@jbrowse/plugin-alignments 2.2.1 → 2.2.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/CramAdapter/CramTestAdapters.js +2 -1
- package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
- package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts +3 -1
- package/dist/LinearPileupDisplay/components/ColorByModifications.js +7 -22
- package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
- package/dist/LinearPileupDisplay/components/ColorByTag.js +2 -22
- package/dist/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
- package/dist/LinearPileupDisplay/components/FilterByTag.js +2 -15
- package/dist/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +2 -19
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js +2 -18
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SortByTag.js +2 -23
- package/dist/LinearPileupDisplay/components/SortByTag.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +13 -9
- package/dist/LinearSNPCoverageDisplay/models/model.js +8 -6
- package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/dist/PileupRenderer/configSchema.js +1 -1
- package/dist/PileupRenderer/configSchema.js.map +1 -1
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +0 -51
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -182
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/dist/SNPCoverageAdapter/generateCoverageBins.d.ts +53 -0
- package/dist/SNPCoverageAdapter/generateCoverageBins.js +185 -0
- package/dist/SNPCoverageAdapter/generateCoverageBins.js.map +1 -0
- package/esm/CramAdapter/CramTestAdapters.js +2 -1
- package/esm/CramAdapter/CramTestAdapters.js.map +1 -1
- package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +3 -1
- package/esm/LinearPileupDisplay/components/ColorByModifications.js +8 -23
- package/esm/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
- package/esm/LinearPileupDisplay/components/ColorByTag.js +3 -20
- package/esm/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
- package/esm/LinearPileupDisplay/components/FilterByTag.js +3 -13
- package/esm/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +3 -17
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js +3 -16
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
- package/esm/LinearPileupDisplay/components/SortByTag.js +3 -21
- package/esm/LinearPileupDisplay/components/SortByTag.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +13 -9
- package/esm/LinearSNPCoverageDisplay/models/model.js +9 -7
- package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/esm/PileupRenderer/configSchema.js +1 -1
- package/esm/PileupRenderer/configSchema.js.map +1 -1
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +0 -51
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +4 -183
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts +53 -0
- package/esm/SNPCoverageAdapter/generateCoverageBins.js +182 -0
- package/esm/SNPCoverageAdapter/generateCoverageBins.js.map +1 -0
- package/package.json +3 -3
- package/src/CramAdapter/CramTestAdapters.ts +1 -0
- package/src/LinearPileupDisplay/components/ColorByModifications.tsx +5 -34
- package/src/LinearPileupDisplay/components/ColorByTag.tsx +2 -29
- package/src/LinearPileupDisplay/components/FilterByTag.tsx +2 -22
- package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +2 -22
- package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +2 -24
- package/src/LinearPileupDisplay/components/SortByTag.tsx +2 -31
- package/src/LinearSNPCoverageDisplay/models/model.ts +12 -8
- package/src/PileupRenderer/configSchema.ts +1 -1
- package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +5 -249
- package/src/SNPCoverageAdapter/generateCoverageBins.ts +245 -0
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@@ -2,33 +2,13 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
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import SimpleFeature from '@jbrowse/core/util/simpleFeature';
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import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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import { toArray } from 'rxjs/operators';
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import
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import {
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function mismatchLen(mismatch) {
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return !isInterbase(mismatch.type) ? mismatch.length : 1;
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}
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function isInterbase(type) {
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return type === 'softclip' || type === 'hardclip' || type === 'insertion';
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}
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// eslint-disable-next-line @typescript-eslint/no-explicit-any
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function inc(bin, strand, type, field) {
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let thisBin = bin[type][field];
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if (thisBin === undefined) {
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thisBin = bin[type][field] = {
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total: 0,
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'-1': 0,
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'0': 0,
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'1': 0,
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};
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}
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thisBin.total++;
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thisBin[strand]++;
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}
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import generateCoverageBins from './generateCoverageBins';
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import { fetchSequence } from '../util';
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export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
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async configure() {
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var _a, _b;
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const subadapterConfig = this.getConf('subadapter');
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const sequenceConf =
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const sequenceConf = subadapterConfig.sequenceAdapter;
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const dataAdapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, subadapterConfig));
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const sequenceAdapter = sequenceConf
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? await ((_b = this.getSubAdapter) === null || _b === void 0 ? void 0 : _b.call(this, sequenceConf))
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@@ -55,7 +35,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
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.getFeatures(region, opts)
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.pipe(toArray())
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.toPromise();
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const { bins, skipmap } = await
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const { bins, skipmap } = await generateCoverageBins(feats, region, opts, arg => this.fetchSequence(arg));
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bins.forEach((bin, index) => {
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const start = region.start + index;
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observer.next(new SimpleFeature({
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@@ -95,165 +75,6 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
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return subadapter.getRefNames(opts);
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}
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freeResources( /* { region } */) { }
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async generateCoverageBins(features, region, opts) {
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var _a;
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const { colorBy } = opts;
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const binMax = Math.ceil(region.end - region.start);
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const skipmap = {};
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const regionSeq = features.length && shouldFetchReferenceSequence((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type)
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? await this.fetchSequence(region)
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: undefined;
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const bins = [];
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for (let i = 0; i < features.length; i++) {
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const feature = features[i];
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const fstart = feature.get('start');
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const fend = feature.get('end');
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const fstrand = feature.get('strand');
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for (let j = fstart; j < fend + 1; j++) {
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const i = j - region.start;
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if (i >= 0 && i < binMax) {
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if (bins[i] === undefined) {
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bins[i] = {
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total: 0,
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all: 0,
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ref: 0,
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'-1': 0,
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'0': 0,
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'1': 0,
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lowqual: {},
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cov: {},
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delskips: {},
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noncov: {},
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};
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}
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if (j !== fend) {
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bins[i].total++;
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bins[i].all++;
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bins[i].ref++;
