jbrowse-plugin-mafviewer 1.2.2 → 1.2.3
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/README.md +6 -1
- package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.d.ts +11 -2
- package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js +123 -94
- package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js.map +1 -1
- package/dist/LinearMafRenderer/LinearMafRenderer.js +1 -1
- package/dist/LinearMafRenderer/LinearMafRenderer.js.map +1 -1
- package/dist/LinearMafRenderer/makeImageData.js +25 -9
- package/dist/LinearMafRenderer/makeImageData.js.map +1 -1
- package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js +1 -1
- package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map +1 -1
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +8 -7
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +4 -4
- package/package.json +2 -1
- package/src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts +135 -99
- package/src/LinearMafRenderer/LinearMafRenderer.ts +1 -1
- package/src/LinearMafRenderer/makeImageData.ts +38 -9
- package/src/MafAddTrackWorkflow/AddTrackWorkflow.tsx +9 -11
package/README.md
CHANGED
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@@ -94,7 +94,12 @@ can use nhLocation or samples array on adapter
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### Example BgzipTaffyAdapter config
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-
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Note: TAF files are actually significantly slower and has known bugs...will
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update once fixed
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This notice will be removed it it is improved
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As with other adapters, you can use nhLocation or samples array on adapter
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```json
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{
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@@ -1,9 +1,18 @@
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import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
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import { Feature, Region } from '@jbrowse/core/util';
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import type { IndexData } from './types';
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import type { IndexData, OrganismRecord } from './types';
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export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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setupP?: Promise<IndexData>;
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private cache;
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getRefNames(): Promise<string[]>;
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getChunk(buffer: Uint8Array, opts?: BaseOptions): Promise<{
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uniqueId: string;
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start: number;
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end: number;
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strand: number;
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alignments: Record<string, OrganismRecord>;
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seq: string;
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} | undefined>;
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setupPre(): Promise<IndexData>;
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setup(opts?: BaseOptions): Promise<IndexData>;
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readTaiFile(): Promise<IndexData>;
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@@ -16,6 +25,6 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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}[];
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tree: Record<string, any> | undefined;
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}>;
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getLines(query: Region, byteRanges: IndexData): Promise<
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getLines(query: Region, byteRanges: IndexData): Promise<unknown>;
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freeResources(): void;
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}
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@@ -1,8 +1,10 @@
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import { unzip } from '@gmod/bgzf-filehandle';
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import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
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import { SimpleFeature, updateStatus, } from '@jbrowse/core/util';
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import QuickLRU from '@jbrowse/core/util/QuickLRU';
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import { openLocation } from '@jbrowse/core/util/io';
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import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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import AbortablePromiseCache from 'abortable-promise-cache';
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import Long from 'long';
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import VirtualOffset from './virtualOffset';
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import parseNewick from '../parseNewick';
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@@ -12,10 +14,116 @@ import { parseLineByLine } from './util';
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const toP = (s = 0) => +(+s).toFixed(1);
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export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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setupP;
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cache = new AbortablePromiseCache({
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cache: new QuickLRU({ maxSize: 50 }),
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// @ts-expect-error
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fill: async ({ nextEntry, firstEntry }, signal, statusCallback) => {
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const file = openLocation(this.getConf('tafGzLocation'));
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const response = await file.read(nextEntry.virtualOffset.blockPosition -
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firstEntry.virtualOffset.blockPosition, firstEntry.virtualOffset.blockPosition);
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const buffer = await unzip(response);
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const slice = buffer.slice(firstEntry.virtualOffset.dataPosition);
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return this.getChunk(slice, {
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statusCallback: statusCallback,
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signal,
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});
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},
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});
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async getRefNames() {
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const data = await this.setup();
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return Object.keys(data);
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}
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async getChunk(buffer, opts) {
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const { statusCallback = () => { } } = opts || {};
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const alignments = {};
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const data = [];
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let a0;
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let j = 0;
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let b = 0;
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parseLineByLine(buffer, line => {
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if (j++ % 100 === 0) {
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statusCallback(`Processing ${toP(b / 1_000_000)}/${toP(buffer.length / 1_000_000)}Mb`);
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}
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b += line.length;
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if (line) {
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const [lineData, rowInstructions] = line.split(' ; ');
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if (rowInstructions) {
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for (const ins of parseRowInstructions(rowInstructions)) {
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if (ins.type === 'i') {
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data.splice(ins.row, 0, ins);
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if (!alignments[ins.asm]) {
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alignments[ins.asm] = {
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start: ins.start,
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strand: ins.strand,
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srcSize: ins.length,
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chr: ins.ref,
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data: '',
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};
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}
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const e = alignments[ins.asm];
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e.data += ' '.repeat(Math.max(0, j - e.data.length - 1)); // catch it up
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}
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else if (ins.type === 's') {
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if (!alignments[ins.asm]) {
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alignments[ins.asm] = {
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start: ins.start,
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strand: ins.strand,
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srcSize: ins.length,
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chr: ins.ref,
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data: '',
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};
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}
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const e = alignments[ins.asm];
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e.data += ' '.repeat(Math.max(0, j - e.data.length - 1)); // catch it up
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data[ins.row] = ins;
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}
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else if (ins.type === 'd') {
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data.splice(ins.row, 1);
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}
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// no gaps for now(?)
