@jbrowse/plugin-comparative-adapters 3.6.2 → 3.6.4

package/dist/BlastTabularAdapter/BlastTabularAdapter.js

@@ -7,9 +7,9 @@ const configuration_1 = require("@jbrowse/core/configuration");
 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 parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const SyntenyFeature_1 = __importDefault(require("../SyntenyFeature"));
-const util_2 = require("../util");
 function createBlastLineParser(columns) {
     const columnNames = columns.trim().split(' ');
     const qseqidIndex = columnNames.indexOf('qseqid');
@@ -85,7 +85,16 @@ class BlastTabularAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async setup(opts) {
         const columns = (0, configuration_1.readConfObject)(this.config, 'columns');
-        return (0, util_2.parseLineByLine)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)((0, configuration_1.readConfObject)(this.config, 'blastTableLocation'), this.pluginManager), opts), createBlastLineParser(columns), opts);
+        const lines = [];
+        const cb = createBlastLineParser(columns);
+        (0, parseLineByLine_1.parseLineByLine)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)((0, configuration_1.readConfObject)(this.config, 'blastTableLocation'), this.pluginManager), opts), line => {
+            const res = cb(line);
+            if (res) {
+                lines.push(res);
+            }
+            return true;
+        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
+        return lines;
     }
     async hasDataForRefName() {
         return true;

package/dist/ChainAdapter/util.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.paf_chain2paf = paf_chain2paf;
-const util_1 = require("@jbrowse/core/util");
+const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
 function generate_record(qname, qstart, qend, qstrand, tname, tstart, tend, cigar, numMatches) {
     return {
         qname,
@@ -32,24 +32,9 @@ function paf_chain2paf(buffer, opts) {
     let num_matches = 0;
     let cigar = '';
     const records = [];
-    let blockStart = 0;
-    const decoder = new TextDecoder('utf8');
-    let s = performance.now();
-    let i = 0;
-    while (blockStart < buffer.length) {
-        if (i++ % 10000 === 0 && performance.now() - s > 50) {
-            statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
-            s = performance.now();
-        }
-        const n = buffer.indexOf(10, blockStart);
-        if (n === -1) {
-            break;
-        }
-        const b = buffer.subarray(blockStart, n);
-        const line = decoder.decode(b).trim();
-        blockStart = n + 1;
+    (0, parseLineByLine_1.parseLineByLine)(buffer, line => {
         if (!line || line.startsWith('#')) {
-            continue;
+            return true;
         }
         const l_vec = line.split(/[ \t]+/);
         if (l_vec[0] === 'chain') {
@@ -87,7 +72,8 @@ function paf_chain2paf(buffer, opts) {
                 cigar += `${diff_in_target}D`;
             }
         }
-    }
+        return true;
+    }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
     if (cigar) {
         generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches);
     }

package/dist/DeltaAdapter/DeltaAdapter.d.ts

@@ -9,12 +9,6 @@ export default class DeltaAdapter extends PAFAdapter {
         tstart: number;
         tend: number;
         strand: number;
-        extra: {
-            numMatches: number;
-            blockLen: number;
-            mappingQual: number;
-            NM: number;
-            cg: string;
-        };
+        extra: Record<string, unknown>;
     }[]>;
 }

package/dist/DeltaAdapter/util.d.ts

@@ -7,11 +7,5 @@ export declare function paf_delta2paf(buffer: Uint8Array, opts?: BaseOptions): {
     tstart: number;
     tend: number;
     strand: number;
-    extra: {
-        numMatches: number;
-        blockLen: number;
-        mappingQual: number;
-        NM: number;
-        cg: string;
-    };
+    extra: Record<string, unknown>;
 }[];