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bins[i][fstrand]++;
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}
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}
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}
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if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
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const seq = feature.get('seq');
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const mm = getTagAlt(feature, 'MM', 'Mm') || '';
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const ops = parseCigar(feature.get('CIGAR'));
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const fend = feature.get('end');
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getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
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const mod = `mod_${type}`;
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for (const pos of getNextRefPos(ops, positions)) {
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const epos = pos + fstart - region.start;
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if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
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const bin = bins[epos];
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if (bin) {
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inc(bin, fstrand, 'cov', mod);
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}
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else {
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console.warn('Undefined position in modifications snpcoverage encountered');
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}
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}
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}
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});
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}
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// methylation based coloring takes into account both reference
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// sequence CpG detection and reads
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else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
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if (!regionSeq) {
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throw new Error('no region sequence detected, need sequenceAdapter configuration');
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}
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const seq = feature.get('seq');
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const mm = getTagAlt(feature, 'MM', 'Mm') || '';
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const methBins = new Array(region.end - region.start).fill(0);
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const ops = parseCigar(feature.get('CIGAR'));
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getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
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// we are processing methylation
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if (type === 'm') {
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for (const pos of getNextRefPos(ops, positions)) {
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const epos = pos + fstart - region.start;
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if (epos >= 0 && epos < methBins.length) {
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methBins[epos] = 1;
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}
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}
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}
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});
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for (let j = fstart; j < fend; j++) {
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const i = j - region.start;
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if (i >= 0 && i < bins.length - 1) {
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const l1 = regionSeq[i].toLowerCase();
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const l2 = regionSeq[i + 1].toLowerCase();
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const bin = bins[i];
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const bin1 = bins[i + 1];
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// color
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if (l1 === 'c' && l2 === 'g') {
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if (methBins[i] || methBins[i + 1]) {
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inc(bin, fstrand, 'cov', 'meth');
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inc(bin1, fstrand, 'cov', 'meth');
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bins[i].ref--;
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bins[i][fstrand]--;
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bins[i + 1].ref--;
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bins[i + 1][fstrand]--;
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}
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else {
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inc(bin, fstrand, 'cov', 'unmeth');
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inc(bin1, fstrand, 'cov', 'unmeth');
