@jbrowse/plugin-breakpoint-split-view 2.16.1 → 2.17.0

package/dist/BreakpointSplitView/components/AlignmentConnections.js

@@ -49,9 +49,9 @@ const AlignmentConnections = (0, mobx_react_1.observer)(function ({ model, track
             ? (0, util_2.getBadlyPairedAlignments)(allFeatures)
             : (0, util_2.getMatchedAlignmentFeatures)(allFeatures));
         if (!hasPaired) {
-            layoutMatches.forEach(m => {
-                m.sort((a, b) => a.feature.get('clipPos') - b.feature.get('clipPos'));
-            });
+            for (const m of layoutMatches) {
+                m.sort((a, b) => a.clipPos - b.clipPos);
+            }
         }
         return layoutMatches;
     }, [allFeatures, trackId, hasPaired, model]);

package/dist/BreakpointSplitView/components/util.js

@@ -33,20 +33,17 @@ function getBadlyPairedAlignments(features) {
     }
     return [...candidates.values()].filter(v => v.length > 1);
 }
-function getTag(f, tag) {
-    const tags = f.get('tags');
-    return tags ? tags[tag] : f.get(tag);
-}
 // this finds candidate alignment features, aimed at plotting split reads from
 // BAM/CRAM files
 function getMatchedAlignmentFeatures(features) {
+    var _a;
     const candidates = new Map();
     const alreadySeen = new Set();
     // this finds candidate features that share the same name
     for (const feature of features.values()) {
         const id = feature.id();
         const unmapped = feature.get('flags') & 4;
-        const hasSA = !!getTag(feature, 'SA');
+        const hasSA = !!((_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a.SA);
         if (!alreadySeen.has(id) && !unmapped && hasSA) {
             const n = feature.get('name');
             let val = candidates.get(n);

package/dist/BreakpointSplitView/model.d.ts

@@ -3,6 +3,7 @@ import { Instance } from 'mobx-state-tree';
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { Feature } from '@jbrowse/core/util';
+export declare function getClip(cigar: string, strand: number): number;
 export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
     filename?: string;
@@ -319,6 +320,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         feature: Feature;
         layout: LayoutRecord | undefined;
         level: number;
+        clipPos: number;
     }[][];
 } & {
     afterAttach(): void;

package/dist/BreakpointSplitView/model.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.getClip = getClip;
 exports.default = stateModelFactory;
 const react_1 = require("react");
 const mobx_state_tree_1 = require("mobx-state-tree");
@@ -41,6 +42,13 @@ const Link_1 = __importDefault(require("@mui/icons-material/Link"));
 const util_2 = require("./util");
 // lazies
 const ExportSvgDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ExportSvgDialog'))));
+const startClip = new RegExp(/(\d+)[SH]$/);
+const endClip = new RegExp(/^(\d+)([SH])/);
+function getClip(cigar, strand) {
+    return strand === -1
+        ? +(startClip.exec(cigar) || [])[1] || 0
+        : +(endClip.exec(cigar) || [])[1] || 0;
+}
 function calc(track, f) {
     var _a, _b;
     return (_b = (_a = track.displays[0]).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, f.id());
@@ -178,6 +186,7 @@ function stateModelFactory(pluginManager) {
                         feature,
                         layout: calc(tracks[level], feature),
                         level,
+                        clipPos: getClip(feature.get('CIGAR'), feature.get('strand')),
                     }
                     : undefined;
             })

package/esm/BreakpointSplitView/components/AlignmentConnections.js

@@ -24,9 +24,9 @@ const AlignmentConnections = observer(function ({ model, trackId, parentRef, get
             ? getBadlyPairedAlignments(allFeatures)
             : getMatchedAlignmentFeatures(allFeatures));
         if (!hasPaired) {
-            layoutMatches.forEach(m => {
-                m.sort((a, b) => a.feature.get('clipPos') - b.feature.get('clipPos'));
-            });
+            for (const m of layoutMatches) {
+                m.sort((a, b) => a.clipPos - b.clipPos);
+            }
         }
         return layoutMatches;
     }, [allFeatures, trackId, hasPaired, model]);

package/esm/BreakpointSplitView/components/util.js

@@ -24,20 +24,17 @@ export function getBadlyPairedAlignments(features) {
     }
     return [...candidates.values()].filter(v => v.length > 1);
 }
-function getTag(f, tag) {
-    const tags = f.get('tags');
-    return tags ? tags[tag] : f.get(tag);
-}
 // this finds candidate alignment features, aimed at plotting split reads from
 // BAM/CRAM files
 export function getMatchedAlignmentFeatures(features) {
+    var _a;
     const candidates = new Map();
     const alreadySeen = new Set();
     // this finds candidate features that share the same name
     for (const feature of features.values()) {
         const id = feature.id();
         const unmapped = feature.get('flags') & 4;
-        const hasSA = !!getTag(feature, 'SA');
+        const hasSA = !!((_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a.SA);
         if (!alreadySeen.has(id) && !unmapped && hasSA) {
             const n = feature.get('name');
             let val = candidates.get(n);

package/esm/BreakpointSplitView/model.d.ts

@@ -3,6 +3,7 @@ import { Instance } from 'mobx-state-tree';
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { Feature } from '@jbrowse/core/util';
+export declare function getClip(cigar: string, strand: number): number;
 export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
     filename?: string;
@@ -319,6 +320,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         feature: Feature;
         layout: LayoutRecord | undefined;
         level: number;
+        clipPos: number;
     }[][];
 } & {
     afterAttach(): void;

package/esm/BreakpointSplitView/model.js

@@ -12,6 +12,13 @@ import LinkIcon from '@mui/icons-material/Link';
 import { intersect } from './util';
 // lazies
 const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
+const startClip = new RegExp(/(\d+)[SH]$/);
+const endClip = new RegExp(/^(\d+)([SH])/);
+export function getClip(cigar, strand) {
+    return strand === -1
+        ? +(startClip.exec(cigar) || [])[1] || 0
+        : +(endClip.exec(cigar) || [])[1] || 0;
+}
 function calc(track, f) {
     var _a, _b;
     return (_b = (_a = track.displays[0]).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, f.id());
@@ -149,6 +156,7 @@ export default function stateModelFactory(pluginManager) {
                         feature,
                         layout: calc(tracks[level], feature),
                         level,
+                        clipPos: getClip(feature.get('CIGAR'), feature.get('strand')),
                     }
                     : undefined;
             })

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-breakpoint-split-view",
-  "version": "2.16.1",
+  "version": "2.17.0",
   "description": "JBrowse 2 breakpoint detail split view",
   "keywords": [
     "jbrowse",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }