@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/dist/SNPCoverageAdapter/util.d.ts

@@ -0,0 +1,29 @@
+export interface SkipMap {
+    [key: string]: {
+        score: number;
+        feature: unknown;
+        start: number;
+        end: number;
+        strand: number;
+        xs: string;
+    };
+}
+export interface BinType {
+    total?: number;
+    strands?: {
+        [key: string]: number;
+    };
+}
+export interface Bin {
+    refbase?: string;
+    total: number;
+    all: number;
+    ref: number;
+    '-1': number;
+    '0': number;
+    '1': number;
+    lowqual: BinType;
+    cov: BinType;
+    delskips: BinType;
+    noncov: BinType;
+}

package/dist/SNPCoverageAdapter/util.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=util.js.map

package/dist/SNPCoverageAdapter/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/util.ts"],"names":[],"mappings":""}

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts

@@ -13,7 +13,7 @@ export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserializ
         values: number[];
     };
     displayCrossHatches: boolean;
-    modificationTagMap?: Record<string, string>;
+    modificationTagMap?: Record<string, string | undefined>;
 }
 export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -48,10 +48,10 @@ class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
             C: bases.C.main,
             G: bases.G.main,
             T: bases.T.main,
-            total: 'lightgrey',
             insertion: 'purple',
             softclip: 'blue',
             hardclip: 'red',
+            total: (0, configuration_1.readConfObject)(cfg, 'color'),
             meth: 'red',
             unmeth: 'blue',
         };
@@ -95,7 +95,7 @@ class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
                 ctx.fillStyle =
                     colorForBase[base] ||
                         modificationTagMap[base.replace('mod_', '')] ||
-                        '#888';
+                        'black';
                 const height = toHeight(score);
                 const bottom = toY(score) + height;
                 ctx.fillRect(Math.round(leftPx), bottom - ((total + curr) / score) * height, w, (total / score) * height);