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bins[i].ref--;
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bins[i][fstrand]--;
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bins[i + 1].ref--;
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bins[i + 1][fstrand]--;
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}
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}
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}
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}
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}
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// normal SNP based coloring
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const mismatches = feature.get('mismatches') || [];
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const colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
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for (let i = 0; i < mismatches.length; i++) {
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const mismatch = mismatches[i];
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const mstart = fstart + mismatch.start;
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const mlen = mismatchLen(mismatch);
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const mend = mstart + mlen;
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for (let j = mstart; j < mstart + mlen; j++) {
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const epos = j - region.start;
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if (epos >= 0 && epos < bins.length) {
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const bin = bins[epos];
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const { base, type } = mismatch;
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const interbase = isInterbase(type);
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if (!interbase) {
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bin.ref--;
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bin[fstrand]--;
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}
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else {
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inc(bin, fstrand, 'noncov', type);
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}
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if (type === 'deletion' || type === 'skip') {
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inc(bin, fstrand, 'delskips', type);
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bin.total--;
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}
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else if (!interbase && colorSNPs) {
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inc(bin, fstrand, 'cov', base);
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bin.refbase = mismatch.altbase;
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}
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}
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}
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const hash = `${mstart}_${mend}_${fstrand}`;
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if (skipmap[hash] === undefined) {
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skipmap[hash] = {
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feature: feature,
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start: mstart,
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end: mend,
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strand: fstrand,
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xs: getTag(feature, 'XS') || getTag(feature, 'TS'),
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score: 0,
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};
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}
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skipmap[hash].score++;
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}
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}
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}
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return { bins, skipmap };
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}
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}
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const { capabilities } = SNPCoverageAdapter;
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export { capabilities };
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{"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,
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{"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,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,EAAE,aAAa,EAAE,MAAM,SAAS,CAAA;AAEvC,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,gBAAgB,CAAC,eAAe,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,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,oBAAoB,CAClD,KAAK,EACL,MAAM,EACN,IAAI,EACJ,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAC/B,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;gBAClC,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE;oBACzB,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK;wBACL,GAAG,EAAE,KAAK,GAAG,CAAC;wBACd,OAAO,EAAE,MAAM,CAAC,OAAO;qBACxB;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,uCAAuC;YACvC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE;gBAC9C,QAAQ,CAAC,IAAI,CACX,IAAI,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;CACzC;AAED,MAAM,EAAE,YAAY,EAAE,GAAG,kBAAkB,CAAA;AAC3C,OAAO,EAAE,YAAY,EAAE,CAAA"}
