@jbrowse/plugin-comparative-adapters 3.3.0 → 3.5.0

package/dist/BlastTabularAdapter/BlastTabularAdapter.d.ts

@@ -61,6 +61,5 @@ export default class BlastTabularAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }
 export {};

package/dist/BlastTabularAdapter/BlastTabularAdapter.js

@@ -84,10 +84,8 @@ class BlastTabularAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return this.data;
     }
     async setup(opts) {
-        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), opts);
+        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);
     }
     async hasDataForRefName() {
         return true;
@@ -194,7 +192,6 @@ class BlastTabularAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 BlastTabularAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BlastTabularAdapter;

package/dist/ChainAdapter/ChainAdapter.js

@@ -9,9 +9,7 @@ const util_2 = require("./util");
 const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
 class ChainAdapter extends PAFAdapter_1.default {
     async setupPre(opts) {
-        const loc = (0, io_1.openLocation)(this.getConf('chainLocation'), this.pluginManager);
-        const buf = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
-        return (0, util_2.paf_chain2paf)(buf);
+        return (0, util_2.paf_chain2paf)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('chainLocation'), this.pluginManager), opts), opts);
     }
 }
 exports.default = ChainAdapter;

package/dist/ChainAdapter/util.js

@@ -32,22 +32,26 @@ function paf_chain2paf(buffer, opts) {
     let num_matches = 0;
     let cigar = '';
     const records = [];
-    let i = 0;
     let blockStart = 0;
     const decoder = new TextDecoder('utf8');
+    let s = performance.now();
+    let i = 0;
     while (blockStart < buffer.length) {
-        if (i++ % 10000 === 0) {
+        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 l = decoder.decode(b).trim();
+        const line = decoder.decode(b).trim();
         blockStart = n + 1;
-        const l_tab = l.replaceAll(' ', '\t');
-        const l_vec = l_tab.split('\t');
+        if (!line || line.startsWith('#')) {
+            continue;
+        }
+        const l_vec = line.split(/[ \t]+/);
         if (l_vec[0] === 'chain') {
             if (cigar) {
                 records.push(generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches));
@@ -87,5 +91,6 @@ function paf_chain2paf(buffer, opts) {
     if (cigar) {
         generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches);
     }
+    statusCallback('');
     return records;
 }

package/dist/DeltaAdapter/DeltaAdapter.js

@@ -9,9 +9,7 @@ const util_2 = require("./util");
 const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
 class DeltaAdapter extends PAFAdapter_1.default {
     async setupPre(opts) {
-        const loc = (0, io_1.openLocation)(this.getConf('deltaLocation'), this.pluginManager);
-        const buf = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
-        return (0, util_2.paf_delta2paf)(buf);
+        return (0, util_2.paf_delta2paf)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('deltaLocation'), this.pluginManager), opts), opts);
     }
 }
 exports.default = DeltaAdapter;

package/dist/DeltaAdapter/util.js

@@ -22,9 +22,11 @@ function paf_delta2paf(buffer, opts) {
     let i = 0;
     let j = 0;
     const decoder = new TextDecoder('utf8');
+    let s = performance.now();
     while (blockStart < buffer.length) {
-        if (j++ % 10000 === 0) {
+        if (j++ % 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) {
@@ -123,5 +125,6 @@ function paf_delta2paf(buffer, opts) {
             }
         }
     }
+    statusCallback('');
     return records;
 }

package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts

@@ -25,6 +25,5 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }
 export {};

package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -16,12 +16,13 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return this.setupP;
     }
     async setupPre(opts) {
+        const { statusCallback = () => { } } = opts;
         const assemblyNames = this.getConf('assemblyNames');
         const pm = this.pluginManager;
         const bed1 = (0, io_1.openLocation)(this.getConf('bed1Location'), pm);
         const bed2 = (0, io_1.openLocation)(this.getConf('bed2Location'), pm);
         const mcscan = (0, io_1.openLocation)(this.getConf('mcscanAnchorsLocation'), pm);
-        const [bed1text, bed2text, mcscantext] = await Promise.all([bed1, bed2, mcscan].map(r => (0, util_2.readFile)(r, opts)));
+        const [bed1text, bed2text, mcscantext] = await (0, util_1.updateStatus)('Downloading data', statusCallback, () => Promise.all([bed1, bed2, mcscan].map(r => (0, util_2.readFile)(r, opts))));
         const bed1Map = (0, util_2.parseBed)(bed1text);
         const bed2Map = (0, util_2.parseBed)(bed2text);
         const feats = mcscantext
@@ -92,7 +93,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = MCScanAnchorsAdapter;