package/dist/DeltaAdapter/util.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.paf_delta2paf = paf_delta2paf;
-const util_1 = require("@jbrowse/core/util");
+const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
 function paf_delta2paf(buffer, opts) {
     const { statusCallback = () => { } } = opts || {};
     let rname = '';
@@ -18,113 +18,94 @@ function paf_delta2paf(buffer, opts) {
     let seen_gt = false;
     const records = [];
     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');
-    let s = performance.now();
-    while (blockStart < buffer.length) {
-        if (j++ % 10000 === 0 && performance.now() - s > 50) {
-            statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
-            s = performance.now();
+    (0, parseLineByLine_1.parseLineByLine)(buffer, line => {
+        const m = regex.exec(line);
+        if (m !== null) {
+            rname = m[1];
+            qname = m[2];
+            seen_gt = true;
+            return true;
         }
-        const n = buffer.indexOf(10, blockStart);
-        if (n === -1) {
-            break;
+        if (!seen_gt) {
+            return true;
         }
-        const b = buffer.subarray(blockStart, n);
-        const line = decoder.decode(b).trim();
-        blockStart = n + 1;
-        i++;
-        if (line) {
-            const m = regex.exec(line);
-            if (m !== null) {
-                rname = m[1];
-                qname = m[2];
-                seen_gt = true;
-                continue;
-            }
-            if (!seen_gt) {
-                continue;
+        const t = line.split(' ');
+        if (t.length === 7) {
+            const t0 = +t[0];
+            const t1 = +t[1];
+            const t2 = +t[2];
+            const t3 = +t[3];
+            const t4 = +t[4];
+            strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1;
+            rs = +Math.min(t0, t1) - 1;
+            re = +Math.max(t1, t0);
+            qs = +Math.min(t2, t3) - 1;
+            qe = +Math.max(t3, t2);
+            x = y = 0;
+            NM = t4;
+            cigar = [];
+        }
+        else if (t.length === 1) {
+            const d = +t[0];
+            if (d === 0) {
+                let blen = 0;
+                const cigar_str = [];
+                if (re - rs - x !== qe - qs - y) {
+                    throw new Error(`inconsistent alignment on line ${line}`);
+                }
+                cigar.push((re - rs - x) << 4);
+                for (const entry of cigar) {
+                    const rlen = entry >> 4;
+                    blen += rlen;
+                    cigar_str.push(rlen + 'MID'.charAt(entry & 0xf));
+                }
+                records.push({
+                    qname,
+                    qstart: qs,
+                    qend: qe,
+                    tname: rname,
+                    tstart: rs,
+                    tend: re,
+                    strand,
+                    extra: {
+                        numMatches: blen - NM,
+                        blockLen: blen,
+                        mappingQual: 0,
+                        NM,
+                        cg: cigar_str.join(''),
+                    },
+                });
             }
-            const t = line.split(' ');
-            if (t.length === 7) {
-                const t0 = +t[0];
-                const t1 = +t[1];
-                const t2 = +t[2];
-                const t3 = +t[3];
-                const t4 = +t[4];
-                strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1;
-                rs = +Math.min(t0, t1) - 1;
-                re = +Math.max(t1, t0);
-                qs = +Math.min(t2, t3) - 1;
-                qe = +Math.max(t3, t2);
-                x = y = 0;
-                NM = t4;
-                cigar = [];
+            else if (d > 0) {
+                const l = d - 1;
+                x += l + 1;
+                y += l;
+                if (l > 0) {
+                    cigar.push(l << 4);
+                }
+                if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 2) {
+                    cigar[cigar.length - 1] += 1 << 4;
+                }
+                else {
+                    cigar.push((1 << 4) | 2);
+                }
             }
-            else if (t.length === 1) {
-                const d = +t[0];
-                if (d === 0) {
-                    let blen = 0;
-                    const cigar_str = [];
-                    if (re - rs - x !== qe - qs - y) {
-                        throw new Error(`inconsistent alignment on line ${i}`);
-                    }
-                    cigar.push((re - rs - x) << 4);
-                    for (const entry of cigar) {
-                        const rlen = entry >> 4;
-                        blen += rlen;
-                        cigar_str.push(rlen + 'MID'.charAt(cigar[i] & 0xf));
-                    }
-                    records.push({
-                        qname,
-                        qstart: qs,
-                        qend: qe,
-                        tname: rname,
-                        tstart: rs,
-                        tend: re,
-                        strand,
-                        extra: {
-                            numMatches: blen - NM,
-                            blockLen: blen,
-                            mappingQual: 0,
-                            NM,
-                            cg: cigar_str.join(''),
-                        },
-                    });
+            else {
+                const l = -d - 1;
+                x += l;
+                y += l + 1;
+                if (l > 0) {
+                    cigar.push(l << 4);
                 }
-                else if (d > 0) {
-                    const l = d - 1;
-                    x += l + 1;
-                    y += l;
-                    if (l > 0) {
-                        cigar.push(l << 4);
-                    }
-                    if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 2) {
-                        cigar[cigar.length - 1] += 1 << 4;
-                    }
-                    else {
-                        cigar.push((1 << 4) | 2);
-                    }
+                if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 1) {
+                    cigar[cigar.length - 1] += 1 << 4;
                 }
                 else {
-                    const l = -d - 1;
-                    x += l;
-                    y += l + 1;
-                    if (l > 0) {
-                        cigar.push(l << 4);
-                    }
-                    if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 1) {
-                        cigar[cigar.length - 1] += 1 << 4;
-                    }
-                    else {
-                        cigar.push((1 << 4) | 1);
-                    }
+                    cigar.push((1 << 4) | 1);
                 }
             }
         }
-    }
-    statusCallback('');
+        return true;
+    }, statusCallback);
     return records;
 }