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@@ -0,0 +1,53 @@
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1
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+
import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
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2
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import { Feature } from '@jbrowse/core/util/simpleFeature';
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export default function generateCoverageBins(features: Feature[], region: Region, opts: {
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bpPerPx?: number;
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colorBy?: {
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type: string;
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tag?: string;
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};
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}, fetchSequence: (arg: Region) => Promise<string>): Promise<{
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bins: {
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refbase?: string | undefined;
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total: number;
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all: number;
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ref: number;
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'-1': 0;
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'0': 0;
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'1': 0;
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lowqual: {
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total: number;
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strands: {
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[key: string]: number;
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};
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};
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cov: {
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total: number;
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strands: {
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[key: string]: number;
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};
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};
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+
delskips: {
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total: number;
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strands: {
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[key: string]: number;
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};
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+
};
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36
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+
noncov: {
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+
total: number;
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+
strands: {
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+
[key: string]: number;
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+
};
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41
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+
};
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42
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+
}[];
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43
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+
skipmap: {
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44
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+
[key: string]: {
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45
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+
score: number;
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46
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+
feature: unknown;
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47
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+
start: number;
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|
48
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+
end: number;
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|
49
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+
strand: number;
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50
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+
xs: string;
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51
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+
};
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+
};
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53
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+
}>;
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@@ -0,0 +1,182 @@
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1
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+
import { getTag, getTagAlt, shouldFetchReferenceSequence } from '../util';
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2
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+
import { parseCigar, getNextRefPos, getModificationPositions, } from '../BamAdapter/MismatchParser';
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|
3
|
+
function mismatchLen(mismatch) {
|
|
4
|
+
return !isInterbase(mismatch.type) ? mismatch.length : 1;
|
|
5
|
+
}
|
|
6
|
+
function isInterbase(type) {