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// else if (ins.type === 'g') {
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// console.log('g??')
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// } else if (ins.type === 'G') {
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// console.log('G??')
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// }
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}
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if (!a0) {
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a0 = data[0];
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}
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}
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const lineLen = lineData.length;
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for (let i = 0; i < lineLen; i++) {
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const letter = lineData[i];
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const r = data[i];
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if (r) {
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alignments[r.asm].data += letter;
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}
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else {
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// not sure why but chr22_KI270731v1_random.taf.gz ends up here
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}
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}
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}
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});
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if (a0) {
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const row0 = alignments[a0.asm];
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// see
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// https://github.com/ComparativeGenomicsToolkit/taffy/blob/f5a5354/docs/taffy_utilities.md#referenced-based-maftaf-and-indexing
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// for the significance of row[0]:
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//
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// "An anchor line in TAF is a column from which all sequence
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// coordinates can be deduced without scanning backwards to previous
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// lines "
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return {
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uniqueId: `${row0.start}-${row0.data.length}`,
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start: row0.start,
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end: row0.start + row0.data.length,
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strand: row0.strand,
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alignments,
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seq: row0.data,
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};
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}
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return undefined;
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}
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setupPre() {
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if (!this.setupP) {
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this.setupP = this.readTaiFile().catch((e) => {
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return ObservableCreate(async (observer) => {
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try {
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const byteRanges = await this.setup();
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const
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if (
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b += line.length;
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if (line) {
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const [lineData, rowInstructions] = line.split(' ; ');
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if (rowInstructions) {
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for (const ins of parseRowInstructions(rowInstructions)) {
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if (ins.type === 'i') {
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data.splice(ins.row, 0, ins);
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if (!alignments[ins.asm]) {
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alignments[ins.asm] = {
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start: ins.start,
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strand: ins.strand,
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srcSize: ins.length,
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chr: ins.ref,
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data: '',
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};
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}
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const e = alignments[ins.asm];
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e.data += ' '.repeat(Math.max(0, j - e.data.length)); // catch it up
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}
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else if (ins.type === 's') {
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if (!alignments[ins.asm]) {
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alignments[ins.asm] = {
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start: ins.start,
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strand: ins.strand,
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srcSize: ins.length,
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chr: ins.ref,
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data: '',
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};
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}
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const e = alignments[ins.asm];
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e.data += ' '.repeat(Math.max(0, j - e.data.length)); // catch it up
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data[ins.row] = ins;
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}
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else if (ins.type === 'd') {
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data.splice(ins.row, 1);
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}
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// no gaps for now(?)