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map

@@ -1 +1 @@
-{"version":3,"file":"SNPCoverageRenderer.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/SNPCoverageRenderer.ts"],"names":[],"mappings":";;AAAA,yCAAqD;AACrD,6CAAqE;AACrE,+DAA4D;AAE5D,0DAM+B;AA2B/B,MAAM,WAAW,GAAG,GAAG,CAAA;AAEvB,MAAqB,mBAAoB,SAAQ,kCAAkB;IACjE,4EAA4E;IAC5E,kDAAkD;IAClD,KAAK,CAAC,IAAI,CACR,GAA6B,EAC7B,KAAyC;QAEzC,MAAM,EACJ,QAAQ,EACR,OAAO,EACP,OAAO,EACP,mBAAmB,EACnB,kBAAkB,GAAG,EAAE,EACvB,SAAS,EACT,MAAM,EAAE,gBAAgB,EACxB,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,GAAG,EACX,KAAK,GACN,GAAG,KAAK,CAAA;QACT,MAAM,KAAK,GAAG,IAAA,uBAAkB,EAAC,WAAW,CAAC,CAAA;QAC7C,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;QACxB,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QAEnD,yEAAyE;QACzE,oEAAoE;QACpE,iDAAiD;QACjD,MAAM,MAAM,GAAG,sCAAsB,CAAA;QACrC,MAAM,MAAM,GAAG,gBAAgB,GAAG,MAAM,GAAG,CAAC,CAAA;QAE5C,MAAM,EAAE,MAAM,EAAE,GAAG,SAAS,CAAA;QAC5B,IAAI,CAAC,MAAM,EAAE;YACX,OAAM;SACP;QACD,MAAM,IAAI,GAAG,EAAE,GAAG,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,CAAC,EAAE,CAAA;QACjD,MAAM,SAAS,GAAG,IAAA,wBAAQ,EAAC,IAAI,CAAC,CAAA;QAEhC,mEAAmE;QACnE,MAAM,kBAAkB,GAAG,IAAA,wBAAQ,EAAC;YAClC,GAAG,IAAI;YACP,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,GAAG,CAAC,CAAC;YACtB,SAAS,EAAE,QAAQ;SACpB,CAAC,CAAA;QACF,MAAM,OAAO,GAAG,IAAA,yBAAS,EAAC,SAAS,CAAC,SAAS,CAAC,CAAA;QAC9C,MAAM,YAAY,GAAG,IAAA,yBAAS,EAAC,QAAQ,CAAC,CAAA;QAExC,MAAM,kBAAkB,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,oBAAoB,CAAC,CAAA;QACpE,MAAM,mBAAmB,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,qBAAqB,CAAC,CAAA;QACtE,MAAM,QAAQ,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,UAAU,CAAC,CAAA;QAChD,MAAM,cAAc,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,gBAAgB,CAAC,CAAA;QAE5D,sEAAsE;QACtE,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAChE,MAAM,QAAQ,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QACrD,kCAAkC;QAClC,MAAM,IAAI,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,kBAAkB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAC1E,MAAM,SAAS,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QAE7D,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,OAAO,CAAA;QAC/B,MAAM,YAAY,GAA8B;YAC9C,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,KAAK,EAAE,WAAW;YAClB,SAAS,EAAE,QAAQ;YACnB,QAAQ,EAAE,MAAM;YAChB,QAAQ,EAAE,KAAK;YACf,IAAI,EAAE,KAAK;YACX,MAAM,EAAE,MAAM;SACf,CAAA;QAED,MAAM,KAAK,GAAG,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;QACpC,MAAM,QAAQ,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAC5D,MAAM,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAEzD,wEAAwE;QACxE,+CAA+C;QAC/C,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,KAAK,CAAA;QAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAA,oBAAa,EAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YACjE,MAAM,CAAC,GAAG,OAAO,GAAG,MAAM,GAAG,WAAW,CAAA;YACxC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAA;SACrD;QAED,0EAA0E;QAC1E,2EAA2E;QAC3E,0EAA0E;QAC1E,0EAA0E;QAC1E,wEAAwE;QACxE,IAAI,SAAS,GAAG,CAAC,CAAA;QAEjB,wEAAwE;QACxE,+DAA+D;QAC/D,MAAM,8BAA8B,GAAG,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAExE,yEAAyE;QACzE,yEAAyE;QACzE,oCAAoC;QAEpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAA,oBAAa,EAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YAEjE,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAY,CAAA;YACjD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,GAAG,MAAM,EAAE,CAAC,CAAC,CAAA;YACvC,MAAM,UAAU,GAAG,OAAO,CAAC,KAAK,CAAA;YAChC,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAA;YAE5C,IAAI,IAAI,GAAG,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACpC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;gBACpB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;gBACnC,GAAG,CAAC,SAAS;oBACX,YAAY,CAAC,IAAI,CAAC;wBAClB,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;wBAC5C,MAAM,CAAA;gBAER,MAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;gBAC9B,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,MAAM,CAAA;gBAClC,GAAG,CAAC,QAAQ,CACV,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,EAClB,MAAM,GAAG,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,KAAK,CAAC,GAAG,MAAM,EAC1C,CAAC,EACD,CAAC,KAAK,GAAG,KAAK,CAAC,GAAG,MAAM,CACzB,CAAA;gBACD,IAAI,IAAI,KAAK,CAAA;aACd;YAED,MAAM,eAAe,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YACnD,MAAM,eAAe,GAAG,GAAG,CAAA;YAC3B,IAAI,mBAAmB,EAAE;gBACvB,IAAI,IAAI,GAAG,CAAC,CAAA;gBACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/C,MAAM,IAAI,GAAG,eAAe,CAAC,CAAC,CAAC,CAAA;oBAC/B,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;oBACtC,MAAM,CAAC,GAAG,GAAG,CAAA;oBACb,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;oBAClC,GAAG,CAAC,QAAQ,CACV,MAAM,GAAG,CAAC,GAAG,8BAA8B,EAC3C,eAAe,GAAG,SAAS,CAAC,IAAI,CAAC,EACjC,CAAC,GAAG,CAAC,EACL,SAAS,CAAC,KAAK,CAAC,CACjB,CAAA;oBACD,IAAI,IAAI,KAAK,CAAA;iBACd;aACF;YAED,IAAI,cAAc,EAAE;gBAClB,IAAI,KAAK,GAAG,CAAC,CAAA;gBACb,IAAI,GAAG,GAAG,CAAC,CAAA;gBACX,IAAI,OAAO,GAAG,EAAE,CAAA;gBAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/C,MAAM,IAAI,GAAG,eAAe,CAAC,CAAC,CAAC,CAAA;oBAC/B,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;oBACtC,KAAK,IAAI,KAAK,CAAA;oBACd,IAAI,KAAK,GAAG,GAAG,EAAE;wBACf,GAAG,GAAG,KAAK,CAAA;wBACX,OAAO,GAAG,IAAI,CAAA;qBACf;iBACF;gBAED,mEAAmE;gBACnE,8DAA8D;gBAC9D,MAAM,wBAAwB,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,EAAE,SAAS,CAAC,CAAA;gBAChE,IACE,KAAK,GAAG,wBAAwB,GAAG,kBAAkB;oBACrD,wBAAwB,GAAG,CAAC,EAC5B;oBACA,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;oBACrC,GAAG,CAAC,SAAS,EAAE,CAAA;oBACf,MAAM,CAAC,GAAG,MAAM,GAAG,8BAA8B,CAAA;oBACjD,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;oBACtB,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;oBACtB,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,eAAe,CAAC,CAAA;oBAC9B,GAAG,CAAC,IAAI,EAAE,CAAA;iBACX;aACF;YACD,SAAS,GAAG,UAAU,CAAA;SACvB;QAED,IAAI,QAAQ,EAAE;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACrC,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBAClB,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,GAAG,IAAA,eAAQ,EAC5B,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EACd,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EACZ,MAAM,EACN,OAAO,CACR,CAAA;gBAED,GAAG,CAAC,SAAS,EAAE,CAAA;gBACf,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAW,CAAA;gBACrC,MAAM,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,IAAI,CAAW,CAAA;gBAChC,MAAM,GAAG,GAAG,uBAAuB,CAAA;gBACnC,MAAM,GAAG,GAAG,uBAAuB,CAAA;gBACnC,MAAM,OAAO,GAAG,uBAAuB,CAAA;gBAEvC,IAAI,EAAE,KAAK,GAAG,EAAE;oBACd,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,EAAE,KAAK,GAAG,EAAE;oBACrB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,GAAG,KAAK,CAAC,EAAE;oBACpB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,GAAG,KAAK,CAAC,CAAC,EAAE;oBACrB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM;oBACL,GAAG,CAAC,WAAW,GAAG,OAAO,CAAA;iBAC1B;gBAED,GAAG,CAAC,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAA;gBAC5C,GAAG,CAAC,MAAM,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAC,CAAA;gBACrC,GAAG,CAAC,aAAa,CAAC,IAAI,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAC,CAAA;gBAChE,GAAG,CAAC,MAAM,EAAE,CAAA;aACb;SACF;QAED,IAAI,mBAAmB,EAAE;YACvB,GAAG,CAAC,SAAS,GAAG,CAAC,CAAA;YACjB,GAAG,CAAC,WAAW,GAAG,uBAAuB,CAAA;YACzC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;gBAC1B,GAAG,CAAC,SAAS,EAAE,CAAA;gBACf,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACpC,GAAG,CAAC,MAAM,CAAC,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACxC,GAAG,CAAC,MAAM,EAAE,CAAA;YACd,CAAC,CAAC,CAAA;SACH;IACH,CAAC;CACF;AAtOD,sCAsOC"}