|
|
7
|
+
return type === 'softclip' || type === 'hardclip' || type === 'insertion';
|
|
8
|
+
}
|
|
9
|
+
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
10
|
+
function inc(bin, strand, type, field) {
|
|
11
|
+
let thisBin = bin[type][field];
|
|
12
|
+
if (thisBin === undefined) {
|
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13
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+
thisBin = bin[type][field] = {
|
|
14
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+
total: 0,
|
|
15
|
+
'-1': 0,
|
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16
|
+
'0': 0,
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17
|
+
'1': 0,
|
|
18
|
+
};
|
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19
|
+
}
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20
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+
thisBin.total++;
|
|
21
|
+
thisBin[strand]++;
|
|
22
|
+
}
|
|
23
|
+
export default async function generateCoverageBins(features, region, opts, fetchSequence) {
|
|
24
|
+
var _a;
|
|
25
|
+
const { colorBy } = opts;
|
|
26
|
+
const binMax = Math.ceil(region.end - region.start);
|
|
27
|
+
const skipmap = {};
|
|
28
|
+
const regionSeq = features.length && shouldFetchReferenceSequence((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type)
|
|
29
|
+
? await fetchSequence(region)
|
|
30
|
+
: undefined;
|
|
31
|
+
const bins = [];
|
|
32
|
+
for (let i = 0; i < features.length; i++) {
|
|
33
|
+
const feature = features[i];
|
|
34
|
+
const fstart = feature.get('start');
|
|
35
|
+
const fend = feature.get('end');
|
|
36
|
+
const fstrand = feature.get('strand');
|
|
37
|
+
for (let j = fstart; j < fend + 1; j++) {
|
|
38
|
+
const i = j - region.start;
|
|
39
|
+
if (i >= 0 && i < binMax) {
|
|
40
|
+
if (bins[i] === undefined) {
|
|
41
|
+
bins[i] = {
|
|
42
|
+
total: 0,
|
|
43
|
+
all: 0,
|
|
44
|
+
ref: 0,
|
|
45
|
+
'-1': 0,
|
|
46
|
+
'0': 0,
|
|
47
|
+
'1': 0,
|
|
48
|
+
lowqual: {},
|
|
49
|
+
cov: {},
|
|
50
|
+
delskips: {},
|
|
51
|
+
noncov: {},
|
|
52
|
+
};
|
|
53
|
+
}
|
|
54
|
+
if (j !== fend) {
|
|
55
|
+
bins[i].total++;
|
|
56
|
+
bins[i].all++;
|
|
57
|
+
bins[i].ref++;
|
|
58
|
+
bins[i][fstrand]++;
|
|
59
|
+
}
|
|
60
|
+
}
|
|
61
|
+
}
|
|
62
|
+
if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
|
|
63
|
+
const seq = feature.get('seq');
|
|
64
|
+
const mm = getTagAlt(feature, 'MM', 'Mm') || '';
|
|
65
|
+
const ops = parseCigar(feature.get('CIGAR'));
|
|
66
|
+
const fend = feature.get('end');
|
|
67
|
+
getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
|
|
68
|
+
const mod = `mod_${type}`;
|
|
69
|
+
for (const pos of getNextRefPos(ops, positions)) {
|
|
70
|
+
const epos = pos + fstart - region.start;
|
|
71
|
+
if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
|
|
72
|
+
const bin = bins[epos];
|
|
73
|
+
if (bin) {
|
|
74
|
+
inc(bin, fstrand, 'cov', mod);
|
|
75
|
+
}
|
|
76
|
+
else {
|
|
77
|
+
console.warn('Undefined position in modifications snpcoverage encountered');
|
|
78
|
+
}
|
|
79
|
+
}
|
|
80
|
+
}
|
|
81
|
+
});
|
|
82
|
+
}
|
|
83
|
+
// methylation based coloring takes into account both reference
|
|
84
|
+
// sequence CpG detection and reads
|
|
85
|
+
else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
|
|
86
|
+
if (!regionSeq) {
|
|
87
|
+
throw new Error('no region sequence detected, need sequenceAdapter configuration');
|
|
88
|
+
}
|
|
89
|
+
const seq = feature.get('seq');
|
|
90
|
+
const mm = getTagAlt(feature, 'MM', 'Mm') || '';
|
|
91
|
+
const methBins = new Array(region.end - region.start).fill(0);
|
|
92
|
+
const ops = parseCigar(feature.get('CIGAR'));
|
|
93
|
+
getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
|
|
94
|
+
// we are processing methylation
|
|
95
|
+
if (type === 'm') {
|
|
96
|
+
for (const pos of getNextRefPos(ops, positions)) {
|
|
97
|
+
const epos = pos + fstart - region.start;
|
|
98
|
+
if (epos >= 0 && epos < methBins.length) {
|
|
99
|
+
methBins[epos] = 1;
|
|
100
|
+
}
|
|
101
|
+
}
|
|
102
|
+
}
|
|
103
|
+
});
|
|
104
|
+
for (let j = fstart; j < fend; j++) {
|
|
105
|
+
const i = j - region.start;
|
|
106
|
+
if (i >= 0 && i < bins.length - 1) {
|
|
107
|
+
const l1 = regionSeq[i].toLowerCase();
|
|
108
|
+
const l2 = regionSeq[i + 1].toLowerCase();
|
|
109
|
+
const bin = bins[i];
|
|
110
|
+
const bin1 = bins[i + 1];
|
|
111
|
+
// color
|
|
112
|
+
if (l1 === 'c' && l2 === 'g') {
|
|
113
|
+
if (methBins[i] || methBins[i + 1]) {
|
|
114
|
+
inc(bin, fstrand, 'cov', 'meth');
|
|
115
|
+
inc(bin1, fstrand, 'cov', 'meth');
|
|
116
|
+
bins[i].ref--;
|
|
117
|
+
bins[i][fstrand]--;
|
|
118
|
+
bins[i + 1].ref--;
|
|
119
|
+
bins[i + 1][fstrand]--;
|
|
120
|
+
}
|
|
121
|
+
else {
|
|
122
|
+
inc(bin, fstrand, 'cov', 'unmeth');
|
|
123
|
+
inc(bin1, fstrand, 'cov', 'unmeth');
|
|
124
|
+
bins[i].ref--;
|
|
125
|
+
bins[i][fstrand]--;
|
|
126
|
+
bins[i + 1].ref--;
|
|
127
|
+
bins[i + 1][fstrand]--;
|
|
128
|
+
}
|
|
129
|
+
}
|
|
130
|
+
}
|
|
131
|
+
}
|
|
132
|
+
}
|
|
133
|
+
// normal SNP based coloring
|
|
134
|
+
const mismatches = feature.get('mismatches') || [];
|
|
135
|
+
const colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
|
|
136
|
+
for (let i = 0; i < mismatches.length; i++) {
|
|
137
|
+
const mismatch = mismatches[i];
|
|
138
|
+
const mstart = fstart + mismatch.start;
|
|
139
|
+
const mlen = mismatchLen(mismatch);