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.d.ts

@@ -33,6 +33,5 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }
 export {};

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -20,12 +20,13 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return this.setupP;
     }
     async setupPre(opts) {
+        const { statusCallback = () => { } } = opts;
         const assemblyNames = this.getConf('assemblyNames');
         const pm = this.pluginManager;
         const bed1 = (0, io_1.openLocation)(this.getConf('bed1Location'), pm);
         const bed2 = (0, io_1.openLocation)(this.getConf('bed2Location'), pm);
         const mcscan = (0, io_1.openLocation)(this.getConf('mcscanSimpleAnchorsLocation'), pm);
-        const [bed1text, bed2text, mcscantext] = await Promise.all([bed1, bed2, mcscan].map(r => (0, util_2.readFile)(r, opts)));
+        const [bed1text, bed2text, mcscantext] = await (0, util_1.updateStatus)('Downloading data', statusCallback, () => Promise.all([bed1, bed2, mcscan].map(r => (0, util_2.readFile)(r, opts))));
         const bed1Map = (0, util_2.parseBed)(bed1text);
         const bed2Map = (0, util_2.parseBed)(bed2text);
         const feats = mcscantext
@@ -126,7 +127,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = MCScanAnchorsAdapter;

package/dist/MashMapAdapter/MashMapAdapter.js

@@ -9,9 +9,7 @@ const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
 const util_2 = require("../util");
 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, opts);
+        return (0, util_2.parseLineByLine)(await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('outLocation'), this.pluginManager), opts), parseMashMapLine, opts);
     }
 }
 exports.default = MashMapAdapter;

package/dist/PAFAdapter/PAFAdapter.d.ts

@@ -16,6 +16,5 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(query: Region, opts?: PAFOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }
 export {};

package/dist/PAFAdapter/PAFAdapter.js

@@ -25,10 +25,7 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return this.setupP;
     }
     async setupPre(opts) {
-        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, 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);
     }
     async hasDataForRefName() {
         return true;
@@ -134,7 +131,6 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = PAFAdapter;

package/dist/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.d.ts

@@ -20,6 +20,5 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
         regions?: Region[];
     }): Promise<string[]>;
     getFeatures(query: Region, opts?: PAFOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }
 export {};

package/dist/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -104,7 +104,6 @@ class PAFAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = PAFAdapter;

package/dist/util.js

@@ -39,6 +39,7 @@ function parseLineByLine(buffer, cb, opts) {
     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) {
@@ -52,11 +53,13 @@ function parseLineByLine(buffer, cb, opts) {
                 entries.push(entry);
             }
         }
-        if (i++ % 10000 === 0) {
+        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) {

package/esm/BlastTabularAdapter/BlastTabularAdapter.d.ts

@@ -61,6 +61,5 @@ export default class BlastTabularAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }
 export {};

package/esm/BlastTabularAdapter/BlastTabularAdapter.js

@@ -79,10 +79,8 @@ class BlastTabularAdapter extends BaseFeatureDataAdapter {
         return this.data;
     }
     async setup(opts) {
-        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), opts);
+        return parseLineByLine(await fetchAndMaybeUnzip(openLocation(readConfObject(this.config, 'blastTableLocation'), this.pluginManager), opts), createBlastLineParser(columns), opts);
     }
     async hasDataForRefName() {
         return true;
@@ -189,7 +187,6 @@ class BlastTabularAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 BlastTabularAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BlastTabularAdapter;