+{"version":3,"file":"SNPCoverageRenderer.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/SNPCoverageRenderer.ts"],"names":[],"mappings":";;AAAA,yCAAqD;AACrD,6CAAqE;AACrE,+DAA4D;AAE5D,0DAM+B;AA2B/B,MAAM,WAAW,GAAG,GAAG,CAAA;AAEvB,MAAqB,mBAAoB,SAAQ,kCAAkB;IACjE,4EAA4E;IAC5E,kDAAkD;IAClD,KAAK,CAAC,IAAI,CACR,GAA6B,EAC7B,KAAyC;QAEzC,MAAM,EACJ,QAAQ,EACR,OAAO,EACP,OAAO,EACP,mBAAmB,EACnB,kBAAkB,GAAG,EAAE,EACvB,SAAS,EACT,MAAM,EAAE,gBAAgB,EACxB,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,GAAG,EACX,KAAK,GACN,GAAG,KAAK,CAAA;QACT,MAAM,KAAK,GAAG,IAAA,uBAAkB,EAAC,WAAW,CAAC,CAAA;QAC7C,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;QACxB,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;QAEnD,yEAAyE;QACzE,oEAAoE;QACpE,iDAAiD;QACjD,MAAM,MAAM,GAAG,sCAAsB,CAAA;QACrC,MAAM,MAAM,GAAG,gBAAgB,GAAG,MAAM,GAAG,CAAC,CAAA;QAE5C,MAAM,EAAE,MAAM,EAAE,GAAG,SAAS,CAAA;QAC5B,IAAI,CAAC,MAAM,EAAE;YACX,OAAM;SACP;QACD,MAAM,IAAI,GAAG,EAAE,GAAG,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,CAAC,EAAE,CAAA;QACjD,MAAM,SAAS,GAAG,IAAA,wBAAQ,EAAC,IAAI,CAAC,CAAA;QAEhC,mEAAmE;QACnE,MAAM,kBAAkB,GAAG,IAAA,wBAAQ,EAAC;YAClC,GAAG,IAAI;YACP,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,GAAG,CAAC,CAAC;YACtB,SAAS,EAAE,QAAQ;SACpB,CAAC,CAAA;QACF,MAAM,OAAO,GAAG,IAAA,yBAAS,EAAC,SAAS,CAAC,SAAS,CAAC,CAAA;QAC9C,MAAM,YAAY,GAAG,IAAA,yBAAS,EAAC,QAAQ,CAAC,CAAA;QAExC,MAAM,kBAAkB,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,oBAAoB,CAAC,CAAA;QACpE,MAAM,mBAAmB,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,qBAAqB,CAAC,CAAA;QACtE,MAAM,QAAQ,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,UAAU,CAAC,CAAA;QAChD,MAAM,cAAc,GAAG,IAAA,8BAAc,EAAC,GAAG,EAAE,gBAAgB,CAAC,CAAA;QAE5D,sEAAsE;QACtE,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAChE,MAAM,QAAQ,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QACrD,kCAAkC;QAClC,MAAM,IAAI,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,MAAM,GAAG,CAAC,kBAAkB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QAC1E,MAAM,SAAS,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QAE7D,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,OAAO,CAAA;QAC/B,MAAM,YAAY,GAA8B;YAC9C,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;YACf,SAAS,EAAE,QAAQ;YACnB,QAAQ,EAAE,MAAM;YAChB,QAAQ,EAAE,KAAK;YACf,KAAK,EAAE,IAAA,8BAAc,EAAC,GAAG,EAAE,OAAO,CAAC;YACnC,IAAI,EAAE,KAAK;YACX,MAAM,EAAE,MAAM;SACf,CAAA;QAED,MAAM,KAAK,GAAG,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;QACpC,MAAM,QAAQ,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAC5D,MAAM,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAA;QAEzD,wEAAwE;QACxE,+CAA+C;QAC/C,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,KAAK,CAAA;QAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAA,oBAAa,EAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YACjE,MAAM,CAAC,GAAG,OAAO,GAAG,MAAM,GAAG,WAAW,CAAA;YACxC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAA;SACrD;QAED,0EAA0E;QAC1E,2EAA2E;QAC3E,0EAA0E;QAC1E,0EAA0E;QAC1E,wEAAwE;QACxE,IAAI,SAAS,GAAG,CAAC,CAAA;QAEjB,wEAAwE;QACxE,+DAA+D;QAC/D,MAAM,8BAA8B,GAAG,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAExE,yEAAyE;QACzE,yEAAyE;QACzE,oCAAoC;QAEpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAA,oBAAa,EAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YAEjE,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAW,CAAA;YAC5C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAY,CAAA;YACjD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,GAAG,MAAM,EAAE,CAAC,CAAC,CAAA;YACvC,MAAM,UAAU,GAAG,OAAO,CAAC,KAAK,CAAA;YAChC,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAA;YAE5C,IAAI,IAAI,GAAG,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACpC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;gBACpB,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;gBACnC,GAAG,CAAC,SAAS;oBACX,YAAY,CAAC,IAAI,CAAC;wBAClB,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;wBAC5C,OAAO,CAAA;gBAET,MAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;gBAC9B,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,MAAM,CAAA;gBAClC,GAAG,CAAC,QAAQ,CACV,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,EAClB,MAAM,GAAG,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,KAAK,CAAC,GAAG,MAAM,EAC1C,CAAC,EACD,CAAC,KAAK,GAAG,KAAK,CAAC,GAAG,MAAM,CACzB,CAAA;gBACD,IAAI,IAAI,KAAK,CAAA;aACd;YAED,MAAM,eAAe,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YACnD,MAAM,eAAe,GAAG,GAAG,CAAA;YAC3B,IAAI,mBAAmB,EAAE;gBACvB,IAAI,IAAI,GAAG,CAAC,CAAA;gBACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/C,MAAM,IAAI,GAAG,eAAe,CAAC,CAAC,CAAC,CAAA;oBAC/B,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;oBACtC,MAAM,CAAC,GAAG,GAAG,CAAA;oBACb,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;oBAClC,GAAG,CAAC,QAAQ,CACV,MAAM,GAAG,CAAC,GAAG,8BAA8B,EAC3C,eAAe,GAAG,SAAS,CAAC,IAAI,CAAC,EACjC,CAAC,GAAG,CAAC,EACL,SAAS,CAAC,KAAK,CAAC,CACjB,CAAA;oBACD,IAAI,IAAI,KAAK,CAAA;iBACd;aACF;YAED,IAAI,cAAc,EAAE;gBAClB,IAAI,KAAK,GAAG,CAAC,CAAA;gBACb,IAAI,GAAG,GAAG,CAAC,CAAA;gBACX,IAAI,OAAO,GAAG,EAAE,CAAA;gBAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/C,MAAM,IAAI,GAAG,eAAe,CAAC,CAAC,CAAC,CAAA;oBAC/B,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;oBACtC,KAAK,IAAI,KAAK,CAAA;oBACd,IAAI,KAAK,GAAG,GAAG,EAAE;wBACf,GAAG,GAAG,KAAK,CAAA;wBACX,OAAO,GAAG,IAAI,CAAA;qBACf;iBACF;gBAED,mEAAmE;gBACnE,8DAA8D;gBAC9D,MAAM,wBAAwB,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,EAAE,SAAS,CAAC,CAAA;gBAChE,IACE,KAAK,GAAG,wBAAwB,GAAG,kBAAkB;oBACrD,wBAAwB,GAAG,CAAC,EAC5B;oBACA,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;oBACrC,GAAG,CAAC,SAAS,EAAE,CAAA;oBACf,MAAM,CAAC,GAAG,MAAM,GAAG,8BAA8B,CAAA;oBACjD,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;oBACtB,GAAG,CAAC,MAAM,CAAC,CAAC,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;oBACtB,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,eAAe,CAAC,CAAA;oBAC9B,GAAG,CAAC,IAAI,EAAE,CAAA;iBACX;aACF;YACD,SAAS,GAAG,UAAU,CAAA;SACvB;QAED,IAAI,QAAQ,EAAE;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACrC,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBAClB,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,GAAG,IAAA,eAAQ,EAC5B,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EACd,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EACZ,MAAM,EACN,OAAO,CACR,CAAA;gBAED,GAAG,CAAC,SAAS,EAAE,CAAA;gBACf,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAW,CAAA;gBACrC,MAAM,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,IAAI,CAAW,CAAA;gBAChC,MAAM,GAAG,GAAG,uBAAuB,CAAA;gBACnC,MAAM,GAAG,GAAG,uBAAuB,CAAA;gBACnC,MAAM,OAAO,GAAG,uBAAuB,CAAA;gBAEvC,IAAI,EAAE,KAAK,GAAG,EAAE;oBACd,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,EAAE,KAAK,GAAG,EAAE;oBACrB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,GAAG,KAAK,CAAC,EAAE;oBACpB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM,IAAI,GAAG,KAAK,CAAC,CAAC,EAAE;oBACrB,GAAG,CAAC,WAAW,GAAG,GAAG,CAAA;iBACtB;qBAAM;oBACL,GAAG,CAAC,WAAW,GAAG,OAAO,CAAA;iBAC1B;gBAED,GAAG,CAAC,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAA;gBAC5C,GAAG,CAAC,MAAM,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAC,CAAA;gBACrC,GAAG,CAAC,aAAa,CAAC,IAAI,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAC,CAAA;gBAChE,GAAG,CAAC,MAAM,EAAE,CAAA;aACb;SACF;QAED,IAAI,mBAAmB,EAAE;YACvB,GAAG,CAAC,SAAS,GAAG,CAAC,CAAA;YACjB,GAAG,CAAC,WAAW,GAAG,uBAAuB,CAAA;YACzC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;gBAC1B,GAAG,CAAC,SAAS,EAAE,CAAA;gBACf,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACpC,GAAG,CAAC,MAAM,CAAC,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACxC,GAAG,CAAC,MAAM,EAAE,CAAA;YACd,CAAC,CAAC,CAAA;SACH;IACH,CAAC;CACF;AAtOD,sCAsOC"}