package/dist/MashMapAdapter/MashMapAdapter.js

@@ -5,11 +5,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
+const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
 const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
-const util_2 = require("../util");
 class MashMapAdapter extends PAFAdapter_1.default {
     async setupPre(opts) {
-        return (0, util_2.parseLineByLine)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('outLocation'), this.pluginManager), opts), parseMashMapLine, opts);
+        const lines = [];
+        (0, parseLineByLine_1.parseLineByLine)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('outLocation'), this.pluginManager), opts), line => {
+            lines.push(parseMashMapLine(line));
+            return true;
+        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
+        return lines;
     }
 }
 exports.default = MashMapAdapter;

package/dist/PAFAdapter/PAFAdapter.js

@@ -7,6 +7,7 @@ const configuration_1 = require("@jbrowse/core/configuration");
 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 parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
 const range_1 = require("@jbrowse/core/util/range");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
@@ -25,7 +26,12 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return this.setupP;
     }
     async setupPre(opts) {
-        return (0, util_2.parseLineByLine)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('pafLocation'), this.pluginManager), opts), util_2.parsePAFLine, opts);
+        const lines = [];
+        (0, parseLineByLine_1.parseLineByLine)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('pafLocation'), this.pluginManager), opts), line => {
+            lines.push((0, util_2.parsePAFLine)(line));
+            return true;
+        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
+        return lines;
     }
     async hasDataForRefName() {
         return true;

package/dist/util.d.ts

@@ -11,7 +11,6 @@ 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, 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

@@ -3,7 +3,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseBed = parseBed;
 exports.readFile = readFile;
 exports.zip = zip;
-exports.parseLineByLine = parseLineByLine;
 exports.parsePAFLine = parsePAFLine;
 exports.flipCigar = flipCigar;
 exports.swapIndelCigar = swapIndelCigar;
@@ -33,35 +32,6 @@ async function readFile(file, opts) {
 function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
 }
-function parseLineByLine(buffer, cb, opts) {
-    const { statusCallback = () => { } } = opts || {};
-    let blockStart = 0;
-    const entries = [];
-    const decoder = new TextDecoder('utf8');
-    let i = 0;
-    let s = performance.now();
-    while (blockStart < buffer.length) {
-        const n = buffer.indexOf(10, blockStart);
-        if (n === -1) {
-            break;
-        }
-        const b = buffer.subarray(blockStart, n);
-        const line = decoder.decode(b).trim();
-        if (line) {
-            const entry = cb(line);
-            if (entry) {
-                entries.push(entry);
-            }
-        }
-        if (i++ % 10000 === 0 && performance.now() - s > 50) {
-            statusCallback(`Loading ${(0, util_1.getProgressDisplayStr)(blockStart, buffer.length)}`);
-            s = performance.now();
-        }
-        blockStart = n + 1;
-    }
-    statusCallback('');
-    return entries;
-}
 function parsePAFLine(line) {
     const parts = line.split('\t');
     const extraFields = parts.slice(12);

package/esm/BlastTabularAdapter/BlastTabularAdapter.js

@@ -2,9 +2,9 @@ import { readConfObject } from '@jbrowse/core/configuration';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { doesIntersect2, fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
+import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SyntenyFeature from '../SyntenyFeature';
-import { parseLineByLine } from '../util';
 function createBlastLineParser(columns) {
     const columnNames = columns.trim().split(' ');
     const qseqidIndex = columnNames.indexOf('qseqid');
@@ -80,7 +80,16 @@ class BlastTabularAdapter extends BaseFeatureDataAdapter {
     }
     async setup(opts) {
         const columns = readConfObject(this.config, 'columns');
-        return parseLineByLine(await fetchAndMaybeUnzip(openLocation(readConfObject(this.config, 'blastTableLocation'), this.pluginManager), opts), createBlastLineParser(columns), opts);
+        const lines = [];
+        const cb = createBlastLineParser(columns);
+        parseLineByLine(await fetchAndMaybeUnzip(openLocation(readConfObject(this.config, 'blastTableLocation'), this.pluginManager), opts), line => {
+            const res = cb(line);
+            if (res) {
+                lines.push(res);
+            }
+            return true;
+        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
+        return lines;
     }
     async hasDataForRefName() {
         return true;

package/esm/ChainAdapter/util.js

@@ -1,4 +1,4 @@
-import { getProgressDisplayStr } from '@jbrowse/core/util';
+import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
 function generate_record(qname, qstart, qend, qstrand, tname, tstart, tend, cigar, numMatches) {
     return {
         qname,
@@ -29,24 +29,9 @@ export function paf_chain2paf(buffer, opts) {
     let num_matches = 0;
     let cigar = '';
     const records = [];
-    let blockStart = 0;
-    const decoder = new TextDecoder('utf8');
-    let s = performance.now();
-    let i = 0;
-    while (blockStart < buffer.length) {
-        if (i++ % 10000 === 0 && performance.now() - s > 50) {
-            statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
-            s = performance.now();
-        }
-        const n = buffer.indexOf(10, blockStart);
-        if (n === -1) {
-            break;
-        }
-        const b = buffer.subarray(blockStart, n);
-        const line = decoder.decode(b).trim();
-        blockStart = n + 1;
+    parseLineByLine(buffer, line => {
         if (!line || line.startsWith('#')) {
-            continue;
+            return true;
         }
         const l_vec = line.split(/[ \t]+/);
         if (l_vec[0] === 'chain') {
@@ -84,7 +69,8 @@ export function paf_chain2paf(buffer, opts) {
                 cigar += `${diff_in_target}D`;
             }
         }
-    }
+        return true;
+    }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
     if (cigar) {
         generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches);
     }

package/esm/DeltaAdapter/DeltaAdapter.d.ts

@@ -9,12 +9,6 @@ export default class DeltaAdapter extends PAFAdapter {
         tstart: number;
         tend: number;
         strand: number;
-        extra: {
-            numMatches: number;
-            blockLen: number;
-            mappingQual: number;
-            NM: number;
-            cg: string;
-        };
+        extra: Record<string, unknown>;
     }[]>;
 }

package/esm/DeltaAdapter/util.d.ts

@@ -7,11 +7,5 @@ export declare function paf_delta2paf(buffer: Uint8Array, opts?: BaseOptions): {
     tstart: number;
     tend: number;
     strand: number;
-    extra: {
-        numMatches: number;
-        blockLen: number;
-        mappingQual: number;
-        NM: number;
-        cg: string;
-    };
+    extra: Record<string, unknown>;
 }[];

package/esm/DeltaAdapter/util.js

@@ -1,4 +1,4 @@
-import { getProgressDisplayStr } from '@jbrowse/core/util';
+import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
 export function paf_delta2paf(buffer, opts) {
     const { statusCallback = () => { } } = opts || {};
     let rname = '';
@@ -15,113 +15,94 @@ export function paf_delta2paf(buffer, opts) {
     let seen_gt = false;
     const records = [];
     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');
-    let s = performance.now();
-    while (blockStart < buffer.length) {
-        if (j++ % 10000 === 0 && performance.now() - s > 50) {
-            statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
-            s = performance.now();
+    parseLineByLine(buffer, line => {
+        const m = regex.exec(line);
+        if (m !== null) {
+            rname = m[1];
+            qname = m[2];
+            seen_gt = true;
+            return true;
         }
-        const n = buffer.indexOf(10, blockStart);
-        if (n === -1) {
-            break;
+        if (!seen_gt) {
+            return true;
         }
-        const b = buffer.subarray(blockStart, n);
-        const line = decoder.decode(b).trim();
-        blockStart = n + 1;
-        i++;
-        if (line) {
-            const m = regex.exec(line);
-            if (m !== null) {
-                rname = m[1];
-                qname = m[2];
-                seen_gt = true;
-                continue;
-            }
-            if (!seen_gt) {
-                continue;
+        const t = line.split(' ');
+        if (t.length === 7) {
+            const t0 = +t[0];
+            const t1 = +t[1];
+            const t2 = +t[2];
+            const t3 = +t[3];
+            const t4 = +t[4];
+            strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1;
+            rs = +Math.min(t0, t1) - 1;
+            re = +Math.max(t1, t0);
+            qs = +Math.min(t2, t3) - 1;
+            qe = +Math.max(t3, t2);
+            x = y = 0;
+            NM = t4;
+            cigar = [];
+        }
+        else if (t.length === 1) {
+            const d = +t[0];
+            if (d === 0) {
+                let blen = 0;
+                const cigar_str = [];
+                if (re - rs - x !== qe - qs - y) {
+                    throw new Error(`inconsistent alignment on line ${line}`);
+                }
+                cigar.push((re - rs - x) << 4);
+                for (const entry of cigar) {
+                    const rlen = entry >> 4;
+                    blen += rlen;
+                    cigar_str.push(rlen + 'MID'.charAt(entry & 0xf));
+                }
+                records.push({
+                    qname,
+                    qstart: qs,
+                    qend: qe,
+                    tname: rname,
+                    tstart: rs,
+                    tend: re,
+                    strand,
+                    extra: {
+                        numMatches: blen - NM,
+                        blockLen: blen,
+                        mappingQual: 0,
+                        NM,
+                        cg: cigar_str.join(''),
+                    },
+                });
             }
-            const t = line.split(' ');
-            if (t.length === 7) {
-                const t0 = +t[0];
-                const t1 = +t[1];
-                const t2 = +t[2];
-                const t3 = +t[3];
-                const t4 = +t[4];
-                strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1;
-                rs = +Math.min(t0, t1) - 1;
-                re = +Math.max(t1, t0);
-                qs = +Math.min(t2, t3) - 1;
-                qe = +Math.max(t3, t2);
-                x = y = 0;
-                NM = t4;
-                cigar = [];
+            else if (d > 0) {
+                const l = d - 1;
+                x += l + 1;
+                y += l;
+                if (l > 0) {
+                    cigar.push(l << 4);
+                }
+                if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 2) {
+                    cigar[cigar.length - 1] += 1 << 4;
+                }
+                else {
+                    cigar.push((1 << 4) | 2);
+                }
             }
-            else if (t.length === 1) {
-                const d = +t[0];
-                if (d === 0) {
-                    let blen = 0;
-                    const cigar_str = [];
-                    if (re - rs - x !== qe - qs - y) {
-                        throw new Error(`inconsistent alignment on line ${i}`);
-                    }
-                    cigar.push((re - rs - x) << 4);
-                    for (const entry of cigar) {
-                        const rlen = entry >> 4;
-                        blen += rlen;
-                        cigar_str.push(rlen + 'MID'.charAt(cigar[i] & 0xf));
-                    }
-                    records.push({
-                        qname,
-                        qstart: qs,
-                        qend: qe,
-                        tname: rname,
-                        tstart: rs,
-                        tend: re,
-                        strand,
-                        extra: {
-                            numMatches: blen - NM,
-                            blockLen: blen,
-                            mappingQual: 0,
-                            NM,
-                            cg: cigar_str.join(''),
-                        },
-                    });
+            else {
+                const l = -d - 1;
+                x += l;
+                y += l + 1;
+                if (l > 0) {
+                    cigar.push(l << 4);
                 }
-                else if (d > 0) {
-                    const l = d - 1;
-                    x += l + 1;
-                    y += l;
-                    if (l > 0) {
-                        cigar.push(l << 4);
-                    }
-                    if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 2) {
-                        cigar[cigar.length - 1] += 1 << 4;
-                    }
-                    else {
-                        cigar.push((1 << 4) | 2);
-                    }
+                if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 1) {
+                    cigar[cigar.length - 1] += 1 << 4;
                 }
                 else {
-                    const l = -d - 1;
-                    x += l;
-                    y += l + 1;
-                    if (l > 0) {
-                        cigar.push(l << 4);
-                    }
-                    if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 1) {
-                        cigar[cigar.length - 1] += 1 << 4;
-                    }
-                    else {
-                        cigar.push((1 << 4) | 1);
-                    }
+                    cigar.push((1 << 4) | 1);
                 }
             }
         }
-    }
-    statusCallback('');
+        return true;
+    }, statusCallback);
     return records;
 }