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// else if (ins.type === 'g') {
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// }
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// else if (ins.type === 'G') {
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// }
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}
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if (!a0) {
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a0 = data[0];
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}
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}
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const lineLen = lineData.length;
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for (let i = 0; i < lineLen; i++) {
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const letter = lineData[i];
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const r = data[i];
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if (r) {
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alignments[r.asm].data += letter;
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}
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else {
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// not sure why but chr22_KI270731v1_random.taf.gz ends up here
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}
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}
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}
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});
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if (a0) {
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const row0 = alignments[a0.asm];
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// see
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// https://github.com/ComparativeGenomicsToolkit/taffy/blob/f5a5354/docs/taffy_utilities.md#referenced-based-maftaf-and-indexing
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// for the significance of row[0]:
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//
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// "An anchor line in TAF is a column from which all sequence
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// coordinates can be deduced without scanning backwards to previous
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// lines "
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observer.next(new SimpleFeature({
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uniqueId: `${row0.start}-${row0.data.length}`,
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refName: query.refName,
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start: row0.start,
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end: row0.start + row0.data.length,
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strand: row0.strand,
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alignments,
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seq: row0.data,
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}));
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}
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const feat = await updateStatus('Downloading alignments', statusCallback, () => this.getLines(query, byteRanges));
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if (feat) {
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observer.next(
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// @ts-expect-error
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new SimpleFeature({
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...feat,
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refName: query.refName,
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}));
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}
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else {
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console.error('no feature found');
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}
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statusCallback('');
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observer.complete();
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}