package/dist/SNPCoverageRenderer/configSchema.d.ts

@@ -1,2 +1,48 @@
-declare const SNPCoverageRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const SNPCoverageRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    indicatorThreshold: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    drawArcs: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    drawInterbaseCounts: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    drawIndicators: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default SNPCoverageRenderer;

package/dist/SNPCoverageRenderer/configSchema.js

@@ -46,6 +46,11 @@ const SNPCoverageRenderer = (0, configuration_1.ConfigurationSchema)('SNPCoverag
         description: 'draw a triangular indicator where an event has been detected',
         defaultValue: true,
     },
+    color: {
+        type: 'color',
+        description: 'Background color for the SNPCoverage renderer',
+        defaultValue: '#d3d3d3',
+    },
 }, { explicitlyTyped: true });
 exports.default = SNPCoverageRenderer;
 //# sourceMappingURL=configSchema.js.map

package/dist/SNPCoverageRenderer/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,kCAAkC;QAC/C,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,+DAA+D;QACjE,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,6CAA6C;QAC1D,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,mBAAmB,EAAE;QACnB,IAAI,EAAE,SAAS;QACf,WAAW,EACT,iJAAiJ;QACnJ,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,SAAS;QACf,WAAW,EACT,8DAA8D;QAChE,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,mBAAmB,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,kCAAkC;QAC/C,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,+DAA+D;QACjE,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,6CAA6C;QAC1D,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,mBAAmB,EAAE;QACnB,IAAI,EAAE,SAAS;QACf,WAAW,EACT,iJAAiJ;QACnJ,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,SAAS;QACf,WAAW,EACT,8DAA8D;QAChE,YAAY,EAAE,IAAI;KACnB;IAED,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,+CAA+C;QAC5D,YAAY,EAAE,SAAS;KACxB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,mBAAmB,CAAA"}

package/dist/shared/BaseDisplayComponent.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
+import { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
+declare const _default: ({ model, children, }: {
+    model: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel;
+    children?: React.ReactNode;
+}) => React.JSX.Element | null;
+export default _default;