|
|
140
|
+
const mend = mstart + mlen;
|
|
141
|
+
for (let j = mstart; j < mstart + mlen; j++) {
|
|
142
|
+
const epos = j - region.start;
|
|
143
|
+
if (epos >= 0 && epos < bins.length) {
|
|
144
|
+
const bin = bins[epos];
|
|
145
|
+
const { base, type } = mismatch;
|
|
146
|
+
const interbase = isInterbase(type);
|
|
147
|
+
if (!interbase) {
|
|
148
|
+
bin.ref--;
|
|
149
|
+
bin[fstrand]--;
|
|
150
|
+
}
|
|
151
|
+
else {
|
|
152
|
+
inc(bin, fstrand, 'noncov', type);
|
|
153
|
+
}
|
|
154
|
+
if (type === 'deletion' || type === 'skip') {
|
|
155
|
+
inc(bin, fstrand, 'delskips', type);
|
|
156
|
+
bin.total--;
|
|
157
|
+
}
|
|
158
|
+
else if (!interbase && colorSNPs) {
|
|
159
|
+
inc(bin, fstrand, 'cov', base);
|
|
160
|
+
bin.refbase = mismatch.altbase;
|
|
161
|
+
}
|
|
162
|
+
}
|
|
163
|
+
}
|
|
164
|
+
if (mismatch.type === 'skip') {
|
|
165
|
+
const hash = `${mstart}_${mend}_${fstrand}`;
|
|
166
|
+
if (skipmap[hash] === undefined) {
|
|
167
|
+
skipmap[hash] = {
|
|
168
|
+
feature: feature,
|
|
169
|
+
start: mstart,
|
|
170
|
+
end: mend,
|
|
171
|
+
strand: fstrand,
|
|
172
|
+
xs: getTag(feature, 'XS') || getTag(feature, 'TS'),
|
|
173
|
+
score: 0,
|
|
174
|
+
};
|
|
175
|
+
}
|
|
176
|
+
skipmap[hash].score++;
|
|
177
|
+
}
|
|
178
|
+
}
|
|
179
|
+
}
|
|
180
|
+
return { bins, skipmap };
|
|
181
|
+
}
|
|
182
|
+
//# sourceMappingURL=generateCoverageBins.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-alignments",
|
|
3
|
-
"version": "2.2.
|
|
3
|
+
"version": "2.2.2",
|
|
4
4
|
"description": "JBrowse 2 alignments adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -27,7 +27,7 @@
|
|
|
27
27
|
"build": "npm-run-all build:*",
|
|
28
28
|
"test": "cd ../..; jest plugins/alignments",
|
|
29
29
|
"prepublishOnly": "yarn test",
|
|
30
|
-
"prepack": "yarn build
|
|
30
|
+
"prepack": "yarn build && yarn useDist",
|
|
31
31
|
"postpack": "yarn useSrc",
|
|
32
32
|
"useDist": "node ../../scripts/useDist.js",
|
|
33
33
|
"useSrc": "node ../../scripts/useSrc.js",
|
|
@@ -65,5 +65,5 @@
|
|
|
65
65
|
"distModule": "esm/index.js",
|
|
66
66
|
"srcModule": "src/index.ts",
|
|
67
67
|
"module": "esm/index.js",
|
|
68
|
-
"gitHead": "
|
|
68
|
+
"gitHead": "abbc00e8feedbc58de84a7a3e735ec0224909b29"
|
|
69
69
|
}
|
|
@@ -4,23 +4,14 @@ import { ObservableMap } from 'mobx'
|
|
|
4
4
|
import {
|
|
5
5
|
Button,
|
|
6
6
|
CircularProgress,
|
|
7
|
-
Dialog,
|
|
8
7
|
DialogActions,
|
|
9
8
|
DialogContent,
|
|
10
|
-
DialogTitle,
|
|
11
|
-
IconButton,
|
|
12
9
|
Typography,
|
|
13
10
|
} from '@mui/material'
|
|
11
|
+
import { Dialog } from '@jbrowse/core/ui'
|
|
14
12
|
import { makeStyles } from 'tss-react/mui'
|
|
15
|
-
import CloseIcon from '@mui/icons-material/Close'
|
|
16
13
|
|
|
17
14
|
const useStyles = makeStyles()(theme => ({
|
|
18
|
-
closeButton: {
|
|
19
|
-
position: 'absolute',
|
|
20
|
-
right: theme.spacing(1),
|
|
21
|
-
top: theme.spacing(1),
|
|
22
|
-
color: theme.palette.grey[500],
|
|
23
|
-
},
|
|
24
15
|
table: {
|
|
25
16
|
border: '1px solid #888',
|
|
26
17
|
margin: theme.spacing(4),
|
|
@@ -58,30 +49,19 @@ function ModificationTable({
|
|
|
58
49
|
|
|
59
50
|
function ColorByTagDlg(props: {
|
|
60
51
|
model: {
|
|
61
|
-
setColorScheme:
|
|
52
|
+
setColorScheme: (arg: { type: string }) => void
|
|
62
53
|
modificationTagMap: ObservableMap<string, string>
|
|
63
54
|
colorBy?: { type: string }
|
|
64
55
|
}
|
|
65
56
|
handleClose: () => void
|
|
66
57
|
}) {
|
|
67
|
-
const { classes } = useStyles()
|
|
68
58
|
const { model, handleClose } = props
|
|
69
59
|
const { colorBy, modificationTagMap } = model
|
|
70
60
|
|
|
71
61
|
const modifications = [...modificationTagMap.entries()]
|
|
72
62
|
|
|
73
63
|
return (
|
|
74
|
-
<Dialog open onClose={handleClose}>
|
|
75
|
-
<DialogTitle>
|
|
76
|
-
Color by modifications
|
|
77
|
-
<IconButton
|
|
78
|
-
aria-label="close"
|
|
79
|
-
className={classes.closeButton}
|
|
80
|
-
onClick={handleClose}
|
|
81
|
-
>
|
|
82
|
-
<CloseIcon />
|
|
83
|
-
</IconButton>
|
|
84
|
-
</DialogTitle>
|
|
64
|
+
<Dialog open onClose={handleClose} title="Color by modifications">
|
|
85
65
|
<DialogContent>
|
|
86
66
|
<Typography>
|
|
87
67
|
You can choose to color the modifications in the BAM/CRAM MM/ML
|
|
@@ -126,12 +106,8 @@ function ColorByTagDlg(props: {
|
|
|
126
106
|
<DialogActions>
|
|
127
107
|
<Button
|
|
128
108
|
variant="contained"
|
|
129
|
-
color="primary"
|
|
130
|
-
style={{ margin: 5 }}
|
|
131
109
|
onClick={() => {
|
|
132
|
-
model.setColorScheme({
|
|
133
|
-
type: 'modifications',
|
|
134
|
-
})
|
|
110
|
+
model.setColorScheme({ type: 'modifications' })
|
|
135
111
|
handleClose()
|
|
136
112
|
}}
|
|
137
113
|
>
|
|
@@ -139,12 +115,8 @@ function ColorByTagDlg(props: {
|
|
|
139
115
|
</Button>
|
|
140
116
|
<Button
|
|
141
117
|
variant="contained"
|
|
142
|
-
color="primary"
|
|
143
|
-
style={{ margin: 5 }}
|
|
144
118
|
onClick={() => {
|
|
145
|
-
model.setColorScheme({
|
|
146
|
-
type: 'methylation',
|
|
147
|
-
})
|
|
119
|
+
model.setColorScheme({ type: 'methylation' })
|
|
148
120
|
handleClose()
|
|
149
121
|
}}
|
|
150
122
|
>
|
|
@@ -153,7 +125,6 @@ function ColorByTagDlg(props: {
|
|
|
153
125
|
<Button
|
|
154
126
|
variant="contained"
|
|
155
127
|
color="secondary"
|
|
156
|
-
style={{ margin: 5 }}
|
|
157
128
|
onClick={() => handleClose()}
|
|
158
129
|
>
|
|
159
130
|
Cancel
|