@jbrowse/plugin-comparative-adapters 3.0.2 → 3.0.4

package/dist/BlastTabularAdapter/BlastTabularAdapter.js

@@ -87,7 +87,7 @@ class BlastTabularAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const buf = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)((0, configuration_1.readConfObject)(this.config, 'blastTableLocation'), pm), opts);
         const columns = (0, configuration_1.readConfObject)(this.config, 'columns');
-        return (0, util_2.parseLineByLine)(buf, createBlastLineParser(columns));
+        return (0, util_2.parseLineByLine)(buf, createBlastLineParser(columns), opts);
     }
     async hasDataForRefName() {
         return true;

package/dist/ChainAdapter/util.d.ts

@@ -1,4 +1,5 @@
-export declare function paf_chain2paf(buffer: Uint8Array): {
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+export declare function paf_chain2paf(buffer: Uint8Array, opts?: BaseOptions): {
     qname: string;
     qstart: number;
     qend: number;

package/dist/ChainAdapter/util.js

@@ -18,7 +18,8 @@ function generate_record(qname, qstart, qend, qstrand, tname, tstart, tend, ciga
         },
     };
 }
-function paf_chain2paf(buffer) {
+function paf_chain2paf(buffer, opts) {
+    const { statusCallback = () => { } } = opts || {};
     let t_name = '';
     let t_start = 0;
     let t_end = 0;
@@ -30,9 +31,13 @@ function paf_chain2paf(buffer) {
     let num_matches = 0;
     let cigar = '';
     const records = [];
+    let i = 0;
     let blockStart = 0;
     const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
+        if (i++ % 10000 === 0) {
+            statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
+        }
         const n = buffer.indexOf(10, blockStart);
         if (n === -1) {
             break;

package/dist/DeltaAdapter/util.d.ts

@@ -1,4 +1,5 @@
-export declare function paf_delta2paf(buffer: Uint8Array): {
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter/BaseOptions';
+export declare function paf_delta2paf(buffer: Uint8Array, opts?: BaseOptions): {
     qname: string;
     qstart: number;
     qend: number;

package/dist/DeltaAdapter/util.js

@@ -1,7 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.paf_delta2paf = paf_delta2paf;
-function paf_delta2paf(buffer) {
+function paf_delta2paf(buffer, opts) {
+    const { statusCallback = () => { } } = opts || {};
     let rname = '';
     let qname = '';
     let qs = 0;
@@ -18,8 +19,12 @@ function paf_delta2paf(buffer) {
     const regex = new RegExp(/^>(\S+)\s+(\S+)\s+(\d+)\s+(\d+)/);
     let blockStart = 0;
     let i = 0;
+    let j = 0;
     const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
+        if (j++ % 10000 === 0) {
+            statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
+        }
         const n = buffer.indexOf(10, blockStart);
         if (n === -1) {
             break;

package/dist/MashMapAdapter/MashMapAdapter.js

@@ -11,7 +11,7 @@ class MashMapAdapter extends PAFAdapter_1.default {
     async setupPre(opts) {
         const outLoc = (0, io_1.openLocation)(this.getConf('outLocation'), this.pluginManager);
         const buf = await (0, util_1.fetchAndMaybeUnzip)(outLoc, opts);
-        return (0, util_2.parseLineByLine)(buf, parseMashMapLine);
+        return (0, util_2.parseLineByLine)(buf, parseMashMapLine, opts);
     }
 }
 exports.default = MashMapAdapter;

package/dist/PAFAdapter/PAFAdapter.js

@@ -28,7 +28,7 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const pafLocation = (0, io_1.openLocation)(this.getConf('pafLocation'), pm);
         const buf = await (0, util_1.fetchAndMaybeUnzip)(pafLocation, opts);
-        return (0, util_2.parseLineByLine)(buf, util_2.parsePAFLine);
+        return (0, util_2.parseLineByLine)(buf, util_2.parsePAFLine, opts);
     }
     async hasDataForRefName() {
         return true;

package/dist/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -5,10 +5,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const tabix_1 = require("@gmod/tabix");
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const SyntenyFeature_1 = __importDefault(require("../SyntenyFeature"));
-const util_1 = require("../util");
+const util_2 = require("../util");
 class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -58,15 +59,16 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }
     }
     getFeatures(query, opts = {}) {
+        const { statusCallback = () => { } } = opts;
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { assemblyName } = query;
             const assemblyNames = this.getAssemblyNames();
             const index = assemblyNames.indexOf(assemblyName);
             const flip = index === 0;
             const letter = flip ? 'q' : 't';
-            await this.pif.getLines(letter + query.refName, query.start, query.end, {
+            await (0, util_1.updateStatus)('Downloading features', statusCallback, () => this.pif.getLines(letter + query.refName, query.start, query.end, {
                 lineCallback: (line, fileOffset) => {
-                    const r = (0, util_1.parsePAFLine)(line);
+                    const r = (0, util_2.parsePAFLine)(line);
                     const refName = r.qname.slice(1);
                     const start = r.qstart;
                     const end = r.qend;
@@ -98,7 +100,7 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     }));
                 },
                 stopToken: opts.stopToken,
-            });
+            }));
             observer.complete();
         });
     }

package/dist/util.d.ts

@@ -11,7 +11,7 @@ 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<T>(buffer: Uint8Array, cb: (line: string) => T | undefined): T[];
+export declare function parseLineByLine<T>(buffer: Uint8Array, cb: (line: string) => T | undefined, opts?: BaseOptions): T[];
 export declare function parsePAFLine(line: string): PAFRecord;
 export declare function flipCigar(cigar: string[]): (string | undefined)[];
 export declare function swapIndelCigar(cigar: string): string;

package/dist/util.js

@@ -33,10 +33,12 @@ async function readFile(file, opts) {
 function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
 }
-function parseLineByLine(buffer, cb) {
+function parseLineByLine(buffer, cb, opts) {
+    const { statusCallback = () => { } } = opts || {};
     let blockStart = 0;
     const entries = [];
     const decoder = new TextDecoder('utf8');
+    let i = 0;
     while (blockStart < buffer.length) {
         const n = buffer.indexOf(10, blockStart);
         if (n === -1) {
@@ -50,32 +52,36 @@ function parseLineByLine(buffer, cb) {
                 entries.push(entry);
             }
         }
+        if (i++ % 10000 === 0) {
+            statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
+        }
         blockStart = n + 1;
     }
     return entries;
 }
 function parsePAFLine(line) {
-    const [qname, , qstart, qend, strand, tname, , tstart, tend, numMatches, blockLen, mappingQual, ...fields] = line.split('\t');
-    const rest = Object.fromEntries(fields.map(field => {
-        const r = field.indexOf(':');
-        const fieldName = field.slice(0, r);
-        const fieldValue = field.slice(r + 3);
-        return [fieldName, fieldValue];
-    }));
+    const parts = line.split('\t');
+    const extraFields = parts.slice(12);
+    const extra = {
+        numMatches: +parts[9],
+        blockLen: +parts[10],
+        mappingQual: +parts[11],
+    };
+    if (extraFields.length) {
+        for (const field of extraFields) {
+            const colonIndex = field.indexOf(':');
+            extra[field.slice(0, colonIndex)] = field.slice(colonIndex + 3);
+        }
+    }
     return {
-        tname,
-        tstart: +tstart,
-        tend: +tend,
-        qname,
-        qstart: +qstart,
-        qend: +qend,
-        strand: strand === '-' ? -1 : 1,
-        extra: {
-            numMatches: +numMatches,
-            blockLen: +blockLen,
-            mappingQual: +mappingQual,
-            ...rest,
-        },
+        tname: parts[5],
+        tstart: +parts[7],
+        tend: +parts[8],
+        qname: parts[0],
+        qstart: +parts[2],
+        qend: +parts[3],
+        strand: parts[4] === '-' ? -1 : 1,
+        extra,
     };
 }
 function flipCigar(cigar) {