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// TODO: cache processed large chunks
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async getLines(query, byteRanges) {
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const file = openLocation(this.getConf('tafGzLocation'));
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const records = byteRanges[query.refName];
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if (records) {
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let firstEntry;
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@@ -211,10 +240,10 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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// file whn you request e.g. out of range region (e.g. taf in chr22:1-100
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// and you are at chr22:200-300)
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if (firstEntry && nextEntry) {
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return this.cache.get(`${JSON.stringify(nextEntry)}_${JSON.stringify(firstEntry)}`, {
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nextEntry,
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firstEntry,
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});
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}
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}
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return undefined;
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@@ -1 +1 @@
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|
-
{"version":3,"file":"BgzipTaffyAdapter.js","sourceRoot":"","sources":["../../src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAGL,aAAa,EACb,YAAY,GACb,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,IAAI,MAAM,MAAM,CAAA;AAEvB,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAC3C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,oBAAoB,EAAE,MAAM,mBAAmB,CAAA;AACxD,OAAO,EAAE,eAAe,EAAE,MAAM,QAAQ,CAAA;
|
|
1
|
+
{"version":3,"file":"BgzipTaffyAdapter.js","sourceRoot":"","sources":["../../src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAGL,aAAa,EACb,YAAY,GACb,MAAM,oBAAoB,CAAA;AAC3B,OAAO,QAAQ,MAAM,6BAA6B,CAAA;AAClD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,IAAI,MAAM,MAAM,CAAA;AAEvB,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAC3C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,oBAAoB,EAAE,MAAM,mBAAmB,CAAA;AACxD,OAAO,EAAE,eAAe,EAAE,MAAM,QAAQ,CAAA;AAcxC,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,sBAAsB;IAC5D,MAAM,CAAqB;IAE1B,KAAK,GAAG,IAAI,qBAAqB,CAAC;QACxC,KAAK,EAAE,IAAI,QAAQ,CAAC,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC;QACpC,mBAAmB;QACnB,IAAI,EAAE,KAAK,EAAE,EAAE,SAAS,EAAE,UAAU,EAAE,EAAE,MAAM,EAAE,cAAc,EAAE,EAAE;YAChE,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAC,CAAA;YACxD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,IAAI,CAC9B,SAAS,CAAC,aAAa,CAAC,aAAa;gBACnC,UAAU,CAAC,aAAa,CAAC,aAAa,EACxC,UAAU,CAAC,aAAa,CAAC,aAAa,CACvC,CAAA;YACD,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,QAAQ,CAAC,CAAA;YACpC,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,aAAa,CAAC,YAAY,CAAC,CAAA;YACjE,OAAO,IAAI,CAAC,QAAQ,CAAC,KAAK,EAAE;gBAC1B,cAAc,EAAE,cAAuC;gBACvD,MAAM;aACP,CAAC,CAAA;QACJ,CAAC;KACF,CAAC,CAAA;IAEF,KAAK,CAAC,WAAW;QACf,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC/B,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,QAAQ,CAAC,MAAkB,EAAE,IAAkB;QACnD,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,UAAU,GAAG,EAAoC,CAAA;QACvD,MAAM,IAAI,GAAG,EAAa,CAAA;QAC1B,IAAI,EAAO,CAAA;QACX,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,eAAe,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE;YAC7B,IAAI,CAAC,EAAE,GAAG,GAAG,KAAK,CAAC,EAAE,CAAC;gBACpB,cAAc,CACZ,cAAc,GAAG,CAAC,CAAC,GAAG,SAAS,CAAC,IAAI,GAAG,CAAC,MAAM,CAAC,MAAM,GAAG,SAAS,CAAC,IAAI,CACvE,CAAA;YACH,CAAC;YACD,CAAC,IAAI,IAAI,CAAC,MAAM,CAAA;YAChB,IAAI,IAAI,EAAE,CAAC;gBACT,MAAM,CAAC,QAAQ,EAAE,eAAe,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACrD,IAAI,eAAe,EAAE,CAAC;oBACpB,KAAK,MAAM,GAAG,IAAI,oBAAoB,CAAC,eAAe,CAAC,EAAE,CAAC;wBACxD,IAAI,GAAG,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;4BACrB,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;4BAC5B,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gCACzB,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG;oCACpB,KAAK,EAAE,GAAG,CAAC,KAAK;oCAChB,MAAM,EAAE,GAAG,CAAC,MAAM;oCAClB,OAAO,EAAE,GAAG,CAAC,MAAM;oCACnB,GAAG,EAAE,GAAG,CAAC,GAAG;oCACZ,IAAI,EAAE,EAAE;iCACT,CAAA;4BACH,CAAC;4BACD,MAAM,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,GAAG,CAAE,CAAA;4BAC9B,CAAC,CAAC,IAAI,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA,CAAC,cAAc;wBACzE,CAAC;6BAAM,IAAI,GAAG,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;4BAC5B,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gCACzB,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG;oCACpB,KAAK,EAAE,GAAG,CAAC,KAAK;oCAChB,MAAM,EAAE,GAAG,CAAC,MAAM;oCAClB,OAAO,EAAE,GAAG,CAAC,MAAM;oCACnB,GAAG,EAAE,GAAG,CAAC,GAAG;oCACZ,IAAI,EAAE,EAAE;iCACT,CAAA;4BACH,CAAC;4BACD,MAAM,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,GAAG,CAAE,CAAA;4BAC9B,CAAC,CAAC,IAAI,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA,CAAC,cAAc;4BACvE,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,GAAG,CAAA;wBACrB,CAAC;6BAAM,IAAI,GAAG,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;4BAC5B,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;wBACzB,CAAC;wBAED,qBAAqB;wBACrB,+BAA+B;wBAC/B,uBAAuB;wBACvB,iCAAiC;wBACjC,uBAAuB;wBACvB,IAAI;oBACN,CAAC;oBACD,IAAI,CAAC,EAAE,EAAE,CAAC;wBACR,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;oBACd,CAAC;gBACH,CAAC;gBACD,MAAM,OAAO,GAAG,QAAS,CAAC,MAAM,CAAA;gBAEhC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE,CAAC;oBACjC,MAAM,MAAM,GAAG,QAAS,CAAC,CAAC,CAAC,CAAA;oBAC3B,MAAM,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;oBAEjB,IAAI,CAAC,EAAE,CAAC;wBACN,UAAU,CAAC,CAAC,CAAC,GAAG,CAAE,CAAC,IAAI,IAAI,MAAM,CAAA;oBACnC,CAAC;yBAAM,CAAC;wBACN,+DAA+D;oBACjE,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC,CAAC,CAAA;QACF,IAAI,EAAE,EAAE,CAAC;YACP,MAAM,IAAI,GAAG,UAAU,CAAC,EAAE,CAAC,GAAG,CAAE,CAAA;YAEhC,MAAM;YACN,gIAAgI;YAChI,kCAAkC;YAClC,EAAE;YACF,6DAA6D;YAC7D,oEAAoE;YACpE,UAAU;YACV,OAAO;gBACL,QAAQ,EAAE,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;gBAC7C,KAAK,EAAE,IAAI,CAAC,KAAK;gBACjB,GAAG,EAAE,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM;gBAClC,MAAM,EAAE,IAAI,CAAC,MAAM;gBACnB,UAAU;gBACV,GAAG,EAAE,IAAI,CAAC,IAAI;aACf,CAAA;QACH,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACpD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IACD,KAAK,CAAC,IAAkB;QACtB,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI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@@ -15,7 +15,7 @@ export default class LinearMafRenderer extends FeatureRendererType {
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15
15
|
async render(renderProps) {
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16
16
|
const { statusCallback = () => { }, regions, bpPerPx, samples, rowHeight, } = renderProps;
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17
17
|
const region = regions[0];
|
|
18
|
-
const height = samples.length *
|
|
18
|
+
const height = samples.length * rowHeight + 100;
|
|
19
19
|
const width = (region.end - region.start) / bpPerPx;
|
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20
20
|
const features = await this.getFeatures(renderProps);
|
|
21
21
|
const res = await renderToAbstractCanvas(width, height, renderProps, async (ctx) => {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"LinearMafRenderer.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/LinearMafRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAA;AAEzE,OAAO,EAEL,sBAAsB,EACtB,YAAY,GACb,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAe/C,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,mBAAmB;IAChE,iBAAiB,CAAC,MAAc;QAC9B,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QAC7B,MAAM,WAAW,GAAG,CAAC,CAAA;QAErB,OAAO;YACL,sEAAsE;YACtE,GAAI,MAAsC;YAC1C,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,WAAW,EAAE,CAAC,CAAC,CAAC;YACnD,GAAG,EAAE,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC;SAClC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,MAAM,CAAC,WAAuB;QAClC,MAAM,EACJ,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EACzB,OAAO,EACP,OAAO,EACP,OAAO,EACP,SAAS,GACV,GAAG,WAAW,CAAA;QACf,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,
|
|