package/esm/MashMapAdapter/MashMapAdapter.js

@@ -1,10 +1,15 @@
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
+import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
-import { parseLineByLine } from '../util';
 export default class MashMapAdapter extends PAFAdapter {
     async setupPre(opts) {
-        return parseLineByLine(await fetchAndMaybeUnzip(openLocation(this.getConf('outLocation'), this.pluginManager), opts), parseMashMapLine, opts);
+        const lines = [];
+        parseLineByLine(await fetchAndMaybeUnzip(openLocation(this.getConf('outLocation'), this.pluginManager), opts), line => {
+            lines.push(parseMashMapLine(line));
+            return true;
+        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
+        return lines;
     }
 }
 function parseMashMapLine(line) {

package/esm/PAFAdapter/PAFAdapter.js

@@ -2,11 +2,12 @@ import { readConfObject } from '@jbrowse/core/configuration';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
+import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
 import { doesIntersect2 } from '@jbrowse/core/util/range';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { MismatchParser } from '@jbrowse/plugin-alignments';
 import SyntenyFeature from '../SyntenyFeature';
-import { flipCigar, parseLineByLine, parsePAFLine, swapIndelCigar, } from '../util';
+import { flipCigar, parsePAFLine, swapIndelCigar } from '../util';
 import { getWeightedMeans } from './util';
 const { parseCigar } = MismatchParser;
 class PAFAdapter extends BaseFeatureDataAdapter {
@@ -20,7 +21,12 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         return this.setupP;
     }
     async setupPre(opts) {
-        return parseLineByLine(await fetchAndMaybeUnzip(openLocation(this.getConf('pafLocation'), this.pluginManager), opts), parsePAFLine, opts);
+        const lines = [];
+        parseLineByLine(await fetchAndMaybeUnzip(openLocation(this.getConf('pafLocation'), this.pluginManager), opts), line => {
+            lines.push(parsePAFLine(line));
+            return true;
+        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
+        return lines;
     }
     async hasDataForRefName() {
         return true;

package/esm/util.d.ts

@@ -11,7 +11,6 @@ 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, 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

@@ -1,4 +1,4 @@
-import { fetchAndMaybeUnzipText, getProgressDisplayStr, } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
 export function parseBed(text) {
     return new Map(text
         .split(/\n|\r\n|\r/)
@@ -24,35 +24,6 @@ export async function readFile(file, opts) {
 export function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
 }
-export function parseLineByLine(buffer, cb, opts) {
-    const { statusCallback = () => { } } = opts || {};
-    let blockStart = 0;
-    const entries = [];
-    const decoder = new TextDecoder('utf8');
-    let i = 0;
-    let s = performance.now();
-    while (blockStart < buffer.length) {
-        const n = buffer.indexOf(10, blockStart);
-        if (n === -1) {
-            break;
-        }
-        const b = buffer.subarray(blockStart, n);
-        const line = decoder.decode(b).trim();
-        if (line) {
-            const entry = cb(line);
-            if (entry) {
-                entries.push(entry);
-            }
-        }
-        if (i++ % 10000 === 0 && performance.now() - s > 50) {
-            statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
-            s = performance.now();
-        }
-        blockStart = n + 1;
-    }
-    statusCallback('');
-    return entries;
-}
 export function parsePAFLine(line) {
     const parts = line.split('\t');
     const extraFields = parts.slice(12);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "3.6.2",
+  "version": "3.6.4",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -38,9 +38,9 @@
   "dependencies": {
     "@gmod/bgzf-filehandle": "^4.0.0",
     "@gmod/tabix": "^3.0.1",
-    "@jbrowse/core": "^3.6.2",
-    "@jbrowse/plugin-alignments": "^3.6.2",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.2",
+    "@jbrowse/core": "^3.6.4",
+    "@jbrowse/plugin-alignments": "^3.6.4",
+    "@jbrowse/plugin-linear-genome-view": "^3.6.4",
     "@mui/material": "^7.0.0",
     "generic-filehandle2": "^2.0.1",
     "mobx": "^6.0.0",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "2a2c52face5f1b8fe899f48d5903e5c5f06dba63"
+  "gitHead": "3db8e50ce2bd9c081efbf6c2e7ae5f342380a25a"
 }