package/dist/shared/BaseDisplayComponent.js

@@ -0,0 +1,49 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const ui_1 = require("@jbrowse/core/ui");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const mui_1 = require("tss-react/mui");
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("@jbrowse/core/util");
+const useStyles = (0, mui_1.makeStyles)()(theme => {
+    const bg = theme.palette.action.disabledBackground;
+    return {
+        loading: {
+            backgroundColor: theme.palette.background.default,
+            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
+            position: 'absolute',
+            bottom: 0,
+            height: 50,
+            width: 300,
+            right: 0,
+            pointerEvents: 'none',
+            textAlign: 'center',
+        },
+    };
+});
+exports.default = (0, mobx_react_1.observer)(function ({ model, children, }) {
+    const { error, regionTooLarge } = model;
+    return error ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", buttonText: "Reload", action: model.reload })) : regionTooLarge ? (model.regionCannotBeRendered()) : (react_1.default.createElement(DataDisplay, { model: model }, children));
+});
+const DataDisplay = (0, mobx_react_1.observer)(function ({ model, children, }) {
+    const { drawn, loading } = model;
+    const view = (0, util_1.getContainingView)(model);
+    const left = (model.lastDrawnOffsetPx || 0) - view.offsetPx;
+    return (
+    // this data-testid is located here because changing props on the canvas
+    // itself is very sensitive to triggering ref invalidation
+    react_1.default.createElement("div", { "data-testid": `drawn-${drawn}` },
+        react_1.default.createElement("div", { style: { position: 'absolute', left } }, children),
+        left !== 0 || loading ? react_1.default.createElement(LoadingBar, { model: model }) : null));
+});
+const LoadingBar = (0, mobx_react_1.observer)(function ({ model, }) {
+    const { classes } = useStyles();
+    const { message } = model;
+    return (react_1.default.createElement("div", { className: classes.loading },
+        react_1.default.createElement(ui_1.LoadingEllipses, { message: message })));
+});
+//# sourceMappingURL=BaseDisplayComponent.js.map

package/dist/shared/BaseDisplayComponent.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"BaseDisplayComponent.js","sourceRoot":"","sources":["../../src/shared/BaseDisplayComponent.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,yCAAkD;AAClD,kFAA6D;AAC7D,uCAA0C;AAC1C,2CAAqC;AAKrC,6CAAsD;AAEtD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE;IACrC,MAAM,EAAE,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,kBAAkB,CAAA;IAClD,OAAO;QACL,OAAO,EAAE;YACP,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO;YACjD,eAAe,EAAE,kEAAkE,EAAE,SAAS,EAAE,QAAQ;YACxG,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,CAAC;YACT,MAAM,EAAE,EAAE;YACV,KAAK,EAAE,GAAG;YACV,KAAK,EAAE,CAAC;YACR,aAAa,EAAE,MAAM;YACrB,SAAS,EAAE,QAAQ;SACpB;KACF,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,kBAAe,IAAA,qBAAQ,EAAC,UAAU,EAChC,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EAAE,KAAK,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IACvC,OAAO,KAAK,CAAC,CAAC,CAAC,CACb,8BAAC,oCAAQ,IACP,OAAO,EAAE,GAAG,KAAK,EAAE,EACnB,QAAQ,EAAC,OAAO,EAChB,UAAU,EAAC,QAAQ,EACnB,MAAM,EAAE,KAAK,CAAC,MAAM,GACpB,CACH,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,CACnB,KAAK,CAAC,sBAAsB,EAAE,CAC/B,CAAC,CAAC,CAAC,CACF,8BAAC,WAAW,IAAC,KAAK,EAAE,KAAK,IAAG,QAAQ,CAAe,CACpD,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,WAAW,GAAG,IAAA,qBAAQ,EAAC,UAAU,EACrC,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,KAAK,CAAC,CAAA;IACrC,MAAM,IAAI,GAAG,CAAC,KAAK,CAAC,iBAAiB,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAA;IAC3D,OAAO;IACL,wEAAwE;IACxE,0DAA0D;IAC1D,sDAAkB,SAAS,KAAK,EAAE;QAChC,uCAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE,IAAI,EAAE,IAAG,QAAQ,CAAO;QAC3D,IAAI,KAAK,CAAC,IAAI,OAAO,CAAC,CAAC,CAAC,8BAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CACxD,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,UAAU,GAAG,IAAA,qBAAQ,EAAC,UAAU,EACpC,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACzB,OAAO,CACL,uCAAK,SAAS,EAAE,OAAO,CAAC,OAAO;QAC7B,8BAAC,oBAAe,IAAC,OAAO,EAAE,OAAO,GAAI,CACjC,CACP,CAAA;AACH,CAAC,CAAC,CAAA"}

package/dist/shared/FilterByTag.d.ts

@@ -1,18 +1,19 @@
-/// <reference types="react" />
+import React from 'react';
+interface FilterBy {
+    flagExclude: number;
+    flagInclude: number;
+    readName?: string;
+    tagFilter?: {
+        tag: string;
+        value: string;
+    };
+}
 declare function FilterByTagDlg(props: {
     model: {
-        filterBy?: {
-            flagExclude: number;
-            flagInclude: number;
-            readName?: string;
-            tagFilter?: {
-                tag: string;
-                value: string;
-            };
-        };
-        setFilterBy: Function;
+        filterBy: FilterBy;
+        setFilterBy: (arg: FilterBy) => void;
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof FilterByTagDlg;
 export default _default;

package/dist/shared/FilterByTag.js

@@ -75,11 +75,11 @@ function FilterByTagDlg(props) {
     const { model, handleClose } = props;
     const { classes } = useStyles();
     const { filterBy } = model;
-    const [flagInclude, setFlagInclude] = (0, react_1.useState)(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagInclude);
-    const [flagExclude, setFlagExclude] = (0, react_1.useState)(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagExclude);
-    const [tag, setTag] = (0, react_1.useState)(((_a = filterBy === null || filterBy === void 0 ? void 0 : filterBy.tagFilter) === null || _a === void 0 ? void 0 : _a.tag) || '');
-    const [tagValue, setTagValue] = (0, react_1.useState)(((_b = filterBy === null || filterBy === void 0 ? void 0 : filterBy.tagFilter) === null || _b === void 0 ? void 0 : _b.value) || '');
-    const [readName, setReadName] = (0, react_1.useState)((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || '');
+    const [flagInclude, setFlagInclude] = (0, react_1.useState)(filterBy.flagInclude);
+    const [flagExclude, setFlagExclude] = (0, react_1.useState)(filterBy.flagExclude);
+    const [tag, setTag] = (0, react_1.useState)(((_a = filterBy.tagFilter) === null || _a === void 0 ? void 0 : _a.tag) || '');
+    const [tagValue, setTagValue] = (0, react_1.useState)(((_b = filterBy.tagFilter) === null || _b === void 0 ? void 0 : _b.value) || '');
+    const [readName, setReadName] = (0, react_1.useState)(filterBy.readName || '');
     const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
     const site = 'https://broadinstitute.github.io/picard/explain-flags.html';
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options" },
@@ -101,16 +101,11 @@ function FilterByTagDlg(props) {
                 react_1.default.createElement(material_1.Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"),
                 react_1.default.createElement(material_1.TextField, { className: classes.field, value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: {
                         maxLength: 2,
-                        'data-testid': 'color-tag-name-input',
-                    }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', "data-testid": "color-tag-name" }),
-                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tagValue, onChange: event => setTagValue(event.target.value), placeholder: "Enter tag value", inputProps: {
-                        'data-testid': 'color-tag-name-input',
-                    }, "data-testid": "color-tag-value" })),
+                    }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '' }),
+                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tagValue, onChange: event => setTagValue(event.target.value), placeholder: "Enter tag value" })),
             react_1.default.createElement(material_1.Paper, { className: classes.paper, variant: "outlined" },
                 react_1.default.createElement(material_1.Typography, null, "Filter by read name"),
-                react_1.default.createElement(material_1.TextField, { className: classes.field, value: readName, onChange: event => setReadName(event.target.value), placeholder: "Enter read name", inputProps: {
-                        'data-testid': 'color-tag-readname-input',
-                    }, "data-testid": "color-tag-readname" })),
+                react_1.default.createElement(material_1.TextField, { className: classes.field, value: readName, onChange: event => setReadName(event.target.value), placeholder: "Enter read name" })),
             react_1.default.createElement(material_1.DialogActions, null,
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", autoFocus: true, type: "submit", onClick: () => {
                         model.setFilterBy({

package/dist/shared/FilterByTag.js.map

@@ -1 +1 @@
-{"version":3,"file":"FilterByTag.js","sourceRoot":"","sources":["../../src/shared/FilterByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAQsB;AACtB,yCAAyC;AACzC,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACzB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,SAAS,GAAG;IAChB,aAAa;IACb,4BAA4B;IAC5B,eAAe;IACf,eAAe;IACf,qBAAqB;IACrB,qBAAqB;IACrB,eAAe;IACf,gBAAgB;IAChB,uBAAuB;IACvB,2CAA2C;IAC3C,kCAAkC;IAClC,yBAAyB;CAC1B,CAAA;AAED,SAAS,OAAO,CAAC,KAA2C;IAC1D,MAAM,EAAE,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACnC,OAAO,CACL;QACE,8BAAC,oBAAS,IACR,IAAI,EAAC,QAAQ,EACb,KAAK,EAAE,IAAI,EACX,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GAC/C;QACD,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE;YAC7B,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAA;YAC/B,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,uCAAK,GAAG,EAAE,GAAG;gBACX,yCACE,IAAI,EAAC,UAAU,EACf,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,EAAE;4BACxB,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC7B;6BAAM;4BACL,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC9B;oBACH,CAAC,GACD;gBACF,yCAAO,OAAO,EAAE,GAAG,IAAG,IAAI,CAAS,CAC/B,CACP,CAAA;QACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAS,cAAc,CAAC,KAWvB;;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,EAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,EAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,GAAG,KAAI,EAAE,CAAC,CAAA;IAC9D,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,KAAK,KAAI,EAAE,CAAC,CAAA;IAC1E,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,QAAQ,KAAI,EAAE,CAAC,CAAA;IAClE,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,MAAM,IAAI,GAAG,4DAA4D,CAAA;IAEzE,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa;YACZ,8BAAC,qBAAU;;gBAC4B,8BAAC,eAAI,IAAC,IAAI,EAAE,IAAI,IAAG,IAAI,CAAQ;gBAAC,GAAG;8BAE7D;YACb,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,uCAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;oBAC7B;wBACE,8BAAC,qBAAU,yCAA4C;wBACvD,8BAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD;oBACN;wBACE,8BAAC,qBAAU,6CAAgD;wBAC3D,8BAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD,CACF,CACA;YACR,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,8BAAC,qBAAU,kQAKE;gBACb,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;wBACV,SAAS,EAAE,CAAC;wBACZ,aAAa,EAAE,sBAAsB;qBACtC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,iBACtD,gBAAgB,GAC5B;gBACF,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAClD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,sBAAsB;qBACtC,iBACW,iBAAiB,GAC7B,CACI;YACR,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,8BAAC,qBAAU,8BAAiC;gBAC5C,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAClD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,0BAA0B;qBAC1C,iBACW,oBAAoB,GAChC,CACI;YACR,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,QACT,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC;4BAChB,WAAW;4BACX,WAAW;4BACX,QAAQ;4BACR,SAAS,EACP,GAAG,KAAK,EAAE;gCACR,CAAC,CAAC;oCACE,GAAG;oCACH,KAAK,EAAE,QAAQ;iCAChB;gCACH,CAAC,CAAC,SAAS;yBAChB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,cAAc,CAAC,CAAA"}
+{"version":3,"file":"FilterByTag.js","sourceRoot":"","sources":["../../src/shared/FilterByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAQsB;AACtB,yCAAyC;AACzC,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACzB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,SAAS,GAAG;IAChB,aAAa;IACb,4BAA4B;IAC5B,eAAe;IACf,eAAe;IACf,qBAAqB;IACrB,qBAAqB;IACrB,eAAe;IACf,gBAAgB;IAChB,uBAAuB;IACvB,2CAA2C;IAC3C,kCAAkC;IAClC,yBAAyB;CAC1B,CAAA;AAED,SAAS,OAAO,CAAC,KAA2C;IAC1D,MAAM,EAAE,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACnC,OAAO,CACL;QACE,8BAAC,oBAAS,IACR,IAAI,EAAC,QAAQ,EACb,KAAK,EAAE,IAAI,EACX,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GAC/C;QACD,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE;YAC7B,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAA;YAC/B,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,uCAAK,GAAG,EAAE,GAAG;gBACX,yCACE,IAAI,EAAC,UAAU,EACf,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,EAAE;4BACxB,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC7B;6BAAM;4BACL,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC9B;oBACH,CAAC,GACD;gBACF,yCAAO,OAAO,EAAE,GAAG,IAAG,IAAI,CAAS,CAC/B,CACP,CAAA;QACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAOD,SAAS,cAAc,CAAC,KAMvB;;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,EAAC,QAAQ,CAAC,WAAW,CAAC,CAAA;IACpE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,IAAA,gBAAQ,EAAC,QAAQ,CAAC,WAAW,CAAC,CAAA;IACpE,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,MAAA,QAAQ,CAAC,SAAS,0CAAE,GAAG,KAAI,EAAE,CAAC,CAAA;IAC7D,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,EAAC,CAAA,MAAA,QAAQ,CAAC,SAAS,0CAAE,KAAK,KAAI,EAAE,CAAC,CAAA;IACzE,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,EAAC,QAAQ,CAAC,QAAQ,IAAI,EAAE,CAAC,CAAA;IACjE,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,MAAM,IAAI,GAAG,4DAA4D,CAAA;IAEzE,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa;YACZ,8BAAC,qBAAU;;gBAC4B,8BAAC,eAAI,IAAC,IAAI,EAAE,IAAI,IAAG,IAAI,CAAQ;gBAAC,GAAG;8BAE7D;YACb,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,uCAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;oBAC7B;wBACE,8BAAC,qBAAU,yCAA4C;wBACvD,8BAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD;oBACN;wBACE,8BAAC,qBAAU,6CAAgD;wBAC3D,8BAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD,CACF,CACA;YACR,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,8BAAC,qBAAU,kQAKE;gBACb,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;wBACV,SAAS,EAAE,CAAC;qBACb,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,GAClE;gBACF,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAClD,WAAW,EAAC,iBAAiB,GAC7B,CACI;YACR,8BAAC,gBAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,8BAAC,qBAAU,8BAAiC;gBAC5C,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAClD,WAAW,EAAC,iBAAiB,GAC7B,CACI;YACR,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,QACT,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC;4BAChB,WAAW;4BACX,WAAW;4BACX,QAAQ;4BACR,SAAS,EACP,GAAG,KAAK,EAAE;gCACR,CAAC,CAAC;oCACE,GAAG;oCACH,KAAK,EAAE,QAAQ;iCAChB;gCACH,CAAC,CAAC,SAAS;yBAChB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,cAAc,CAAC,CAAA"}

