@jbrowse/cli 2.4.0 → 2.4.2

package/lib/commands/add-track.js

@@ -10,12 +10,29 @@ const json_parse_better_errors_1 = __importDefault(require("json-parse-better-er
 const base_1 = __importDefault(require("../base"));
 const { copyFile, rename, symlink } = fs_1.default.promises;
 const { COPYFILE_EXCL } = fs_1.default.constants;
+function makeLocationProtocol(protocol) {
+    return (location) => {
+        if (protocol === 'uri') {
+            return {
+                uri: location,
+                locationType: 'UriLocation',
+            };
+        }
+        if (protocol === 'localPath') {
+            return {
+                localPath: location,
+                locationType: 'LocalPathLocation',
+            };
+        }
+        throw new Error(`invalid protocol ${protocol}`);
+    };
+}
 const isUrl = (loc) => loc === null || loc === void 0 ? void 0 : loc.match(/^https?:\/\//);
 class AddTrack extends base_1.default {
     async run() {
         const { args: runArgs, flags: runFlags } = this.parse(AddTrack);
         const { track: argsTrack } = runArgs;
-        const { config, skipCheck, force, overwrite, category, description, load, subDir, target, protocol, out, indexFile: index, } = runFlags;
+        const { config, skipCheck, force, overwrite, category, description, load, subDir, target, protocol, out, indexFile: index, bed1, bed2, } = runFlags;
         const output = target || out || '.';
         const isDir = fs_1.default.lstatSync(output).isDirectory();
         this.target = isDir ? `${output}/config.json` : output;
@@ -31,19 +48,27 @@ class AddTrack extends base_1.default {
             }
         }
         const location = argsTrack;
-        const inPlace = load === 'inPlace';
-        const useIndex = isUrl(index) || inPlace || index;
-        const effectiveLocation = isUrl(location) || inPlace
-            ? location
-            : path_1.default.join(subDir, path_1.default.basename(location));
-        const effectiveIndexLocation = !index || isUrl(index) || inPlace
-            ? index
-            : path_1.default.join(subDir, path_1.default.basename(index));
-        const adapter = useIndex
-            ? this.guessAdapter(effectiveLocation, protocol, effectiveIndexLocation)
-            : this.guessAdapter(effectiveLocation, protocol);
-        if (adapter.type === 'PAFAdapter') {
-            // @ts-ignore
+        const mapLoc = (p) => {
+            return !p || isUrl(p) || load === 'inPlace'
+                ? p
+                : path_1.default.join(subDir, path_1.default.basename(p));
+        };
+        const adapter = this.guessAdapter({
+            protocol,
+            location: mapLoc(location),
+            index: index ? mapLoc(index) : undefined,
+            bed1: bed1 ? mapLoc(bed1) : undefined,
+            bed2: bed2 ? mapLoc(bed2) : undefined,
+        });
+        if ([
+            'PAFAdapter',
+            'DeltaAdapter',
+            'ChainAdapter',
+            'MashMapAdapter',
+            'MCScanAnchorsAdapter',
+            'MCScanSimpleAnchorsAdapter',
+        ].includes(adapter.type)) {
+            // @ts-expect-error
             adapter.assemblyNames = assemblyNames.split(',').map(a => a.trim());
         }
         if (isUrl(location) && load) {
@@ -75,26 +100,18 @@ class AddTrack extends base_1.default {
         trackId = trackId || path_1.default.basename(location, path_1.default.extname(location));
         name = name || trackId;
         assemblyNames = assemblyNames || configContents.assemblies[0].name;
-        this.debug(`Name is: ${name}`);
-        this.debug(`Type is: ${trackType}`);
-        this.debug(`Track is :${trackId}`);
-        this.debug(`Assembly name(s) is :${assemblyNames}`);
         const configObj = config ? (0, json_parse_better_errors_1.default)(config) : {};
         const trackConfig = Object.assign({ type: trackType, trackId,
             name,
             adapter, category: category === null || category === void 0 ? void 0 : category.split(',').map(c => c.trim()), assemblyNames: assemblyNames.split(',').map(a => a.trim()), description }, configObj);
-        this.debug(`Track location: ${location}, index: ${adapter ? adapter.index : ''}`);
         // any special track modifications go here
-        switch (trackType) {
-            case 'AlignmentsTrack': {
-                const assembly = configContents.assemblies.find(asm => asm.name === assemblyNames);
-                if (assembly) {
-                    trackConfig.adapter.sequenceAdapter = assembly.sequence.adapter;
-                }
-                else if (!skipCheck) {
-                    this.error(`Failed to find assemblyName ${assemblyNames}`);
-                }
-                break;
+        if (trackType === 'AlignmentsTrack') {
+            const assembly = configContents.assemblies.find(asm => asm.name === assemblyNames);
+            if (assembly) {
+                trackConfig.adapter.sequenceAdapter = assembly.sequence.adapter;
+            }
+            else if (!skipCheck) {
+                this.error(`Failed to find assemblyName ${assemblyNames}`);
             }
         }
         if (!configContents.tracks) {
@@ -139,276 +156,252 @@ class AddTrack extends base_1.default {
                 /* do nothing */
             },
         };
-        await Promise.all(Object.values(this.guessFileNames(location, index))
+        await Promise.all(Object.values(this.guessFileNames({ location, index, bed1, bed2 }))
             .filter(f => !!f)
             .map(src => callbacks[loadType](src, destinationFn(configDirectory, src))));
         this.debug(`Writing configuration to file ${this.target}`);
         await this.writeJsonFile(this.target, configContents);
         this.log(`${idx !== -1 ? 'Overwrote' : 'Added'} track with name "${name}" and trackId "${trackId}" ${idx !== -1 ? 'in' : 'to'} ${this.target}`);
     }
-    guessFileNames(fileName, index) {
-        if (/\.bam$/i.test(fileName)) {
-            return {
-                file: fileName,
-                index: index || `${fileName}.bai`,
-            };
-        }
-        if (/\.cram$/i.test(fileName)) {
+    guessFileNames({ location, index, bed1, bed2, }) {
+        if (/\.anchors(.simple)?$/i.test(location)) {
             return {
-                file: fileName,
-                index: index || `${fileName}.crai`,
+                file: location,
+                // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+                bed1: bed1,
+                // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+                bed2: bed2,
             };
         }
-        if (/\.gff3?$/i.test(fileName)) {
+        if (/\.bam$/i.test(location)) {
             return {
-                file: fileName,
+                file: location,
+                index: index || `${location}.bai`,
             };
         }
-        if (/\.gff3?\.b?gz$/i.test(fileName)) {
+        if (/\.cram$/i.test(location)) {
             return {
-                file: fileName,
-                index: index || `${fileName}.tbi`,
+                file: location,
+                index: index || `${location}.crai`,
             };
         }
-        if (/\.gtf?$/i.test(fileName)) {
+        if (/\.gff3?\.b?gz$/i.test(location) ||
+            /\.vcf\.b?gz$/i.test(location) ||
+            /\.bed\.b?gz$/i.test(location)) {
             return {
-                file: fileName,
+                file: location,
+                index: index || `${location}.tbi`,
             };
         }
-        if (/\.vcf$/i.test(fileName)) {
+        if (/\.(fa|fasta|fas|fna|mfa)$/i.test(location)) {
             return {
-                file: fileName,
+                file: location,
+                index: index || `${location}.fai`,
             };
         }
-        if (/\.vcf\.b?gz$/i.test(fileName)) {
+        if (/\.(fa|fasta|fas|fna|mfa)\.b?gz$/i.test(location)) {
             return {
-                file: fileName,
-                index: index || `${fileName}.tbi`,
+                file: location,
+                index: `${location}.fai`,
+                index2: `${location}.gzi`,
             };
         }
-        if (/\.vcf\.idx$/i.test(fileName)) {
-            return {};
-        }
-        if (/\.bed$/i.test(fileName)) {
-            return {};
-        }
-        if (/\.bed\.b?gz$/i.test(fileName)) {
+        if (/\.2bit$/i.test(location) ||
+            /\/trackData.jsonz?$/i.test(location) ||
+            /\/sparql$/i.test(location) ||
+            /\.out(.gz)?$/i.test(location) ||
+            /\.paf(.gz)?$/i.test(location) ||
+            /\.delta(.gz)?$/i.test(location) ||
+            /\.(bw|bigwig)$/i.test(location) ||
+            /\.(bb|bigbed)$/i.test(location) ||
+            /\.vcf$/i.test(location) ||
+            /\.gtf?$/i.test(location) ||
+            /\.gff3?$/i.test(location) ||
+            /\.chain(.gz)?$/i.test(location)) {
             return {