package/esm/BlastTabularAdapter/BlastTabularAdapter.js

@@ -82,7 +82,7 @@ class BlastTabularAdapter extends BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const buf = await fetchAndMaybeUnzip(openLocation(readConfObject(this.config, 'blastTableLocation'), pm), opts);
         const columns = readConfObject(this.config, 'columns');
-        return parseLineByLine(buf, createBlastLineParser(columns));
+        return parseLineByLine(buf, createBlastLineParser(columns), opts);
     }
     async hasDataForRefName() {
         return true;

package/esm/ChainAdapter/util.d.ts

@@ -1,4 +1,5 @@
-export declare function paf_chain2paf(buffer: Uint8Array): {
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+export declare function paf_chain2paf(buffer: Uint8Array, opts?: BaseOptions): {
     qname: string;
     qstart: number;
     qend: number;

package/esm/ChainAdapter/util.js

@@ -15,7 +15,8 @@ function generate_record(qname, qstart, qend, qstrand, tname, tstart, tend, ciga
         },
     };
 }
-export function paf_chain2paf(buffer) {
+export function paf_chain2paf(buffer, opts) {
+    const { statusCallback = () => { } } = opts || {};
     let t_name = '';
     let t_start = 0;
     let t_end = 0;
@@ -27,9 +28,13 @@ export function paf_chain2paf(buffer) {
     let num_matches = 0;
     let cigar = '';
     const records = [];
+    let i = 0;
     let blockStart = 0;
     const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
+        if (i++ % 10000 === 0) {
+            statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
+        }
         const n = buffer.indexOf(10, blockStart);
         if (n === -1) {
             break;

package/esm/DeltaAdapter/util.d.ts

@@ -1,4 +1,5 @@
-export declare function paf_delta2paf(buffer: Uint8Array): {
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter/BaseOptions';
+export declare function paf_delta2paf(buffer: Uint8Array, opts?: BaseOptions): {
     qname: string;
     qstart: number;
     qend: number;

package/esm/DeltaAdapter/util.js

@@ -1,4 +1,5 @@
-export function paf_delta2paf(buffer) {
+export function paf_delta2paf(buffer, opts) {
+    const { statusCallback = () => { } } = opts || {};
     let rname = '';
     let qname = '';
     let qs = 0;
@@ -15,8 +16,12 @@ export function paf_delta2paf(buffer) {
     const regex = new RegExp(/^>(\S+)\s+(\S+)\s+(\d+)\s+(\d+)/);
     let blockStart = 0;
     let i = 0;
+    let j = 0;
     const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
+        if (j++ % 10000 === 0) {
+            statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
+        }
         const n = buffer.indexOf(10, blockStart);
         if (n === -1) {
             break;

package/esm/MashMapAdapter/MashMapAdapter.js

@@ -6,7 +6,7 @@ export default class MashMapAdapter extends PAFAdapter {
     async setupPre(opts) {
         const outLoc = openLocation(this.getConf('outLocation'), this.pluginManager);
         const buf = await fetchAndMaybeUnzip(outLoc, opts);
-        return parseLineByLine(buf, parseMashMapLine);
+        return parseLineByLine(buf, parseMashMapLine, opts);
     }
 }
 function parseMashMapLine(line) {

package/esm/PAFAdapter/PAFAdapter.js

@@ -23,7 +23,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const pafLocation = openLocation(this.getConf('pafLocation'), pm);
         const buf = await fetchAndMaybeUnzip(pafLocation, opts);
-        return parseLineByLine(buf, parsePAFLine);
+        return parseLineByLine(buf, parsePAFLine, opts);
     }
     async hasDataForRefName() {
         return true;

