@jbrowse/plugin-comparative-adapters 2.11.2 → 2.12.1

package/dist/ChainAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = ChainAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function ChainAdapterF(pluginManager) {
@@ -39,4 +40,3 @@ function ChainAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./ChainAdapter'))).then(r => r.default),
     }));
 }
-exports.default = ChainAdapterF;

package/dist/ChainAdapter/util.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 export declare function paf_chain2paf(buffer: Buffer): {
     qname: string;
     qstart: number;

package/dist/ChainAdapter/util.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.paf_chain2paf = void 0;
+exports.paf_chain2paf = paf_chain2paf;
 const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 /* adapted from chain2paf by Andrea Guarracino, license reproduced below
  *
@@ -130,4 +130,3 @@ function paf_chain2paf(buffer) {
     }
     return records;
 }
-exports.paf_chain2paf = paf_chain2paf;

package/dist/DeltaAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = DeltaAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function DeltaAdapterF(pluginManager) {
@@ -39,4 +40,3 @@ function DeltaAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./DeltaAdapter'))).then(r => r.default),
     }));
 }
-exports.default = DeltaAdapterF;

package/dist/DeltaAdapter/util.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 export declare function paf_delta2paf(buffer: Buffer): {
     qname: string;
     qstart: number;

package/dist/DeltaAdapter/util.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.paf_delta2paf = void 0;
+exports.paf_delta2paf = paf_delta2paf;
 const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 /* paf2delta from paftools.js in the minimap2 repository, license reproduced below
  *
@@ -148,4 +148,3 @@ function paf_delta2paf(buffer) {
     }
     return records;
 }
-exports.paf_delta2paf = paf_delta2paf;

package/dist/MCScanAnchorsAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = MCScanAnchorsAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function MCScanAnchorsAdapterF(pluginManager) {
@@ -39,4 +40,3 @@ function MCScanAnchorsAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MCScanAnchorsAdapter'))).then(r => r.default),
     }));
 }
-exports.default = MCScanAnchorsAdapterF;

package/dist/MCScanSimpleAnchorsAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = MCScanSimpleAnchorsAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function MCScanSimpleAnchorsAdapterF(pluginManager) {
@@ -39,4 +40,3 @@ function MCScanSimpleAnchorsAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MCScanSimpleAnchorsAdapter'))).then(r => r.default),
     }));
 }
-exports.default = MCScanSimpleAnchorsAdapterF;

package/dist/MashMapAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = MashMapAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function MashMapAdapterF(pluginManager) {
@@ -39,4 +40,3 @@ function MashMapAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MashMapAdapter'))).then(r => r.default),
     }));
 }
-exports.default = MashMapAdapterF;

package/dist/PAFAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = PAFAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function PAFAdapterF(pluginManager) {
@@ -39,4 +40,3 @@ function PAFAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./PAFAdapter'))).then(r => r.default),
     }));
 }
-exports.default = PAFAdapterF;

package/dist/PAFAdapter/util.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getWeightedMeans = void 0;
+exports.getWeightedMeans = getWeightedMeans;
 const util_1 = require("../util");
 // based on "weighted mean" method from https://github.com/tpoorten/dotPlotly
 // License reproduced here
@@ -70,7 +70,6 @@ function getWeightedMeans(ret) {
     }
     return ret;
 }
-exports.getWeightedMeans = getWeightedMeans;
 // https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a
 function weightedMean(tuples) {
     // eslint-disable-next-line unicorn/no-array-reduce

package/dist/PairwiseIndexedPAFAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = PairwiseIndexedPAFAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function PairwiseIndexedPAFAdapterF(pluginManager) {
@@ -39,4 +40,3 @@ function PairwiseIndexedPAFAdapterF(pluginManager) {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./PairwiseIndexedPAFAdapter'))).then(r => r.default),
     }));
 }
-exports.default = PairwiseIndexedPAFAdapterF;

package/dist/util.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { GenericFilehandle } from 'generic-filehandle';
 import { PAFRecord } from './PAFAdapter/util';

package/dist/util.js

@@ -1,11 +1,17 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.swapIndelCigar = exports.flipCigar = exports.parsePAFLine = exports.parseLineByLine = exports.zip = exports.readFile = exports.parseBed = exports.isGzip = void 0;
+exports.isGzip = isGzip;
+exports.parseBed = parseBed;
+exports.readFile = readFile;
+exports.zip = zip;
+exports.parseLineByLine = parseLineByLine;
+exports.parsePAFLine = parsePAFLine;
+exports.flipCigar = flipCigar;
+exports.swapIndelCigar = swapIndelCigar;
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 function isGzip(buf) {
     return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
 }
-exports.isGzip = isGzip;
 function parseBed(text) {
     return new Map(text
         .split(/\n|\r\n|\r/)
@@ -25,16 +31,13 @@ function parseBed(text) {
         ];
     }));
 }
-exports.parseBed = parseBed;
 async function readFile(file, opts) {
     const buffer = (await file.readFile(opts));
     return new TextDecoder('utf8', { fatal: true }).decode(isGzip(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer);
 }
-exports.readFile = readFile;
 function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
 }
-exports.zip = zip;
 const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 function parseLineByLine(buffer, cb) {
     let blockStart = 0;
@@ -53,7 +56,6 @@ function parseLineByLine(buffer, cb) {
     }
     return entries;
 }
-exports.parseLineByLine = parseLineByLine;
 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 => {
@@ -78,7 +80,6 @@ function parsePAFLine(line) {
         },
     };
 }
-exports.parsePAFLine = parsePAFLine;
 function flipCigar(cigar) {
     const arr = [];
     for (let i = cigar.length - 2; i >= 0; i -= 2) {
@@ -96,8 +97,6 @@ function flipCigar(cigar) {
     }
     return arr;
 }
-exports.flipCigar = flipCigar;
 function swapIndelCigar(cigar) {
     return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
 }
-exports.swapIndelCigar = swapIndelCigar;

package/esm/ChainAdapter/util.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 export declare function paf_chain2paf(buffer: Buffer): {
     qname: string;
     qstart: number;

package/esm/DeltaAdapter/util.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 export declare function paf_delta2paf(buffer: Buffer): {
     qname: string;
     qstart: number;

package/esm/util.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { GenericFilehandle } from 'generic-filehandle';
 import { PAFRecord } from './PAFAdapter/util';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "2.11.2",
+  "version": "2.12.1",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -59,5 +59,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
+  "gitHead": "20f16ae5a56ae5e4806aaa373131e540b0b5b0fd"
 }