package/dist/shared/afterAttach.d.ts

@@ -0,0 +1,2 @@
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+export declare function doAfterAttach<T extends IAnyStateTreeNode>(self: T, cb: (self: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): void;

package/dist/shared/afterAttach.js

@@ -0,0 +1,44 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.doAfterAttach = void 0;
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("../util");
+const fetchChains_1 = require("./fetchChains");
+function doAfterAttach(self, cb) {
+    (0, util_2.createAutorun)(self, async () => {
+        await (0, fetchChains_1.fetchChains)(self);
+    }, { delay: 1000 });
+    function draw(view) {
+        const canvas = self.ref;
+        if (!canvas) {
+            return;
+        }
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        if (!self.chainData) {
+            return;
+        }
+        ctx.clearRect(0, 0, canvas.width, self.height * 2);
+        ctx.resetTransform();
+        ctx.scale(2, 2);
+        cb(self, ctx, canvas.width, self.height);
+        self.setLastDrawnOffsetPx(view.offsetPx);
+        self.setLastDrawnBpPerPx(view.bpPerPx);
+    }
+    // first autorun instantly draws if bpPerPx changes
+    (0, util_2.createAutorun)(self, async () => {
+        const view = (0, util_1.getContainingView)(self);
+        if (view.bpPerPx !== self.lastDrawnBpPerPx) {
+            draw(view);
+        }
+    });
+    // second autorun draws after delay 1000 e.g. if offsetPx changes
+    (0, util_2.createAutorun)(self, async () => {
+        const view = (0, util_1.getContainingView)(self);
+        draw(view);
+    }, { delay: 1000 });
+}
+exports.doAfterAttach = doAfterAttach;
+//# sourceMappingURL=afterAttach.js.map

