@jbrowse/plugin-comparative-adapters 2.16.0 → 2.17.0

package/esm/MashMapAdapter/MashMapAdapter.js

@@ -1,13 +1,11 @@
 import { openLocation } from '@jbrowse/core/util/io';
-import { unzip } from '@gmod/bgzf-filehandle';
-import { isGzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
 import { parseLineByLine } from '../util';
 export default class MashMapAdapter extends PAFAdapter {
     async setupPre(opts) {
         const outLoc = openLocation(this.getConf('outLocation'), this.pluginManager);
-        const buffer = (await outLoc.readFile(opts));
-        const buf = isGzip(buffer) ? await unzip(buffer) : buffer;
+        const buf = await fetchAndMaybeUnzip(outLoc, opts);
         return parseLineByLine(buf, parseMashMapLine);
     }
 }

package/esm/MashMapAdapter/configSchema.js

@@ -10,7 +10,7 @@ const MashMapAdapter = ConfigurationSchema('MashMapAdapter', {
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
-        description: 'Target is the first value in the array, query is the second',
+        description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
     /**
      * #slot

package/esm/PAFAdapter/PAFAdapter.js

@@ -2,9 +2,8 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
 import { doesIntersect2 } from '@jbrowse/core/util/range';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { isGzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { readConfObject, } from '@jbrowse/core/configuration';
-import { unzip } from '@gmod/bgzf-filehandle';
 import { MismatchParser } from '@jbrowse/plugin-alignments';
 // locals
 import SyntenyFeature from '../SyntenyFeature';
@@ -24,14 +23,13 @@ class PAFAdapter extends BaseFeatureDataAdapter {
     async setupPre(opts) {
         const pm = this.pluginManager;
         const pafLocation = openLocation(this.getConf('pafLocation'), pm);
-        const buffer = (await pafLocation.readFile(opts));
-        const buf = isGzip(buffer) ? await unzip(buffer) : buffer;
+        const buf = await fetchAndMaybeUnzip(pafLocation, opts);
         return parseLineByLine(buf, parsePAFLine);
     }
     async hasDataForRefName() {
-        // determining this properly is basically a call to getFeatures
-        // so is not really that important, and has to be true or else
-        // getFeatures is never called (BaseAdapter filters it out)
+        // determining this properly is basically a call to getFeatures so is not
+        // really that important, and has to be true or else getFeatures is never
+        // called (BaseAdapter filters it out)
         return true;
     }
     getAssemblyNames() {

package/esm/PAFAdapter/configSchema.js

@@ -10,7 +10,7 @@ const PAFAdapter = ConfigurationSchema('PAFAdapter', {
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
-        description: 'Array of assembly names to use for this file. The target assembly name is the first value in the array, query assembly name is the second',
+        description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
     /**
      * #slot

package/esm/PAFAdapter/util.d.ts

@@ -9,7 +9,7 @@ export interface PAFRecord {
     extra: {
         cg?: string;
         blockLen?: number;
-        mappingQual: number;
+        mappingQual?: number;
         numMatches?: number;
         meanScore?: number;
     };

package/esm/PAFAdapter/util.js

@@ -42,7 +42,7 @@ export function getWeightedMeans(ret) {
         if (!scoreMap[key]) {
             scoreMap[key] = { quals: [], len: [] };
         }
-        scoreMap[key].quals.push(entry.extra.mappingQual);
+        scoreMap[key].quals.push(entry.extra.mappingQual || 1);
         scoreMap[key].len.push(entry.extra.blockLen || 1);
     }
     const meanScoreMap = Object.fromEntries(Object.entries(scoreMap).map(([key, val]) => {

package/esm/PairwiseIndexedPAFAdapter/configSchema.js

@@ -11,7 +11,7 @@ const PairwiseIndexedPAFAdapter = ConfigurationSchema('PairwiseIndexedPAFAdapter
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
-        description: 'Array of assembly names to use for this file. The target assembly name is the first value in the array, query assembly name is the second',
+        description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
     /**
      * #slot

package/esm/index.js

@@ -6,6 +6,7 @@ import MCScanSimpleAnchorsAdapterF from './MCScanSimpleAnchorsAdapter';
 import MashMapAdapterF from './MashMapAdapter';
 import DeltaAdapterF from './DeltaAdapter';
 import ChainAdapterF from './ChainAdapter';
+import BlastTabularAdapter from './BlastTabularAdapter';
 import { getFileName, } from '@jbrowse/core/util/tracks';
 export default class ComparativeAdaptersPlugin extends Plugin {
     constructor() {
@@ -20,6 +21,7 @@ export default class ComparativeAdaptersPlugin extends Plugin {
         MCScanAnchorsAdapterF(pluginManager);
         MCScanSimpleAnchorsAdapterF(pluginManager);
         MashMapAdapterF(pluginManager);
+        BlastTabularAdapter(pluginManager);
         pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
             return (file, index, adapterHint) => {
                 const regexGuess = /\.paf/i;

package/esm/util.d.ts

@@ -12,7 +12,7 @@ export declare function parseBed(text: string): Map<string | undefined, {
 }>;
 export declare function readFile(file: GenericFilehandle, opts?: BaseOptions): Promise<string>;
 export declare function zip(a: number[], b: number[]): [number, number][];
-export declare function parseLineByLine(buffer: Buffer, cb: (line: string) => PAFRecord): PAFRecord[];
+export declare function parseLineByLine<T>(buffer: Buffer, cb: (line: string) => T | undefined): T[];
 export declare function parsePAFLine(line: string): PAFRecord;
 export declare function flipCigar(cigar: string[]): (string | undefined)[];
 export declare function swapIndelCigar(cigar: string): string;

package/esm/util.js

@@ -1,5 +1,4 @@
-import { unzip } from '@gmod/bgzf-filehandle';
-import { isGzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 export function parseBed(text) {
     return new Map(text
         .split(/\n|\r\n|\r/)
@@ -20,25 +19,29 @@ export function parseBed(text) {
     }));
 }
 export async function readFile(file, opts) {
-    const buffer = (await file.readFile(opts));
-    return new TextDecoder('utf8', { fatal: true }).decode(isGzip(buffer) ? await unzip(buffer) : buffer);
+    const buf = await fetchAndMaybeUnzip(file, opts);
+    const decoder = new TextDecoder('utf8');
+    return decoder.decode(buf);
 }
 export function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
 }
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 export function parseLineByLine(buffer, cb) {
     let blockStart = 0;
     const entries = [];
+    const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
         const n = buffer.indexOf('\n', blockStart);
         if (n === -1) {
             break;
         }
         const b = buffer.subarray(blockStart, n);
-        const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+        const line = decoder.decode(b).trim();
         if (line) {
-            entries.push(cb(line));
+            const entry = cb(line);
+            if (entry) {
+                entries.push(entry);
+            }
         }
         blockStart = n + 1;
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "2.16.0",
+  "version": "2.17.0",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }