@jbrowse/plugin-comparative-adapters 2.6.1

package/esm/ChainAdapter/util.js

@@ -0,0 +1,130 @@
+const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+/* adapted from chain2paf by Andrea Guarracino, license reproduced below
+ *
+ * MIT License
+ *
+ * Copyright (c) 2021 Andrea Guarracino
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+function generate_record(qname, qstart, qend, qstrand, tname, tstart, tend, cigar, numMatches) {
+    return {
+        qname,
+        qstart,
+        qend,
+        tname,
+        tstart,
+        tend,
+        strand: qstrand === '-' ? -1 : 1,
+        extra: {
+            numMatches,
+            blockLen: Math.max(qend - qstart, tend - tstart),
+            mappingQual: 0,
+            cg: cigar,
+        },
+    };
+}
+export function paf_chain2paf(buffer) {
+    let t_name = '';
+    let t_start = 0;
+    let t_end = 0;
+    let q_name = '';
+    let q_size = '';
+    let q_strand = '';
+    let q_start = 0;
+    let q_end = 0;
+    let num_matches = 0;
+    let cigar = '';
+    const records = [];
+    let blockStart = 0;
+    while (blockStart < buffer.length) {
+        const n = buffer.indexOf('\n', blockStart);
+        if (n === -1) {
+            break;
+        }
+        const b = buffer.slice(blockStart, n);
+        const l = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+        blockStart = n + 1;
+        const l_tab = l.replaceAll(' ', '\t'); // There are CHAIN files with space-separated fields
+        const l_vec = l_tab.split('\t');
+        if (l_vec[0] === 'chain') {
+            // Emit previous PAF row, if available
+            if (cigar) {
+                records.push(generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches));
+            }
+            // Save query/target information
+            // score -- chain score
+            // tName -- chromosome (reference sequence)
+            // tSize -- chromosome size (reference sequence)
+            // tStrand -- strand (reference sequence)
+            // tStart -- alignment start position (reference sequence)
+            // tEnd -- alignment end position (reference sequence)
+            // qName -- chromosome (query sequence)
+            // qSize -- chromosome size (query sequence)
+            // qStrand -- strand (query sequence)
+            // qStart -- alignment start position (query sequence)
+            // qEnd -- alignment end position (query sequence)
+            // id -- chain ID
+            t_name = l_vec[2];
+            t_start = +l_vec[5];
+            t_end = +l_vec[6];
+            q_name = l_vec[7];
+            q_size = l_vec[8];
+            q_strand = l_vec[9];
+            q_start = +l_vec[10];
+            q_end = +l_vec[11];
+            if (q_strand === '-') {
+                const tmp = q_start;
+                q_start = +q_size - q_end;
+                q_end = +q_size - tmp;
+            }
+            // Initialize PAF fields
+            num_matches = 0;
+            cigar = '';
+        }
+        else {
+            // size -- the size of the ungapped alignment
+            //
+            // dt -- the difference between the end of this block and the beginning
+            //    of the next block (reference sequence)
+            //
+            // dq -- the difference between the end of this block and the beginning
+            //    of the next block (query sequence)
+            const size_ungapped_alignment = +l_vec[0] || 0;
+            const diff_in_target = l_vec.length > 1 ? +l_vec[1] : 0;
+            const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0;
+            if (size_ungapped_alignment !== 0) {
+                num_matches += +size_ungapped_alignment;
+                cigar += size_ungapped_alignment + 'M';
+            }
+            if (diff_in_query !== 0) {
+                cigar += diff_in_query + 'I';
+            }
+            if (diff_in_target !== 0) {
+                cigar += diff_in_target + 'D';
+            }
+        }
+    }
+    // Emit last PAF row, if available
+    if (cigar) {
+        generate_record(q_name, q_start, q_end, q_strand, t_name, t_start, t_end, cigar, num_matches);
+    }
+    return records;
+}
+//# sourceMappingURL=util.js.map

package/esm/ChainAdapter/util.js.map

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package/esm/DeltaAdapter/DeltaAdapter.d.ts

@@ -0,0 +1,20 @@
+import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import PAFAdapter from '../PAFAdapter/PAFAdapter';
+export default class DeltaAdapter extends PAFAdapter {
+    setupPre(opts?: BaseOptions): Promise<{
+        qname: string;
+        qstart: number;
+        qend: number;
+        tname: string;
+        tstart: number;
+        tend: number;
+        strand: number;
+        extra: {
+            numMatches: number;
+            blockLen: number;
+            mappingQual: number;
+            NM: number;
+            cg: string;
+        };
+    }[]>;
+}

package/esm/DeltaAdapter/DeltaAdapter.js

@@ -0,0 +1,16 @@
+import { openLocation } from '@jbrowse/core/util/io';
+import { unzip } from '@gmod/bgzf-filehandle';
+import PAFAdapter from '../PAFAdapter/PAFAdapter';
+import { paf_delta2paf } from './util';
+function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+export default class DeltaAdapter extends PAFAdapter {
+    async setupPre(opts) {
+        const loc = openLocation(this.getConf('deltaLocation'), this.pluginManager);
+        const buffer = (await loc.readFile(opts));
+        const buf = isGzip(buffer) ? await unzip(buffer) : buffer;
+        return paf_delta2paf(buf);
+    }
+}
+//# sourceMappingURL=DeltaAdapter.js.map

package/esm/DeltaAdapter/DeltaAdapter.js.map

@@ -0,0 +1 @@
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package/esm/DeltaAdapter/configSchema.d.ts

@@ -0,0 +1,39 @@
+declare const DeltaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+    /**
+     * #slot
+     * alternative to assembly names
+     */
+    targetAssembly: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    /**
+     * #slot
+     * alternative to assembly names
+     */
+    queryAssembly: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    deltaLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default DeltaAdapter;

package/esm/DeltaAdapter/configSchema.js

@@ -0,0 +1,43 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config DeltaAdapter
+ * #category adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const DeltaAdapter = ConfigurationSchema('DeltaAdapter', {
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'Array of assembly names to use for this file. The target assembly name is the first value in the array, query assembly name is the second',
+    },
+    /**
+     * #slot
+     * alternative to assembly names
+     */
+    targetAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames: the target assembly name',
+    },
+    /**
+     * #slot
+     * alternative to assembly names
+     */
+    queryAssembly: {
+        type: 'string',
+        defaultValue: '',
+        description: 'Alternative to assemblyNames: the query assembly name',
+    },
+    /**
+     * #slot
+     */
+    deltaLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/file.delta', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+export default DeltaAdapter;
+//# sourceMappingURL=configSchema.js.map

package/esm/DeltaAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/DeltaAdapter/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/DeltaAdapter/index.js

@@ -0,0 +1,14 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'DeltaAdapter',
+        displayName: 'MUMmer delta adapter',
+        configSchema,
+        adapterMetadata: {
+            hiddenFromGUI: true,
+        },
+        getAdapterClass: () => import('./DeltaAdapter').then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/DeltaAdapter/index.js.map

@@ -0,0 +1 @@
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package/esm/DeltaAdapter/util.d.ts

@@ -0,0 +1,17 @@
+/// <reference types="node" />
+export declare function paf_delta2paf(buffer: Buffer): {
+    qname: string;
+    qstart: number;
+    qend: number;
+    tname: string;
+    tstart: number;
+    tend: number;
+    strand: number;
+    extra: {
+        numMatches: number;
+        blockLen: number;
+        mappingQual: number;
+        NM: number;
+        cg: string;
+    };
+}[];

package/esm/DeltaAdapter/util.js

@@ -0,0 +1,148 @@
+const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+/* paf2delta from paftools.js in the minimap2 repository, license reproduced below
+ *
+ * The MIT License
+ *
+ * Copyright (c) 2018-     Dana-Farber Cancer Institute
+ *               2017-2018 Broad Institute, Inc.
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject to
+ * the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+export function paf_delta2paf(buffer) {
+    let rname = '';
+    let qname = '';
+    let qs = 0;
+    let qe = 0;
+    let rs = 0;
+    let re = 0;
+    let strand = 0;
+    let NM = 0;
+    let cigar = [];
+    let x = 0;
+    let y = 0;
+    let seen_gt = false;
+    const records = [];
+    const regex = new RegExp(/^>(\S+)\s+(\S+)\s+(\d+)\s+(\d+)/);
+    let blockStart = 0;
+    let i = 0;
+    while (blockStart < buffer.length) {
+        const n = buffer.indexOf('\n', blockStart);
+        if (n === -1) {
+            break;
+        }
+        const b = buffer.slice(blockStart, n);
+        const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).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 = +(t0 < t1 ? t0 : t1) - 1;
+                re = +(t1 > t0 ? t1 : t0);
+                qs = +(t2 < t3 ? t2 : t3) - 1;
+                qe = +(t3 > t2 ? 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 ${i}`);
+                    }
+                    cigar.push((re - rs - x) << 4);
+                    for (let i = 0; i < cigar.length; ++i) {
+                        const rlen = cigar[i] >> 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 if (d > 0) {
+                    const l = d - 1;
+                    x += l + 1;
+                    y += l;
+                    if (l > 0) {
+                        cigar.push(l << 4);
+                    }
+                    // eslint-disable-next-line unicorn/prefer-at
+                    if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 2) {
+                        cigar[cigar.length - 1] += 1 << 4;
+                    }
+                    else {
+                        cigar.push((1 << 4) | 2);
+                    } // deletion
+                }
+                else {
+                    const l = -d - 1;
+                    x += l;
+                    y += l + 1;
+                    if (l > 0) {
+                        cigar.push(l << 4);
+                    }
+                    // eslint-disable-next-line unicorn/prefer-at
+                    if (cigar.length > 0 && (cigar[cigar.length - 1] & 0xf) === 1) {
+                        cigar[cigar.length - 1] += 1 << 4;
+                    }
+                    else {
+                        cigar.push((1 << 4) | 1);
+                    } // insertion
+                }
+            }
+        }
+    }
+    return records;
+}
+//# sourceMappingURL=util.js.map

