@jbrowse/plugin-bed 2.17.0 → 3.0.0

package/esm/BigBedAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     bigBedLocation: {
         type: string;
         defaultValue: {
@@ -9,17 +6,11 @@ declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSc
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     aggregateField: {
         type: string;
         description: string;

package/esm/BigBedAdapter/configSchema.js

@@ -1,31 +1,19 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config BigBedAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
-    /**
-     * #slot
-     */
     bigBedLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },
     },
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: 'string',
         description: 'The column to use as a "score" attribute',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     aggregateField: {
         type: 'string',
         description: 'An attribute to aggregate features with',
-        defaultValue: 'geneName',
+        defaultValue: 'geneName2',
     },
 }, { explicitlyTyped: true });
 export default BigBedAdapter;

package/esm/BigBedAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function BigBedAdapterF(pluginManager: PluginManager): void;

package/esm/GuessAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function GuessAdapterF(pluginManager: PluginManager): void;

package/esm/GuessAdapter/index.js

@@ -0,0 +1,65 @@
+import { testAdapter } from '@jbrowse/core/util';
+import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
+export default function GuessAdapterF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const fileName = getFileName(file);
+            const indexName = index && getFileName(index);
+            if (testAdapter(fileName, /\.bedpe(\.gz)?$/i, adapterHint, 'BedpeAdapter')) {
+                return {
+                    type: 'BedpeAdapter',
+                    bedpeLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.bb$/i, adapterHint, 'BigBedAdapter') ||
+                testAdapter(fileName, /\.bigBed?$/i, adapterHint, 'BigBedAdapter')) {
+                return {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.bed$/i, adapterHint, 'BedAdapter')) {
+                return {
+                    type: 'BedAdapter',
+                    bedLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.bg$/i, adapterHint, 'BedGraphAdapter')) {
+                return {
+                    type: 'BedGraphAdapter',
+                    bedGraphLocation: file,
+                };
+            }
+            else if (testAdapter(fileName, /\.bg(\.gz)?$/i, adapterHint, 'BedGraphTabixAdapter')) {
+                return {
+                    type: 'BedGraphTabixAdapter',
+                    bedGraphGzLocation: file,
+                    index: {
+                        location: index || makeIndex(file, '.tbi'),
+                        indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else if (testAdapter(fileName, /\.bed\.gz$/i, adapterHint, 'BedTabixAdapter')) {
+                return {
+                    type: 'BedTabixAdapter',
+                    bedGzLocation: file,
+                    index: {
+                        location: index || makeIndex(file, '.tbi'),
+                        indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else {
+                return adapterGuesser(file, index, adapterHint);
+            }
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName) => {
+        return ({
+            BedpeAdapter: 'VariantTrack',
+            BedGraphAdapter: 'QuantitativeTrack',
+            BedGraphTabixAdapter: 'QuantitativeTrack',
+        }[adapterName] || trackTypeGuesser(adapterName));
+    });
+}

package/esm/generateBedMethylFeature.d.ts

@@ -3,8 +3,8 @@ export declare function isBedMethylFeature({ splitLine, start, end, }: {
     start: number;
     end: number;
 }): boolean;
-export declare function generateBedMethylFeature({ line, uniqueId, refName, start, end, }: {
-    line: string;
+export declare function generateBedMethylFeature({ splitLine, uniqueId, refName, start, end, }: {
+    splitLine: string[];
     uniqueId: string;
     refName: string;
     start: number;
@@ -15,7 +15,7 @@ export declare function generateBedMethylFeature({ line, uniqueId, refName, star
     start: number;
     end: number;
     code: string | undefined;
-    score: string | undefined;
+    score: number;
     strand: string | undefined;
     color: string | undefined;
     source: string | undefined;

package/esm/generateBedMethylFeature.js

@@ -1,17 +1,17 @@
 export function isBedMethylFeature({ splitLine, start, end, }) {
-    return +(splitLine[6] || 0) === start && +(splitLine[7] || 0) === end;
+    return (+(splitLine[6] || 0) === start &&
+        +(splitLine[7] || 0) === end &&
+        [9, 10, 11, 12, 13, 14, 15, 16, 17].every(r => splitLine[r] && !Number.isNaN(+splitLine[r])));
 }
-export function generateBedMethylFeature({ line, uniqueId, refName, start, end, }) {
-    // see
-    // https://github.com/nanoporetech/modkit?tab=readme-ov-file#description-of-bedmethyl-output
-    const [, , , code, , strand, , , color, n_valid_cov, fraction_modified, n_mod, n_canonical, n_other_mod, n_delete, n_fail, n_diff, n_nocall,] = line.split('\t');
+export function generateBedMethylFeature({ splitLine, uniqueId, refName, start, end, }) {
+    const [, , , code, , strand, , , color, n_valid_cov, fraction_modified, n_mod, n_canonical, n_other_mod, n_delete, n_fail, n_diff, n_nocall,] = splitLine;
     return {
         uniqueId,
         refName,
         start,
         end,
         code,
-        score: fraction_modified,
+        score: +fraction_modified || 0,
         strand,
         color,
         source: code,

