
-import { revcom } from '@jbrowse/core/util';
-import { getNextRefPos } from '../MismatchParser';
-import { getTagAlt } from '../util';
-const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
-export function getModProbabilities(feature) {
-    var _a;
-    const m = getTagAlt(feature, 'ML', 'Ml') || [];
-    return m
-        ? (typeof m === 'string' ? m.split(',').map(e => +e) : m).map(e => e / 255)
-        : (_a = getTagAlt(feature, 'MP', 'Mp')) === null || _a === void 0 ? void 0 : _a.split('').map(s => s.charCodeAt(0) - 33).map(elt => Math.min(1, elt / 50));
-}
-export function getModPositions(mm, fseq, fstrand) {
-    const seq = fstrand === -1 ? revcom(fseq) : fseq;
-    const mods = mm.split(';').filter(mod => !!mod);
-    const result = [];
-    for (const mod of mods) {
-        const [basemod, ...skips] = mod.split(',');
-        const matches = modificationRegex.exec(basemod);
-        if (!matches) {
-            throw new Error('bad format for MM tag');
-        }
-        const [, base, strand, typestr] = matches;
-        const types = typestr.split(/(\d+|.)/).filter(f => !!f);
-        if (strand === '-') {
-            console.warn('unsupported negative strand modifications');
-            result.push({
-                type: 'unsupported',
-                positions: [],
-                base: base,
-                strand: strand,
-            });
-        }
-        for (const type of types) {
-            let i = 0;
-            const positions = [];
-            for (const d of skips) {
-                let delta = +d;
-                do {
-                    if (base === 'N' || base === seq[i]) {
-                        delta--;
-                    }
-                    i++;
-                } while (delta >= 0 && i < seq.length);
-                if (fstrand === -1) {
-                    const pos = seq.length - i;
-                    if (pos >= 0) {
-                        positions.unshift(pos);
-                    }
-                }
-                else {
-                    positions.push(i - 1);
-                }
-            }
-            result.push({
-                type,
-                base: base,
-                strand: strand,
-                positions,
-            });
-        }
-    }
-    return result;
-}
-export function getModTypes(mm) {
-    return mm
-        .split(';')
-        .filter(mod => !!mod)
-        .flatMap(mod => {
-        const basemod = mod.split(',')[0];
-        const matches = modificationRegex.exec(basemod);
-        if (!matches) {
-            throw new Error('bad format for MM tag');
-        }
-        const [, base, strand, typestr] = matches;
-        return typestr
-            .split(/(\d+|.)/)
-            .filter(f => !!f)
-            .map(type => ({
-            type,
-            base: base,
-            strand: strand,
-        }));
-    });
-}
-export function getMethBins(feature, cigarOps) {
-    const fstart = feature.get('start');
-    const fend = feature.get('end');
-    const fstrand = feature.get('strand');
-    const flen = fend - fstart;
-    const mm = getTagAlt(feature, 'MM', 'Mm') || '';
-    const methBins = [];
-    const hydroxyMethBins = [];
-    const methProbs = [];
-    const hydroxyMethProbs = [];
-    const seq = feature.get('seq');
-    if (seq) {
-        const probabilities = getModProbabilities(feature);
-        const modifications = getModPositions(mm, seq, fstrand);
-        let probIndex = 0;
-        for (const { type, positions } of modifications) {
-            for (const { ref, idx } of getNextRefPos(cigarOps, positions)) {
-                const idx2 = probIndex + (fstrand === -1 ? positions.length - 1 - idx : idx);
-                const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[idx2]) || 0;
-                if (type === 'm') {
-                    if (ref >= 0 && ref < flen) {
-                        methBins[ref] = 1;
-                        methProbs[ref] = prob;
-                    }
-                }
-                else if (type === 'h') {
-                    if (ref >= 0 && ref < flen) {
-                        hydroxyMethBins[ref] = 1;
-                        hydroxyMethProbs[ref] = prob;
-                    }
-                }
-            }
-            probIndex += positions.length;
-        }
-    }
-    return { methBins, hydroxyMethBins, methProbs, hydroxyMethProbs };
-}