package/esm/DeltaAdapter/util.js.map

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package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts

@@ -0,0 +1,33 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Feature, Region } from '@jbrowse/core/util';
+interface BareFeature {
+    strand: number;
+    refName: string;
+    start: number;
+    end: number;
+    score: number;
+    name: string;
+}
+type Row = [BareFeature, BareFeature, number, number];
+export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
+    private setupP?;
+    static capabilities: string[];
+    setup(opts: BaseOptions): Promise<{
+        assemblyNames: string[];
+        feats: Row[];
+    }>;
+    setupPre(opts: BaseOptions): Promise<{
+        assemblyNames: string[];
+        feats: Row[];
+    }>;
+    hasDataForRefName(): Promise<boolean>;
+    getRefNames(): Promise<never[]>;
+    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the foreseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources(): void;
+}
+export {};

package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -0,0 +1,94 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { doesIntersect2, SimpleFeature, } from '@jbrowse/core/util';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { readFile, parseBed } from '../util';
+class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
+    async setup(opts) {
+        if (!this.setupP) {
+            this.setupP = this.setupPre(opts).catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
+    }
+    async setupPre(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 bed1Map = parseBed(bed1text);
+        const bed2Map = parseBed(bed2text);
+        const feats = mcscantext
+            .split(/\n|\r\n|\r/)
+            .filter(f => !!f && f !== '###')
+            .map((line, index) => {
+            const [name1, name2, score] = line.split('\t');
+            const r1 = bed1Map.get(name1);
+            const r2 = bed2Map.get(name2);
+            if (!r1 || !r2) {
+                throw new Error(`feature not found, ${name1} ${name2} ${r1} ${r2}`);
+            }
+            return [r1, r2, +score, index];
+        });
+        return {
+            assemblyNames,
+            feats,
+        };
+    }
+    async hasDataForRefName() {
+        // determining this properly is basically a call to getFeatures
+        // so is not really that important, and has to be true or else
+        // getFeatures is never called (BaseFeatureDataAdapter filters it out)
+        return true;
+    }
+    async getRefNames() {
+        // we cannot determine this accurately
+        return [];
+    }
+    getFeatures(region, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { assemblyNames, feats } = await this.setup(opts);
+            // The index of the assembly name in the region list corresponds to
+            // the adapter in the subadapters list
+            const index = assemblyNames.indexOf(region.assemblyName);
+            if (index !== -1) {
+                const flip = index === 0;
+                feats.forEach(f => {
+                    const [r1, r2, score, rowNum] = f;
+                    const [f1, f2] = !flip ? [r2, r1] : [r1, r2];
+                    if (f1.refName === region.refName &&
+                        doesIntersect2(region.start, region.end, f1.start, f1.end)) {
+                        observer.next(new SimpleFeature({
+                            ...f1,
+                            uniqueId: `${index}-${rowNum}`,
+                            syntenyId: rowNum,
+                            // note: strand would be -1 if the two features are on opposite
+                            // strands, indicating inverted alignment
+                            strand: f1.strand * f2.strand,
+                            assemblyName: assemblyNames[+!flip],
+                            score,
+                            mate: {
+                                ...f2,
+                                assemblyName: assemblyNames[+flip],
+                            },
+                        }));
+                    }
+                });
+            }
+            observer.complete();
+        });
+    }
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the foreseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources( /* { region } */) { }
+}
+MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
+export default MCScanAnchorsAdapter;
+//# sourceMappingURL=MCScanAnchorsAdapter.js.map

package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js.map

@@ -0,0 +1 @@
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package/esm/MCScanAnchorsAdapter/configSchema.d.ts

@@ -0,0 +1,40 @@
+declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    mcscanAnchorsLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    bed1Location: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    bed2Location: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: string;
+        defaultValue: never[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default MCScanAnchorsAdapter;