-                file: fileName,
-                index: index || `${fileName}.tbi`,
-            };
-        }
-        if (/\.bed\.idx$/i.test(fileName)) {
-            return {};
-        }
-        if (/\.(bb|bigbed)$/i.test(fileName)) {
-            return {
-                file: fileName,
-            };
-        }
-        if (/\.(bw|bigwig)$/i.test(fileName)) {
-            return {
-                file: fileName,
-            };
-        }
-        if (/\.(fa|fasta|fas|fna|mfa)$/i.test(fileName)) {
-            return {
-                file: fileName,
-                index: index || `${fileName}.fai`,
-            };
-        }
-        if (/\.(fa|fasta|fas|fna|mfa)\.b?gz$/i.test(fileName)) {
-            return {
-                file: fileName,
-                index: `${fileName}.fai`,
-                index2: `${fileName}.gzi`,
-            };
-        }
-        if (/\.2bit$/i.test(fileName)) {
-            return {
-                file: fileName,
-            };
-        }
-        if (/\.sizes$/i.test(fileName)) {
-            return {};
-        }
-        if (/\/trackData.jsonz?$/i.test(fileName)) {
-            return {
-                file: fileName,
-            };
-        }
-        if (/\/sparql$/i.test(fileName)) {
-            return {
-                file: fileName,
-            };
-        }
-        if (/\.hic$/i.test(fileName)) {
-            return {
-                file: fileName,
-            };
-        }
-        if (/\.paf$/i.test(fileName)) {
-            return {
-                file: fileName,
+                file: location,
             };
         }
         return {};
     }
     // find way to import this instead of having to paste it
-    guessAdapter(fileName, protocol, index) {
-        function makeLocation(location) {
-            if (protocol === 'uri') {
-                return { uri: location, locationType: 'UriLocation' };
-            }
-            if (protocol === 'localPath') {
-                return {
-                    localPath: location,
-                    locationType: 'LocalPathLocation',
-                };
-            }
-            throw new Error(`invalid protocol ${protocol}`);
-        }
-        if (/\.bam$/i.test(fileName)) {
+    guessAdapter({ location, protocol, index, bed1, bed2, }) {
+        const makeLocation = makeLocationProtocol(protocol);
+        if (/\.bam$/i.test(location)) {
             return {
                 type: 'BamAdapter',
-                bamLocation: makeLocation(fileName),
+                bamLocation: makeLocation(location),
                 index: {
-                    location: makeLocation(index || `${fileName}.bai`),
-                    indexType: index && index.toUpperCase().endsWith('CSI') ? 'CSI' : 'BAI',
+                    location: makeLocation(index || `${location}.bai`),
+                    indexType: (index === null || index === void 0 ? void 0 : index.toUpperCase().endsWith('CSI')) ? 'CSI' : 'BAI',
                 },
             };
         }
-        if (/\.cram$/i.test(fileName)) {
+        if (/\.cram$/i.test(location)) {
             return {
                 type: 'CramAdapter',
-                cramLocation: makeLocation(fileName),
-                craiLocation: makeLocation(`${fileName}.crai`),
+                cramLocation: makeLocation(location),
+                craiLocation: makeLocation(`${location}.crai`),
             };
         }
-        if (/\.gff3?$/i.test(fileName)) {
+        if (/\.gff3?$/i.test(location)) {
             return {
                 type: 'Gff3Adapter',
-                gffLocation: makeLocation(fileName),
+                gffLocation: makeLocation(location),
             };
         }
-        if (/\.gff3?\.b?gz$/i.test(fileName)) {
+        if (/\.gff3?\.b?gz$/i.test(location)) {
             return {
                 type: 'Gff3TabixAdapter',
-                gffGzLocation: makeLocation(fileName),
+                gffGzLocation: makeLocation(location),
                 index: {
-                    location: makeLocation(index || `${fileName}.tbi`),
-                    indexType: index && index.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
+                    location: makeLocation(index || `${location}.tbi`),
+                    indexType: (index === null || index === void 0 ? void 0 : index.toUpperCase().endsWith('CSI')) ? 'CSI' : 'TBI',
                 },
             };
         }
-        if (/\.gtf?$/i.test(fileName)) {
+        if (/\.gtf?$/i.test(location)) {
             return {
                 type: 'GtfAdapter',
-                gtfLocation: makeLocation(fileName),
+                gtfLocation: makeLocation(location),
             };
         }
-        if (/\.vcf$/i.test(fileName)) {
+        if (/\.vcf$/i.test(location)) {
             return {
                 type: 'VcfAdapter',
-                vcfLocation: makeLocation(fileName),
+                vcfLocation: makeLocation(location),
             };
         }
-        if (/\.vcf\.b?gz$/i.test(fileName)) {
+        if (/\.vcf\.b?gz$/i.test(location)) {
             return {
                 type: 'VcfTabixAdapter',
-                vcfGzLocation: makeLocation(fileName),
+                vcfGzLocation: makeLocation(location),
                 index: {
-                    location: makeLocation(index || `${fileName}.tbi`),
-                    indexType: index && index.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
+                    location: makeLocation(index || `${location}.tbi`),
+                    indexType: (index === null || index === void 0 ? void 0 : index.toUpperCase().endsWith('CSI')) ? 'CSI' : 'TBI',
                 },
             };
         }
-        if (/\.vcf\.idx$/i.test(fileName)) {
+        if (/\.vcf\.idx$/i.test(location)) {
             return {
                 type: 'UNSUPPORTED',
             };
         }
-        if (/\.bed$/i.test(fileName)) {
+        if (/\.bed$/i.test(location)) {
             return {
                 type: 'UNSUPPORTED',
             };
         }
-        if (/\.bed\.b?gz$/i.test(fileName)) {
+        if (/\.bed\.b?gz$/i.test(location)) {
             return {
                 type: 'BedTabixAdapter',
-                bedGzLocation: makeLocation(fileName),
+                bedGzLocation: makeLocation(location),
                 index: {
-                    location: makeLocation(index || `${fileName}.tbi`),
-                    indexType: index && index.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
+                    location: makeLocation(index || `${location}.tbi`),
+                    indexType: (index === null || index === void 0 ? void 0 : index.toUpperCase().endsWith('CSI')) ? 'CSI' : 'TBI',
                 },
             };
         }
-        if (/\.bed$/i.test(fileName)) {
+        if (/\.bed$/i.test(location)) {
             return {
                 type: 'BedAdapter',
-                bedLocation: makeLocation(fileName),
+                bedLocation: makeLocation(location),
             };
         }
-        if (/\.(bb|bigbed)$/i.test(fileName)) {
+        if (/\.(bb|bigbed)$/i.test(location)) {
             return {
                 type: 'BigBedAdapter',
-                bigBedLocation: makeLocation(fileName),
+                bigBedLocation: makeLocation(location),
             };
         }
-        if (/\.(bw|bigwig)$/i.test(fileName)) {
+        if (/\.(bw|bigwig)$/i.test(location)) {
             return {
                 type: 'BigWigAdapter',
-                bigWigLocation: makeLocation(fileName),
+                bigWigLocation: makeLocation(location),
             };
         }
-        if (/\.(fa|fasta|fna|mfa)$/i.test(fileName)) {
+        if (/\.(fa|fasta|fna|mfa)$/i.test(location)) {
             return {
                 type: 'IndexedFastaAdapter',
-                fastaLocation: makeLocation(fileName),
-                faiLocation: makeLocation(index || `${fileName}.fai`),
+                fastaLocation: makeLocation(location),
+                faiLocation: makeLocation(index || `${location}.fai`),
             };
         }
-        if (/\.(fa|fasta|fna|mfa)\.b?gz$/i.test(fileName)) {
+        if (/\.(fa|fasta|fna|mfa)\.b?gz$/i.test(location)) {
             return {
                 type: 'BgzipFastaAdapter',
-                fastaLocation: makeLocation(fileName),
-                faiLocation: makeLocation(`${fileName}.fai`),
-                gziLocation: makeLocation(`${fileName}.gzi`),
+                fastaLocation: makeLocation(location),
+                faiLocation: makeLocation(`${location}.fai`),
+                gziLocation: makeLocation(`${location}.gzi`),
             };
         }
-        if (/\.2bit$/i.test(fileName)) {
+        if (/\.2bit$/i.test(location)) {
             return {
                 type: 'TwoBitAdapter',
-                twoBitLocation: makeLocation(fileName),
+                twoBitLocation: makeLocation(location),