package/esm/generateRepeatMaskerFeature.js

@@ -26,8 +26,9 @@ function makeRepeatTrackDescription(description) {
     return { description };
 }
 export function generateRepeatMaskerFeature({ uniqueId, refName, start, end, description, ...rest }) {
+    const { subfeatures, ...rest2 } = rest;
     return {
-        ...rest,
+        ...rest2,
         ...makeRepeatTrackDescription(description),
         uniqueId,
         refName,

package/esm/generateUcscTranscript.d.ts

@@ -1,4 +1,4 @@
-import { MinimalFeature, TranscriptFeat } from './types';
+import type { MinimalFeature, TranscriptFeat } from './types';
 export declare function isUcscTranscript({ thickStart, blockCount, strand, }: {
     thickStart?: number;
     blockCount?: number;

package/esm/generateUcscTranscript.js

@@ -12,7 +12,6 @@ export function generateUcscTranscript(data) {
         const start = block.start;
         const end = block.end;
         if (thickStart >= end) {
-            // left-side UTR
             subfeatures.push({
                 type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
                 start,
@@ -21,7 +20,6 @@ export function generateUcscTranscript(data) {
             });
         }
         else if (thickStart > start && thickStart < end && thickEnd >= end) {
-            // UTR | CDS
             subfeatures.push({
                 type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
                 start,
@@ -29,22 +27,22 @@ export function generateUcscTranscript(data) {
                 refName,
             }, {
                 type: 'CDS',
+                phase: 0,
                 start: thickStart,
                 end,
                 refName,
             });
         }
         else if (thickStart <= start && thickEnd >= end) {
-            // CDS
             subfeatures.push({
                 type: 'CDS',
+                phase: 0,
                 start,
                 end,
                 refName,
             });
         }
         else if (thickStart > start && thickStart < end && thickEnd < end) {
-            // UTR | CDS | UTR
             subfeatures.push({
                 type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
                 start,
@@ -52,6 +50,7 @@ export function generateUcscTranscript(data) {
                 refName,
             }, {
                 type: 'CDS',
+                phase: 0,
                 start: thickStart,
                 end: thickEnd,
                 refName,
@@ -63,9 +62,9 @@ export function generateUcscTranscript(data) {
             });
         }
         else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-            // CDS | UTR
             subfeatures.push({
                 type: 'CDS',
+                phase: 0,
                 start,
                 end: thickEnd,
                 refName,
@@ -77,7 +76,6 @@ export function generateUcscTranscript(data) {
             });
         }
         else if (thickEnd <= start) {
-            // right-side UTR
             subfeatures.push({
                 type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
                 start,

package/esm/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class BedPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,9 +1,11 @@
 import Plugin from '@jbrowse/core/Plugin';
-import BigBedAdapterF from './BigBedAdapter';
-import BedpeAdapterF from './BedpeAdapter';
-import BedTabixAdapterF from './BedTabixAdapter';
 import BedAdapterF from './BedAdapter';
-import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
+import BedGraphAdapterF from './BedGraphAdapter';
+import BedGraphTabixAdapterF from './BedGraphTabixAdapter';
+import BedTabixAdapterF from './BedTabixAdapter';
+import BedpeAdapterF from './BedpeAdapter';
+import BigBedAdapterF from './BigBedAdapter';
+import GuessAdapterF from './GuessAdapter';
 export default class BedPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -14,73 +16,8 @@ export default class BedPlugin extends Plugin {
         BedAdapterF(pluginManager);
         BedpeAdapterF(pluginManager);
         BedTabixAdapterF(pluginManager);
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.(bb|bigbed)$/i;
-                const adapterName = 'BigBedAdapter';
-                const fileName = getFileName(file);
-                const obj = {
-                    type: adapterName,
-                    bigBedLocation: file,
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.bedpe(\.gz)?$/i;
-                const adapterName = 'BedpeAdapter';
-                const fileName = getFileName(file);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        bedpeLocation: file,
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.bed\.b?gz$/i;
-                const adapterName = 'BedTabixAdapter';
-                const fileName = getFileName(file);
-                const indexName = index && getFileName(index);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        bedGzLocation: file,
-                        index: {
-                            location: index || makeIndex(file, '.tbi'),
-                            indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-                        },
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.bed$/i;
-                const adapterName = 'BedAdapter';
-                const fileName = getFileName(file);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        bedLocation: file,
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName) => adapterName === 'BedpeAdapter'
-            ? 'VariantTrack'
-            : trackTypeGuesser(adapterName));
+        BedGraphAdapterF(pluginManager);
+        BedGraphTabixAdapterF(pluginManager);
+        GuessAdapterF(pluginManager);
     }
 }

package/esm/util.d.ts

@@ -1,5 +1,4 @@
-import BED from '@gmod/bed';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
+import type BED from '@gmod/bed';
 export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
     blockCount: number;
     start: number;
@@ -24,9 +23,92 @@ export declare function featureData({ line, colRef, colStart, colEnd, scoreColum
     parser: BED;
     uniqueId: string;
     names?: string[];
-}): SimpleFeatureSerialized;
-export declare function featureData2({ line, refName, start, end, parser, uniqueId, scoreColumn, names, }: {
-    line: string;
+}): {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    code: string | undefined;
+    score: number;
+    strand: string | undefined;
+    color: string | undefined;
+    source: string | undefined;
+    n_valid_cov: string | undefined;
+    fraction_modified: string | undefined;
+    n_mod: string | undefined;
+    n_canonical: string | undefined;
+    n_other_mod: string | undefined;
+    n_delete: string | undefined;
+    n_fail: string | undefined;
+    n_diff: string | undefined;
+    n_nocall: string | undefined;
+} | {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    bitsw_score: string | undefined;
+    percent_div: string | undefined;
+    percent_del: string | undefined;
+    percent_ins: string | undefined;
+    query_chr: string | undefined;
+    query_begin: string | undefined;
+    query_end: string | undefined;
+    query_remaining: string | undefined;
+    orientation: string | undefined;
+    matching_repeat_name: string | undefined;
+    matching_repeat_class: string | undefined;
+    matching_repeat_begin: string | undefined;
+    matching_repeat_end: string | undefined;
+    matching_repeat_remaining: string | undefined;
+    repeat_id: string | undefined;
+    description?: undefined;
+} | {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    description: undefined;
+    bitsw_score?: undefined;
+    percent_div?: undefined;
+    percent_del?: undefined;
+    percent_ins?: undefined;
+    query_chr?: undefined;
+    query_begin?: undefined;
+    query_end?: undefined;
+    query_remaining?: undefined;
+    orientation?: undefined;
+    matching_repeat_name?: undefined;
+    matching_repeat_class?: undefined;
+    matching_repeat_begin?: undefined;
+    matching_repeat_end?: undefined;
+    matching_repeat_remaining?: undefined;
+    repeat_id?: undefined;
+} | {
+    uniqueId: string;
+    strand: number;
+    type: string;
+    refName: string;
+    subfeatures: import("./types").MinimalFeature[];
+    start: number;
+    end: number;
+} | {
+    uniqueId: string;
+    score: number | undefined;
+    start: number;
+    end: number;
+    strand: any;
+    refName: string;
+    subfeatures: {
+        uniqueId: string;
+        start: number;
+        end: number;
+        refName: string;
+        type: string;
+    }[] | undefined;
+};
+export declare function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }: {
+    splitLine: string[];
     refName: string;
     start: number;
     end: number;
@@ -34,5 +116,88 @@ export declare function featureData2({ line, refName, start, end, parser, unique
     uniqueId: string;
     scoreColumn: string;
     names?: string[];
-}): SimpleFeatureSerialized;
+}): {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    code: string | undefined;
+    score: number;
+    strand: string | undefined;
+    color: string | undefined;
+    source: string | undefined;
+    n_valid_cov: string | undefined;
+    fraction_modified: string | undefined;
+    n_mod: string | undefined;
+    n_canonical: string | undefined;
+    n_other_mod: string | undefined;
+    n_delete: string | undefined;
+    n_fail: string | undefined;
+    n_diff: string | undefined;
+    n_nocall: string | undefined;
+} | {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    bitsw_score: string | undefined;
+    percent_div: string | undefined;
+    percent_del: string | undefined;
+    percent_ins: string | undefined;
+    query_chr: string | undefined;
+    query_begin: string | undefined;
+    query_end: string | undefined;
+    query_remaining: string | undefined;
+    orientation: string | undefined;
+    matching_repeat_name: string | undefined;
+    matching_repeat_class: string | undefined;
+    matching_repeat_begin: string | undefined;
+    matching_repeat_end: string | undefined;
+    matching_repeat_remaining: string | undefined;
+    repeat_id: string | undefined;
+    description?: undefined;
+} | {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    description: undefined;
+    bitsw_score?: undefined;
+    percent_div?: undefined;
+    percent_del?: undefined;
+    percent_ins?: undefined;
+    query_chr?: undefined;
+    query_begin?: undefined;
+    query_end?: undefined;
+    query_remaining?: undefined;
+    orientation?: undefined;
+    matching_repeat_name?: undefined;
+    matching_repeat_class?: undefined;
+    matching_repeat_begin?: undefined;
+    matching_repeat_end?: undefined;
+    matching_repeat_remaining?: undefined;
+    repeat_id?: undefined;
+} | {
+    uniqueId: string;
+    strand: number;
+    type: string;
+    refName: string;
+    subfeatures: import("./types").MinimalFeature[];
+    start: number;
+    end: number;
+} | {
+    uniqueId: string;
+    score: number | undefined;
+    start: number;
+    end: number;
+    strand: any;
+    refName: string;
+    subfeatures: {
+        uniqueId: string;
+        start: number;
+        end: number;
+        refName: string;
+        type: string;
+    }[] | undefined;
+};
 export declare function arrayify(f?: string | number[]): number[] | undefined;