1
|
+
{"version":3,"file":"LinearMafRenderer.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/LinearMafRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAA;AAEzE,OAAO,EAEL,sBAAsB,EACtB,YAAY,GACb,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAe/C,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,mBAAmB;IAChE,iBAAiB,CAAC,MAAc;QAC9B,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QAC7B,MAAM,WAAW,GAAG,CAAC,CAAA;QAErB,OAAO;YACL,sEAAsE;YACtE,GAAI,MAAsC;YAC1C,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,WAAW,EAAE,CAAC,CAAC,CAAC;YACnD,GAAG,EAAE,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC;SAClC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,MAAM,CAAC,WAAuB;QAClC,MAAM,EACJ,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EACzB,OAAO,EACP,OAAO,EACP,OAAO,EACP,SAAS,GACV,GAAG,WAAW,CAAA;QACf,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,SAAS,GAAG,GAAG,CAAA;QAC/C,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QACnD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,WAAW,CAAC,CAAA;QACpD,MAAM,GAAG,GAAG,MAAM,sBAAsB,CACtC,KAAK,EACL,MAAM,EACN,WAAW,EACX,KAAK,EAAC,GAAG,EAAC,EAAE;YACV,MAAM,YAAY,CAAC,qBAAqB,EAAE,cAAc,EAAE,GAAG,EAAE;gBAC7D,aAAa,CAAC;oBACZ,GAAG;oBACH,UAAU,EAAE;wBACV,GAAG,WAAW;wBACd,QAAQ;qBACT;iBACF,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YACF,OAAO,SAAS,CAAA;QAClB,CAAC,CACF,CAAA;QACD,MAAM,OAAO,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC;YACjC,GAAG,WAAW;YACd,GAAG,GAAG;YACN,KAAK;YACL,MAAM;SACP,CAAC,CAAA;QACF,OAAO;YACL,GAAG,OAAO;YACV,GAAG,GAAG;YACN,QAAQ,EAAE,IAAI,GAAG,EAAE;YACnB,KAAK;YACL,MAAM;YACN,uBAAuB,EAAE,IAAI;SAC9B,CAAA;IACH,CAAC;CACF"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { createJBrowseTheme } from '@jbrowse/core/ui';
|
|
2
|
-
import { featureSpanPx } from '@jbrowse/core/util';
|
|
2
|
+
import { featureSpanPx, measureText } from '@jbrowse/core/util';
|
|
3
3
|
import { fillRect, getCharWidthHeight, getColorBaseMap, getContrastBaseMap, } from './util';
|
|
4
4
|
export function makeImageData({ ctx, renderArgs, }) {
|
|
5
5
|
const { regions, bpPerPx, rowHeight, showAllLetters, theme: configTheme, mismatchRendering, samples, rowProportion, features, } = renderArgs;
|
|
@@ -52,7 +52,7 @@ export function makeImageData({ ctx, renderArgs, }) {
|
|
|
52
52
|
if (seq[i] !== '-') {
|
|
53
53
|
const c = alignment[i];
|
|
54
54
|
const l = leftPx + scale * o;
|
|
55
|
-
if (seq[i] === c && c !== '-') {
|
|
55
|
+
if (seq[i] === c && c !== '-' && c !== ' ') {
|
|
56
56
|
fillRect(ctx, l, offset + t, scale + f, h, canvasWidth);
|
|
57
57
|
}
|
|
58
58
|
o++;
|
|
@@ -117,8 +117,6 @@ export function makeImageData({ ctx, renderArgs, }) {
|
|
|
117
117
|
continue;
|
|
118
118
|
}
|
|
119
119
|
const t = rowHeight * row;
|
|
120
|
-
ctx.beginPath();
|
|
121
|
-
ctx.fillStyle = 'purple';
|
|
122
120
|
for (let i = 0, o = 0; i < alignment.length; i++) {
|
|
123
121
|
let ins = '';
|
|
124
122
|
while (seq[i] === '-') {
|
|
@@ -129,15 +127,33 @@ export function makeImageData({ ctx, renderArgs, }) {
|
|
|
129
127
|
}
|
|
130
128
|
if (ins.length > 0) {
|
|
131
129
|
const l = leftPx + scale * o - 1;
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
|
|
130
|
+
if (ins.length > 10) {
|
|
131
|
+
const txt = `${ins.length}`;
|
|
132
|
+
if (bpPerPx > 10) {
|
|
133
|
+
fillRect(ctx, l - 1, t, 2, h, canvasWidth, 'purple');
|
|
134
|
+
}
|
|
135
|
+
else if (h > charHeight) {
|
|
136
|
+
const rwidth = measureText(txt);
|
|
137
|
+
const padding = 5;
|
|
138
|
+
fillRect(ctx, l - rwidth / 2 - padding, t, rwidth + 2 * padding, h, canvasWidth, 'purple');
|
|
139
|
+
ctx.fillStyle = 'white';
|
|
140
|
+
ctx.fillText(txt, l - rwidth / 2, t + h);
|
|
141
|
+
}
|
|
142
|
+
else {
|
|
143
|
+
const padding = 2;
|
|
144
|
+
fillRect(ctx, l - padding, t, 2 * padding, h, canvasWidth, 'purple');
|
|
145
|
+
}
|
|
146
|
+
}
|
|
147
|
+
else {
|
|
148
|
+
fillRect(ctx, l, offset + t, 1, h, canvasWidth, 'purple');
|
|
149
|
+
if (bpPerPx < 0.2 && rowHeight > 5) {
|
|
150
|
+
fillRect(ctx, l - 2, offset + t, 5, 1, canvasWidth);
|
|
151
|
+
fillRect(ctx, l - 2, offset + t + h - 1, 5, 1, canvasWidth);
|
|
152
|
+
}
|
|
136
153
|
}
|
|
137
154
|
}
|
|
138
155
|
o++;
|
|
139
156
|
}
|
|