             };
         }
-        if (/\.sizes$/i.test(fileName)) {
+        if (/\.sizes$/i.test(location)) {
             return {
                 type: 'UNSUPPORTED',
             };
         }
-        if (/\/trackData.jsonz?$/i.test(fileName)) {
+        if (/\/trackData.jsonz?$/i.test(location)) {
             return {
                 type: 'NCListAdapter',
-                rootUrlTemplate: makeLocation(fileName),
+                rootUrlTemplate: makeLocation(location),
             };
         }
-        if (/\/sparql$/i.test(fileName)) {
+        if (/\/sparql$/i.test(location)) {
             return {
                 type: 'SPARQLAdapter',
-                endpoint: fileName,
+                endpoint: location,
             };
         }
-        if (/\.hic/i.test(fileName)) {
+        if (/\.hic$/i.test(location)) {
             return {
                 type: 'HicAdapter',
-                hicLocation: makeLocation(fileName),
+                hicLocation: makeLocation(location),
             };
         }
-        if (/\.paf/i.test(fileName)) {
+        if (/\.paf(.gz)?$/i.test(location)) {
             return {
                 type: 'PAFAdapter',
-                pafLocation: makeLocation(fileName),
+                pafLocation: makeLocation(location),
+            };
+        }
+        if (/\.out(.gz)?$/i.test(location)) {
+            return {
+                type: 'MashMapAdapter',
+                outLocation: makeLocation(location),
+            };
+        }
+        if (/\.chain(.gz)?$/i.test(location)) {
+            return {
+                type: 'ChainAdapter',
+                chainLocation: makeLocation(location),
+            };
+        }
+        if (/\.delta(.gz)?$/i.test(location)) {
+            return {
+                type: 'DeltaAdapter',
+                deltaLocation: makeLocation(location),
+            };
+        }
+        if (/\.anchors(.gz)?$/i.test(location)) {
+            return {
+                type: 'MCScanAnchorsAdapter',
+                mcscanAnchorsLocation: makeLocation(location),
+                bed1Location: bed1 ? makeLocation(bed1) : undefined,
+                bed2Location: bed2 ? makeLocation(bed2) : undefined,
+            };
+        }
+        if (/\.anchors.simple(.gz)?$/i.test(location)) {
+            return {
+                type: 'MCScanSimpleAnchorsAdapter',
+                mcscanSimpleAnchorsLocation: makeLocation(location),
+                bed1Location: bed1 ? makeLocation(bed1) : undefined,
+                bed2Location: bed2 ? makeLocation(bed2) : undefined,
             };
         }
         return {
@@ -427,6 +420,11 @@ class AddTrack extends base_1.default {
             VcfAdapter: 'VariantTrack',
             HicAdapter: 'HicTrack',
             PAFAdapter: 'SyntenyTrack',
+            DeltaAdapter: 'SyntenyTrack',
+            ChainAdapter: 'SyntenyTrack',
+            MashMapAdapter: 'SyntenyTrack',
+            MCScanAnchorsAdapter: 'SyntenyTrack',
+            MCScanSimpleAnchorsAdapter: 'SyntenyTrack',
         };
         return known[adapterType] || 'FeatureTrack';
     }
@@ -518,4 +516,10 @@ AddTrack.flags = {
         description: 'Force protocol to a specific value',
         default: 'uri',
     }),
+    bed1: command_1.flags.string({
+        description: 'Used only for mcscan anchors/simpleAnchors types',
+    }),
+    bed2: command_1.flags.string({
+        description: 'Used only for mcscan anchors/simpleAnchors types',
+    }),
 };

package/lib/commands/create.js

@@ -50,7 +50,7 @@ class Create extends base_1.default {
         }
     }
     async catch(error) {
-        // @ts-ignore
+        // @ts-expect-error
         if (error.parse && error.parse.output.flags.listVersions) {
             const versions = (await this.fetchGithubVersions()).map(version => version.tag_name);
             this.log(`All JBrowse versions:\n${versions.join('\n')}`);

package/lib/types/vcfAdapter.js

@@ -75,7 +75,7 @@ function indexVcf({ config, attributesToIndex, inLocation, outLocation, quiet, }
                         val ? decodeURIComponent(val).trim().split(',').join(' ') : undefined,
                     ]));
                     const end = fields.END;
-                    const locStr = `${ref}:${pos}..${end ? end : +pos + 1}`;
+                    const locStr = `${ref}:${pos}..${end || +pos + 1}`;
                     if (id === '.') {
                         continue;
                     }