package/esm/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -1,5 +1,6 @@
 import { TabixIndexedFile } from '@gmod/tabix';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SyntenyFeature from '../SyntenyFeature';
@@ -53,13 +54,14 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         }
     }
     getFeatures(query, opts = {}) {
+        const { statusCallback = () => { } } = opts;
         return ObservableCreate(async (observer) => {
             const { assemblyName } = query;
             const assemblyNames = this.getAssemblyNames();
             const index = assemblyNames.indexOf(assemblyName);
             const flip = index === 0;
             const letter = flip ? 'q' : 't';
-            await this.pif.getLines(letter + query.refName, query.start, query.end, {
+            await updateStatus('Downloading features', statusCallback, () => this.pif.getLines(letter + query.refName, query.start, query.end, {
                 lineCallback: (line, fileOffset) => {
                     const r = parsePAFLine(line);
                     const refName = r.qname.slice(1);
@@ -93,7 +95,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
                     }));
                 },
                 stopToken: opts.stopToken,
-            });
+            }));
             observer.complete();
         });
     }

package/esm/util.d.ts

@@ -11,7 +11,7 @@ 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<T>(buffer: Uint8Array, cb: (line: string) => T | undefined): T[];
+export declare function parseLineByLine<T>(buffer: Uint8Array, cb: (line: string) => T | undefined, opts?: BaseOptions): 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

@@ -24,10 +24,12 @@ export async function readFile(file, opts) {
 export function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
 }
-export function parseLineByLine(buffer, cb) {
+export function parseLineByLine(buffer, cb, opts) {
+    const { statusCallback = () => { } } = opts || {};
     let blockStart = 0;
     const entries = [];
     const decoder = new TextDecoder('utf8');
+    let i = 0;
     while (blockStart < buffer.length) {
         const n = buffer.indexOf(10, blockStart);
         if (n === -1) {
@@ -41,32 +43,36 @@ export function parseLineByLine(buffer, cb) {
                 entries.push(entry);
             }
         }
+        if (i++ % 10000 === 0) {
+            statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
+        }
         blockStart = n + 1;
     }
     return entries;
 }
 export function parsePAFLine(line) {
-    const [qname, , qstart, qend, strand, tname, , tstart, tend, numMatches, blockLen, mappingQual, ...fields] = line.split('\t');
-    const rest = Object.fromEntries(fields.map(field => {
-        const r = field.indexOf(':');
-        const fieldName = field.slice(0, r);
-        const fieldValue = field.slice(r + 3);
-        return [fieldName, fieldValue];
-    }));
+    const parts = line.split('\t');
+    const extraFields = parts.slice(12);
+    const extra = {
+        numMatches: +parts[9],
+        blockLen: +parts[10],
+        mappingQual: +parts[11],
+    };
+    if (extraFields.length) {
+        for (const field of extraFields) {
+            const colonIndex = field.indexOf(':');
+            extra[field.slice(0, colonIndex)] = field.slice(colonIndex + 3);
+        }
+    }
     return {
-        tname,
-        tstart: +tstart,
-        tend: +tend,
-        qname,
-        qstart: +qstart,
-        qend: +qend,
-        strand: strand === '-' ? -1 : 1,
-        extra: {
-            numMatches: +numMatches,
-            blockLen: +blockLen,
-            mappingQual: +mappingQual,
-            ...rest,
-        },
+        tname: parts[5],
+        tstart: +parts[7],
+        tend: +parts[8],
+        qname: parts[0],
+        qstart: +parts[2],
+        qend: +parts[3],
+        strand: parts[4] === '-' ? -1 : 1,
+        extra,
     };
 }
 export function flipCigar(cigar) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "3.0.2",
+  "version": "3.0.4",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -38,9 +38,9 @@
   "dependencies": {
     "@gmod/bgzf-filehandle": "^2.0.1",
     "@gmod/tabix": "^2.0.0",
-    "@jbrowse/core": "^3.0.2",
-    "@jbrowse/plugin-alignments": "^3.0.2",
-    "@jbrowse/plugin-linear-genome-view": "^3.0.2",
+    "@jbrowse/core": "^3.0.4",
+    "@jbrowse/plugin-alignments": "^3.0.4",
+    "@jbrowse/plugin-linear-genome-view": "^3.0.4",
     "@mui/material": "^6.0.0",
     "generic-filehandle2": "^1.0.0",
     "mobx": "^6.0.0",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c01a35edcb2612e94661af8793f09c95c0b13c75"
+  "gitHead": "61e6d26f83acbf58a946c2add3415bc46b878df9"
 }