@jbrowse/plugin-comparative-adapters 2.15.3 → 2.16.0

package/dist/ChainAdapter/ChainAdapter.js

@@ -6,6 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+// locals
 const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
 const util_2 = require("./util");
 class ChainAdapter extends PAFAdapter_1.default {

package/dist/ChainAdapter/util.d.ts

@@ -1,3 +1,4 @@
+import type { Buffer } from 'buffer';
 export declare function paf_chain2paf(buffer: Buffer): {
     qname: string;
     qstart: number;

package/dist/DeltaAdapter/DeltaAdapter.js

@@ -5,15 +5,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const io_1 = require("@jbrowse/core/util/io");
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const util_1 = require("@jbrowse/core/util");
+// locals
 const PAFAdapter_1 = __importDefault(require("../PAFAdapter/PAFAdapter"));
-const util_1 = require("./util");
-const util_2 = require("@jbrowse/core/util");
+const util_2 = require("./util");
 class DeltaAdapter extends PAFAdapter_1.default {
     async setupPre(opts) {
         const loc = (0, io_1.openLocation)(this.getConf('deltaLocation'), this.pluginManager);
         const buffer = (await loc.readFile(opts));
-        const buf = (0, util_2.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
-        return (0, util_1.paf_delta2paf)(buf);
+        const buf = (0, util_1.isGzip)(buffer) ? await (0, bgzf_filehandle_1.unzip)(buffer) : buffer;
+        return (0, util_2.paf_delta2paf)(buf);
     }
 }
 exports.default = DeltaAdapter;

package/dist/DeltaAdapter/util.d.ts

@@ -1,3 +1,4 @@
+import type { Buffer } from 'buffer';
 export declare function paf_delta2paf(buffer: Buffer): {
     qname: string;
     qstart: number;

package/dist/DeltaAdapter/util.js

@@ -74,10 +74,10 @@ function paf_delta2paf(buffer) {
                 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);
+                rs = +Math.min(t0, t1) - 1;
+                re = +Math.max(t1, t0);
+                qs = +Math.min(t2, t3) - 1;
+                qe = +Math.max(t3, t2);
                 x = y = 0;
                 NM = t4;
                 cigar = [];

package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts

@@ -21,7 +21,8 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         feats: Row[];
     }>;
     hasDataForRefName(): Promise<boolean>;
-    getRefNames(): Promise<never[]>;
+    getAssemblyNames(): string[];
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region

package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -42,13 +42,29 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         };
     }
     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)
+        // 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
+    getAssemblyNames() {
+        const assemblyNames = this.getConf('assemblyNames');
+        return assemblyNames;
+    }
+    async getRefNames(opts = {}) {
+        var _a;
+        // @ts-expect-error
+        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        const { feats } = await this.setup(opts);
+        const idx = this.getAssemblyNames().indexOf(r1);
+        if (idx !== -1) {
+            const set = new Set();
+            for (const feat of feats) {
+                set.add(idx === 0 ? feat[0].refName : feat[1].refName);
+            }
+            return [...set];
+        }
+        console.warn('Unable to do ref renaming on adapter');
         return [];
     }
     getFeatures(region, opts = {}) {

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.d.ts

@@ -29,7 +29,8 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         feats: Row[];
     }>;
     hasDataForRefName(): Promise<boolean>;
-    getRefNames(): Promise<never[]>;
+    getAssemblyNames(): string[];
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -61,8 +61,31 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         // getFeatures is never called (BaseFeatureDataAdapter filters it out)
         return true;
     }
-    async getRefNames() {
-        // we cannot determine this accurately
+    getAssemblyNames() {
+        const assemblyNames = this.getConf('assemblyNames');
+        return assemblyNames;
+    }
+    async getRefNames(opts = {}) {
+        var _a;
+        // @ts-expect-error
+        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        const { feats } = await this.setup(opts);
+        const idx = this.getAssemblyNames().indexOf(r1);
+        if (idx !== -1) {
+            const set = new Set();
+            for (const feat of feats) {
+                if (idx === 0) {
+                    set.add(feat[0].refName);
+                    set.add(feat[1].refName);
+                }
+                else {
+                    set.add(feat[2].refName);
+                    set.add(feat[3].refName);
+                }
+            }
+            return [...set];
+        }
+        console.warn('Unable to do ref renaming on adapter');
         return [];
     }
     getFeatures(region, opts = {}) {

package/dist/util.d.ts

@@ -1,5 +1,6 @@
 import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { GenericFilehandle } from 'generic-filehandle';
+import type { Buffer } from 'buffer';
 import { PAFRecord } from './PAFAdapter/util';
 export declare function parseBed(text: string): Map<string | undefined, {
     refName: string | undefined;

package/esm/ChainAdapter/ChainAdapter.js

@@ -1,6 +1,7 @@
 import { openLocation } from '@jbrowse/core/util/io';
 import { isGzip } from '@jbrowse/core/util';
 import { unzip } from '@gmod/bgzf-filehandle';
+// locals
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
 import { paf_chain2paf } from './util';
 export default class ChainAdapter extends PAFAdapter {

package/esm/ChainAdapter/util.d.ts

@@ -1,3 +1,4 @@
+import type { Buffer } from 'buffer';
 export declare function paf_chain2paf(buffer: Buffer): {
     qname: string;
     qstart: number;

package/esm/DeltaAdapter/DeltaAdapter.js

@@ -1,8 +1,9 @@
 import { openLocation } from '@jbrowse/core/util/io';
 import { unzip } from '@gmod/bgzf-filehandle';
+import { isGzip } from '@jbrowse/core/util';
+// locals
 import PAFAdapter from '../PAFAdapter/PAFAdapter';
 import { paf_delta2paf } from './util';
-import { isGzip } from '@jbrowse/core/util';
 export default class DeltaAdapter extends PAFAdapter {
     async setupPre(opts) {
         const loc = openLocation(this.getConf('deltaLocation'), this.pluginManager);

package/esm/DeltaAdapter/util.d.ts

@@ -1,3 +1,4 @@
+import type { Buffer } from 'buffer';
 export declare function paf_delta2paf(buffer: Buffer): {
     qname: string;
     qstart: number;

package/esm/DeltaAdapter/util.js

@@ -71,10 +71,10 @@ export function paf_delta2paf(buffer) {
                 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);
+                rs = +Math.min(t0, t1) - 1;
+                re = +Math.max(t1, t0);
+                qs = +Math.min(t2, t3) - 1;
+                qe = +Math.max(t3, t2);
                 x = y = 0;
                 NM = t4;
                 cigar = [];

package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts

@@ -21,7 +21,8 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         feats: Row[];
     }>;
     hasDataForRefName(): Promise<boolean>;
-    getRefNames(): Promise<never[]>;
+    getAssemblyNames(): string[];
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region

package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -40,13 +40,29 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         };
     }
     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)
+        // 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
+    getAssemblyNames() {
+        const assemblyNames = this.getConf('assemblyNames');
+        return assemblyNames;
+    }
+    async getRefNames(opts = {}) {
+        var _a;
+        // @ts-expect-error
+        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        const { feats } = await this.setup(opts);
+        const idx = this.getAssemblyNames().indexOf(r1);
+        if (idx !== -1) {
+            const set = new Set();
+            for (const feat of feats) {
+                set.add(idx === 0 ? feat[0].refName : feat[1].refName);
+            }
+            return [...set];
+        }
+        console.warn('Unable to do ref renaming on adapter');
         return [];
     }
     getFeatures(region, opts = {}) {

package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.d.ts

@@ -29,7 +29,8 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         feats: Row[];
     }>;
     hasDataForRefName(): Promise<boolean>;
-    getRefNames(): Promise<never[]>;
+    getAssemblyNames(): string[];
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region

package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -56,8 +56,31 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
         // getFeatures is never called (BaseFeatureDataAdapter filters it out)
         return true;
     }
-    async getRefNames() {
-        // we cannot determine this accurately
+    getAssemblyNames() {
+        const assemblyNames = this.getConf('assemblyNames');
+        return assemblyNames;
+    }
+    async getRefNames(opts = {}) {
+        var _a;
+        // @ts-expect-error
+        const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
+        const { feats } = await this.setup(opts);
+        const idx = this.getAssemblyNames().indexOf(r1);
+        if (idx !== -1) {
+            const set = new Set();
+            for (const feat of feats) {
+                if (idx === 0) {
+                    set.add(feat[0].refName);
+                    set.add(feat[1].refName);
+                }
+                else {
+                    set.add(feat[2].refName);
+                    set.add(feat[3].refName);
+                }
+            }
+            return [...set];
+        }
+        console.warn('Unable to do ref renaming on adapter');
         return [];
     }
     getFeatures(region, opts = {}) {

package/esm/util.d.ts

@@ -1,5 +1,6 @@
 import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { GenericFilehandle } from 'generic-filehandle';
+import type { Buffer } from 'buffer';
 import { PAFRecord } from './PAFAdapter/util';
 export declare function parseBed(text: string): Map<string | undefined, {
     refName: string | undefined;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "2.15.3",
+  "version": "2.16.0",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c0f82fe7b210622dd462e702641cc6da01109c6e"
+  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
 }