140
|
-
ctx.fill();
|
|
141
157
|
}
|
|
142
158
|
}
|
|
143
159
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"makeImageData.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/makeImageData.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EAAW,aAAa,EAAE,MAAM,oBAAoB,CAAA;
|
|
1
|
+
{"version":3,"file":"makeImageData.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/makeImageData.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EAAW,aAAa,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAExE,OAAO,EACL,QAAQ,EACR,kBAAkB,EAClB,eAAe,EACf,kBAAkB,GACnB,MAAM,QAAQ,CAAA;AAgBf,MAAM,UAAU,aAAa,CAAC,EAC5B,GAAG,EACH,UAAU,GAIX;IACC,MAAM,EACJ,OAAO,EACP,OAAO,EACP,SAAS,EACT,cAAc,EACd,KAAK,EAAE,WAAW,EAClB,iBAAiB,EACjB,OAAO,EACP,aAAa,EACb,QAAQ,GACT,GAAG,UAAU,CAAA;IACd,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;IAC1B,MAAM,WAAW,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;IACzD,MAAM,CAAC,GAAG,SAAS,GAAG,aAAa,CAAA;IACnC,MAAM,KAAK,GAAG,kBAAkB,CAAC,WAAW,CAAC,CAAA;IAC7C,MAAM,YAAY,GAAG,eAAe,CAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,eAAe,GAAG,kBAAkB,CAAC,KAAK,CAAC,CAAA;IAEjD,MAAM,EAAE,UAAU,EAAE,GAAG,kBAAkB,EAAE,CAAA;IAC3C,MAAM,cAAc,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;IAChE,MAAM,KAAK,GAAG,CAAC,GAAG,OAAO,CAAA;IACzB,MAAM,CAAC,GAAG,GAAG,CAAA;IACb,MAAM,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;IACxB,MAAM,GAAG,GAAG,CAAC,GAAG,CAAC,CAAA;IACjB,MAAM,MAAM,GAAG,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;IAElC,uBAAuB;IACvB,GAAG,CAAC,IAAI,GAAG,iCAAiC,CAAA;IAE5C,KAAK,MAAM,OAAO,IAAI,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC;QACxC,MAAM,CAAC,MAAM,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;QACxD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAqC,CAAA;QAC1E,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,WAAW,EAAE,CAAA;QAC5C,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;QAC9B,KAAK,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9B,MAAM,aAAa,GAAG,GAAG,CAAC,IAAI,CAAA;YAC9B,MAAM,SAAS,GAAG,aAAa,CAAC,WAAW,EAAE,CAAA;YAE7C,MAAM,GAAG,GAAG,cAAc,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACtC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YAED,MAAM,CAAC,GAAG,SAAS,GAAG,GAAG,CAAA;YAEzB,OAAO;YACP,GAAG,CAAC,SAAS,EAAE,CAAA;YACf,GAAG,CAAC,SAAS,GAAG,OAAO,CAAA;YACvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACjD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;oBACnB,IAAI,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;wBACzB,MAAM,CAAC,GAAG,MAAM,GAAG,KAAK,GAAG,CAAC,CAAA;wBAC5B,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;wBACrB,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,KAAK,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;oBACnC,CAAC;oBACD,CAAC,EAAE,CAAA;gBACL,CAAC;YACH,CAAC;YACD,GAAG,CAAC,MAAM,EAAE,CAAA;YAEZ,IAAI,CAAC,cAAc,EAAE,CAAC;gBACpB,UAAU;gBACV,GAAG,CAAC,SAAS,GAAG,WAAW,CAAA;gBAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;oBACjD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;wBACnB,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,CAAA;wBACtB,MAAM,CAAC,GAAG,MAAM,GAAG,KAAK,GAAG,CAAC,CAAA;wBAC5B,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;4BAC3C,QAAQ,CAAC,GAAG,EAAE,CAAC,EAAE,MAAM,GAAG,CAAC,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,EAAE,WAAW,CAAC,CAAA;wBACzD,CAAC;wBACD,CAAC,EAAE,CAAA;oBACL,CAAC;gBACH,CAAC;YACH,CAAC;YAED,aAAa;YACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACjD,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,CAAA;gBACtB,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;oBACnB,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;wBACd,MAAM,CAAC,GAAG,MAAM,GAAG,KAAK,GAAG,CAAC,CAAA;wBAC5B,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;4BAC9B,QAAQ,CACN,GAAG,EACH,CAAC,EACD,MAAM,GAAG,CAAC,EACV,KAAK,GAAG,CAAC,EACT,CAAC,EACD,WAAW,EACX,iBAAiB;gCACf,CAAC,CAAC,uEAAuE;oCACvE,CAAC,YAAY,CAAC,CAA8B,CAAC,IAAI,OAAO,CAAC;gCAC3D,CAAC,CAAC,QAAQ,CACb,CAAA;wBACH,CAAC;6BAAM,IAAI,cAAc,EAAE,CAAC;4BAC1B,QAAQ,CACN,GAAG,EACH,CAAC,EACD,MAAM,GAAG,CAAC,EACV,KAAK,GAAG,CAAC,EACT,CAAC,EACD,WAAW,EACX,iBAAiB;gCACf,CAAC,CAAC,uEAAuE;oCACvE,CAAC,YAAY,CAAC,CAA8B,CAAC,IAAI,OAAO,CAAC;gCAC3D,CAAC,CAAC,WAAW,CAChB,CAAA;wBACH,CAAC;oBACH,CAAC;oBACD,CAAC,EAAE,CAAA;gBACL,CAAC;YACH,CAAC;YAED,OAAO;YACP,MAAM,SAAS,GAAG,EAAE,CAAA;YACpB,IAAI,KAAK,IAAI,SAAS,EAAE,CAAC;gBACvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;oBACjD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;wBACnB,MAAM,CAAC,GAAG,MAAM,GAAG,KAAK,GAAG,CAAC,CAAA;wBAC5B,MAAM,MAAM,GAAG,CAAC,KAAK,GAAG,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;wBAC1C,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAE,CAAA;wBACvB,IAAI,CAAC,cAAc,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;4BAClD,GAAG,CAAC,SAAS,GAAG,iBAAiB;gCAC/B,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,IAAI,OAAO,CAAC;gCACjC,CAAC,CAAC,OAAO,CAAA;4BACX,IAAI,SAAS,GAAG,UAAU,EAAE,CAAC;gCAC3B,GAAG,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,GAAG,MAAM,EAAE,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;4BAC/D,CAAC;wBACH,CAAC;wBACD,CAAC,EAAE,CAAA;oBACL,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,mEAAmE;IACnE,uDAAuD;IACvD,KAAK,MAAM,OAAO,IAAI,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC;QACxC,MAAM,CAAC,MAAM,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;QACxD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAqC,CAAA;QAC1E,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,WAAW,EAAE,CAAA;QAE5C,KAAK,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YACjD,MAAM,aAAa,GAAG,GAAG,CAAC,IAAI,CAAA;YAC9B,MAAM,SAAS,GAAG,aAAa,CAAC,WAAW,EAAE,CAAA;YAC7C,MAAM,GAAG,GAAG,cAAc,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACtC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YAED,MAAM,CAAC,GAAG,SAAS,GAAG,GAAG,CAAA;YAEzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACjD,IAAI,GAAG,GAAG,EAAE,CAAA;gBACZ,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;oBACtB,IAAI,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;wBACjD,GAAG,IAAI,SAAS,CAAC,CAAC,CAAC,CAAA;oBACrB,CAAC;oBACD,CAAC,EAAE,CAAA;gBACL,CAAC;gBACD,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;oBACnB,MAAM,CAAC,GAAG,MAAM,GAAG,KAAK,GAAG,CAAC,GAAG,CAAC,CAAA;oBAEhC,IAAI,GAAG,CAAC,MAAM,GAAG,EAAE,EAAE,CAAC;wBACpB,MAAM,GAAG,GAAG,GAAG,GAAG,CAAC,MAAM,EAAE,CAAA;wBAC3B,IAAI,OAAO,GAAG,EAAE,EAAE,CAAC;4BACjB,QAAQ,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAA;wBACtD,CAAC;6BAAM,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;4BAC1B,MAAM,MAAM,GAAG,WAAW,CAAC,GAAG,CAAC,CAAA;4BAC/B,MAAM,OAAO,GAAG,CAAC,CAAA;4BACjB,QAAQ,CACN,GAAG,EACH,CAAC,GAAG,MAAM,GAAG,CAAC,GAAG,OAAO,EACxB,CAAC,EACD,MAAM,GAAG,CAAC,GAAG,OAAO,EACpB,CAAC,EACD,WAAW,EACX,QAAQ,CACT,CAAA;4BACD,GAAG,CAAC,SAAS,GAAG,OAAO,CAAA;4BACvB,GAAG,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC,GAAG,MAAM,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;wBAC1C,CAAC;6BAAM,CAAC;4BACN,MAAM,OAAO,GAAG,CAAC,CAAA;4BACjB,QAAQ,CACN,GAAG,EACH,CAAC,GAAG,OAAO,EACX,CAAC,EACD,CAAC,GAAG,OAAO,EACX,CAAC,EACD,WAAW,EACX,QAAQ,CACT,CAAA;wBACH,CAAC;oBACH,CAAC;yBAAM,CAAC;wBACN,QAAQ,CAAC,GAAG,EAAE,CAAC,EAAE,MAAM,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAA;wBACzD,IAAI,OAAO,GAAG,GAAG,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;4BACnC,QAAQ,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,WAAW,CAAC,CAAA;4BACnD,QAAQ,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,WAAW,CAAC,CAAA;wBAC7D,CAAC;oBACH,CAAC;gBACH,CAAC;gBACD,CAAC,EAAE,CAAA;YACL,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}
|
|
@@ -36,7 +36,7 @@ export default function MultiMAFWidget({ model }) {
|
|
|
36
36
|
React.createElement(FormLabel, null, "File type"),
|
|
37
37
|
React.createElement(RadioGroup, { value: fileTypeChoice, onChange: event => {
|
|
38
38
|
setFileTypeChoice(event.target.value);
|
|
39
|
-
} }, ['BigMafAdapter', 'MafTabixAdapter'
|
|
39
|
+
} }, ['BigMafAdapter', 'MafTabixAdapter'].map(r => (React.createElement(FormControlLabel, { key: r, value: r, control: React.createElement(Radio, null), checked: fileTypeChoice === r, label: r }))))),
|
|
40
40
|
fileTypeChoice === 'BigMafAdapter' ? (React.createElement(FileSelector, { location: loc, name: "Path to bigMaf", rootModel: rootModel, setLocation: arg => {
|
|
41
41
|
setLoc(arg);
|
|
42
42
|
} })) : fileTypeChoice === 'MafTabixAdapter' ? (React.createElement(React.Fragment, null,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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