package/esm/ChainAdapter/ChainAdapter.js

@@ -4,8 +4,6 @@ import { paf_chain2paf } from './util';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
 export default class ChainAdapter extends PAFAdapter {
     async setupPre(opts) {
-        const loc = openLocation(this.getConf('chainLocation'), this.pluginManager);
-        const buf = await fetchAndMaybeUnzip(loc, opts);
-        return paf_chain2paf(buf);
+        return paf_chain2paf(await fetchAndMaybeUnzip(openLocation(this.getConf('chainLocation'), this.pluginManager), opts), opts);
     }
 }

package/esm/ChainAdapter/util.js

@@ -29,22 +29,26 @@ export function paf_chain2paf(buffer, opts) {
     let num_matches = 0;
     let cigar = '';
     const records = [];
-    let i = 0;
     let blockStart = 0;
     const decoder = new TextDecoder('utf8');
+    let s = performance.now();
+    let i = 0;
     while (blockStart < buffer.length) {
-        if (i++ % 10000 === 0) {
+        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 l = decoder.decode(b).trim();
+        const line = decoder.decode(b).trim();
         blockStart = n + 1;
-        const l_tab = l.replaceAll(' ', '\t');
-        const l_vec = l_tab.split('\t');
+        if (!line || line.startsWith('#')) {
+            continue;
+        }
+        const l_vec = line.split(/[ \t]+/);
         if (l_vec[0] === 'chain') {
             if (cigar) {
                 records.push(generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches));
@@ -84,5 +88,6 @@ export function paf_chain2paf(buffer, opts) {
     if (cigar) {
         generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches);
     }
+    statusCallback('');
     return records;
 }

package/esm/DeltaAdapter/DeltaAdapter.js

@@ -4,8 +4,6 @@ import { paf_delta2paf } from './util';
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
 export default class DeltaAdapter extends PAFAdapter {
     async setupPre(opts) {
-        const loc = openLocation(this.getConf('deltaLocation'), this.pluginManager);
-        const buf = await fetchAndMaybeUnzip(loc, opts);
-        return paf_delta2paf(buf);
+        return paf_delta2paf(await fetchAndMaybeUnzip(openLocation(this.getConf('deltaLocation'), this.pluginManager), opts), opts);
     }
 }

package/esm/DeltaAdapter/util.js

@@ -19,9 +19,11 @@ export function paf_delta2paf(buffer, opts) {
     let i = 0;
     let j = 0;
     const decoder = new TextDecoder('utf8');
+    let s = performance.now();
     while (blockStart < buffer.length) {
-        if (j++ % 10000 === 0) {
+        if (j++ % 10000 === 0 && performance.now() - s > 50) {
             statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
+            s = performance.now();
         }
         const n = buffer.indexOf(10, blockStart);
         if (n === -1) {
@@ -120,5 +122,6 @@ export function paf_delta2paf(buffer, opts) {
             }
         }
     }
+    statusCallback('');
     return records;
 }

package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts

@@ -25,6 +25,5 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }
 export {};

package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -1,5 +1,5 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { SimpleFeature, doesIntersect2 } from '@jbrowse/core/util';
+import { SimpleFeature, doesIntersect2, updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { parseBed, readFile } from '../util';
@@ -14,12 +14,13 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         return this.setupP;
     }
     async setupPre(opts) {
+        const { statusCallback = () => { } } = opts;
         const assemblyNames = this.getConf('assemblyNames');
         const pm = this.pluginManager;
         const bed1 = openLocation(this.getConf('bed1Location'), pm);
         const bed2 = openLocation(this.getConf('bed2Location'), pm);
         const mcscan = openLocation(this.getConf('mcscanAnchorsLocation'), pm);
-        const [bed1text, bed2text, mcscantext] = await Promise.all([bed1, bed2, mcscan].map(r => readFile(r, opts)));
+        const [bed1text, bed2text, mcscantext] = await updateStatus('Downloading data', statusCallback, () => Promise.all([bed1, bed2, mcscan].map(r => readFile(r, opts))));
         const bed1Map = parseBed(bed1text);
         const bed2Map = parseBed(bed2text);
         const feats = mcscantext
@@ -90,7 +91,6 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default MCScanAnchorsAdapter;

package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.d.ts

@@ -33,6 +33,5 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }
 export {};

package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -1,5 +1,5 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { doesIntersect2 } from '@jbrowse/core/util';
+import { doesIntersect2, updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
@@ -15,12 +15,13 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         return this.setupP;
     }
     async setupPre(opts) {
+        const { statusCallback = () => { } } = opts;
         const assemblyNames = this.getConf('assemblyNames');
         const pm = this.pluginManager;
         const bed1 = openLocation(this.getConf('bed1Location'), pm);
         const bed2 = openLocation(this.getConf('bed2Location'), pm);
         const mcscan = openLocation(this.getConf('mcscanSimpleAnchorsLocation'), pm);
-        const [bed1text, bed2text, mcscantext] = await Promise.all([bed1, bed2, mcscan].map(r => readFile(r, opts)));
+        const [bed1text, bed2text, mcscantext] = await updateStatus('Downloading data', statusCallback, () => Promise.all([bed1, bed2, mcscan].map(r => readFile(r, opts))));
         const bed1Map = parseBed(bed1text);
         const bed2Map = parseBed(bed2text);
         const feats = mcscantext
@@ -121,7 +122,6 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default MCScanAnchorsAdapter;

package/esm/MashMapAdapter/MashMapAdapter.js

@@ -4,9 +4,7 @@ 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 buf = await fetchAndMaybeUnzip(outLoc, opts);
-        return parseLineByLine(buf, parseMashMapLine, opts);
+        return parseLineByLine(await fetchAndMaybeUnzip(openLocation(this.getConf('outLocation'), this.pluginManager), opts), parseMashMapLine, opts);
     }
 }
 function parseMashMapLine(line) {

package/esm/PAFAdapter/PAFAdapter.d.ts

@@ -16,6 +16,5 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(query: Region, opts?: PAFOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }
 export {};

package/esm/PAFAdapter/PAFAdapter.js

@@ -20,10 +20,7 @@ class PAFAdapter extends BaseFeatureDataAdapter {
         return this.setupP;
     }
     async setupPre(opts) {
-        const pm = this.pluginManager;
-        const pafLocation = openLocation(this.getConf('pafLocation'), pm);
-        const buf = await fetchAndMaybeUnzip(pafLocation, opts);
-        return parseLineByLine(buf, parsePAFLine, opts);
+        return parseLineByLine(await fetchAndMaybeUnzip(openLocation(this.getConf('pafLocation'), this.pluginManager), opts), parsePAFLine, opts);
     }
     async hasDataForRefName() {
         return true;
@@ -129,7 +126,6 @@ class PAFAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default PAFAdapter;

package/esm/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.d.ts

@@ -20,6 +20,5 @@ export default class PAFAdapter extends BaseFeatureDataAdapter {
         regions?: Region[];
     }): Promise<string[]>;
     getFeatures(query: Region, opts?: PAFOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
 }
 export {};

package/esm/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -99,7 +99,6 @@ class PAFAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources() { }
 }
 PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default PAFAdapter;

package/esm/util.js

@@ -30,6 +30,7 @@ export function parseLineByLine(buffer, cb, opts) {
     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) {
@@ -43,11 +44,13 @@ export function parseLineByLine(buffer, cb, opts) {
                 entries.push(entry);
             }
         }
-        if (i++ % 10000 === 0) {
+        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) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "3.3.0",
+  "version": "3.5.0",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -36,13 +36,13 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^2.0.1",
-    "@gmod/tabix": "^2.0.0",
-    "@jbrowse/core": "^3.3.0",
-    "@jbrowse/plugin-alignments": "^3.3.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.3.0",
+    "@gmod/bgzf-filehandle": "^4.0.0",
+    "@gmod/tabix": "^3.0.1",
+    "@jbrowse/core": "^3.5.0",
+    "@jbrowse/plugin-alignments": "^3.5.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.5.0",
     "@mui/material": "^7.0.0",
-    "generic-filehandle2": "^1.0.0",
+    "generic-filehandle2": "^2.0.1",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
+  "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
 }