package/dist/shared/afterAttach.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"afterAttach.js","sourceRoot":"","sources":["../../src/shared/afterAttach.tsx"],"names":[],"mappings":";;;AAAA,6CAAsD;AACtD,kCAAuC;AACvC,+CAA2C;AAM3C,SAAgB,aAAa,CAC3B,IAAO,EACP,EAKS;IAET,IAAA,oBAAa,EACX,IAAI,EACJ,KAAK,IAAI,EAAE;QACT,MAAM,IAAA,yBAAW,EAAC,IAAI,CAAC,CAAA;IACzB,CAAC,EACD,EAAE,KAAK,EAAE,IAAI,EAAE,CAChB,CAAA;IAED,SAAS,IAAI,CAAC,IAAS;QACrB,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAA;QACvB,IAAI,CAAC,MAAM,EAAE;YACX,OAAM;SACP;QAED,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QACnC,IAAI,CAAC,GAAG,EAAE;YACR,OAAM;SACP;QAED,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE;YACnB,OAAM;SACP;QAED,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC,KAAK,EAAE,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QAClD,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACf,EAAE,CAAC,IAAI,EAAE,GAAG,EAAE,MAAM,CAAC,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;QACxC,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QACxC,IAAI,CAAC,mBAAmB,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACxC,CAAC;IAED,mDAAmD;IACnD,IAAA,oBAAa,EAAC,IAAI,EAAE,KAAK,IAAI,EAAE;QAC7B,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;QAC3C,IAAI,IAAI,CAAC,OAAO,KAAK,IAAI,CAAC,gBAAgB,EAAE;YAC1C,IAAI,CAAC,IAAI,CAAC,CAAA;SACX;IACH,CAAC,CAAC,CAAA;IAEF,iEAAiE;IACjE,IAAA,oBAAa,EACX,IAAI,EACJ,KAAK,IAAI,EAAE;QACT,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;QAC3C,IAAI,CAAC,IAAI,CAAC,CAAA;IACZ,CAAC,EACD,EAAE,KAAK,EAAE,IAAI,EAAE,CAChB,CAAA;AACH,CAAC;AAzDD,sCAyDC"}

package/dist/shared/color.d.ts

@@ -1,17 +1,55 @@
 import { ChainStats } from './fetchChains';
-export declare function getInsertSizeColor(f1: {
+export declare const fillColor: {
+    color_fwd_strand_not_proper: string;
+    color_rev_strand_not_proper: string;
+    color_fwd_strand: string;
+    color_rev_strand: string;
+    color_fwd_missing_mate: string;
+    color_rev_missing_mate: string;
+    color_fwd_diff_chr: string;
+    color_rev_diff_chr: string;
+    color_pair_lr: string;
+    color_pair_rr: string;
+    color_pair_rl: string;
+    color_pair_ll: string;
+    color_nostrand: string;
+    color_interchrom: string;
+    color_longinsert: string;
+    color_shortinsert: string;
+    color_unknown: string;
+};
+export declare const strokeColor: {
+    color_fwd_strand_not_proper: string;
+    color_rev_strand_not_proper: string;
+    color_fwd_strand: string;
+    color_rev_strand: string;
+    color_fwd_missing_mate: string;
+    color_rev_missing_mate: string;
+    color_fwd_diff_chr: string;
+    color_rev_diff_chr: string;
+    color_pair_lr: string;
+    color_pair_rr: string;
+    color_pair_rl: string;
+    color_pair_ll: string;
+    color_nostrand: string;
+    color_interchrom: string;
+    color_longinsert: string;
+    color_shortinsert: string;
+    color_unknown: string;
+};
+export declare function getPairedInsertSizeColor(f1: {
     refName: string;
     tlen?: number;
 }, f2: {
     refName: string;
-}, stats?: ChainStats): "" | "red" | "purple" | "#f0f";
-export declare function getInsertSizeAndOrientationColor(f1: {
+}, stats?: ChainStats): readonly [string, string] | undefined;
+export declare function getPairedInsertSizeAndOrientationColor(f1: {
     refName: string;
     pair_orientation?: string;
     tlen?: number;
 }, f2: {
     refName: string;
-}, stats?: ChainStats): string;
-export declare function getOrientationColor(f: {
+}, stats?: ChainStats): readonly [string, string];
+export declare function getPairedOrientationColor(f: {
     pair_orientation?: string;
-}): string;
+}): readonly [string, string];

package/dist/shared/color.js

@@ -1,43 +1,77 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getOrientationColor = exports.getInsertSizeAndOrientationColor = exports.getInsertSizeColor = void 0;
+exports.getPairedOrientationColor = exports.getPairedInsertSizeAndOrientationColor = exports.getPairedInsertSizeColor = exports.strokeColor = exports.fillColor = void 0;
 const util_1 = require("../util");
-const alignmentColoring = {
+exports.fillColor = {
+    color_fwd_strand_not_proper: '#ECC8C8',
+    color_rev_strand_not_proper: '#BEBED8',
+    color_fwd_strand: '#EC8B8B',
+    color_rev_strand: '#8F8FD8',
+    color_fwd_missing_mate: '#D11919',
+    color_rev_missing_mate: '#1919D1',
+    color_fwd_diff_chr: '#000',
+    color_rev_diff_chr: '#969696',
     color_pair_lr: '#c8c8c8',
     color_pair_rr: 'navy',
     color_pair_rl: 'teal',
     color_pair_ll: 'green',
+    color_nostrand: '#c8c8c8',
+    color_interchrom: 'purple',
+    color_longinsert: 'red',
+    color_shortinsert: 'pink',
+    color_unknown: 'grey',
 };
-function getInsertSizeColor(f1, f2, stats) {
+// manually calculated by running
+// const color = require('color')
+// Object.fromEntries(Object.entries(fillColor).map(([key,val])=>{
+//   return [key, color(val).darken('0.3').hex()]
+// }))
+// this avoids (expensive) use of Color module at runtime
+exports.strokeColor = {
+    color_fwd_strand_not_proper: '#CA6767',
+    color_rev_strand_not_proper: '#7272AA',
+    color_fwd_strand: '#DC2A2A',
+    color_rev_strand: '#4141BA',
+    color_fwd_missing_mate: '#921111',
+    color_rev_missing_mate: '#111192',
+    color_fwd_diff_chr: '#000000',
+    color_rev_diff_chr: '#696969',
+    color_pair_lr: '#8C8C8C',
+    color_pair_rr: '#00005A',
+    color_pair_rl: '#005A5A',
+    color_pair_ll: '#005A00',
+    color_nostrand: '#8C8C8C',
+    color_interchrom: '#5A005A',
+    color_longinsert: '#B30000',
+    color_shortinsert: '#FF3A5C',
+    color_unknown: 'grey',
+};
+function getPairedInsertSizeColor(f1, f2, stats) {
     const sameRef = f1.refName === f2.refName;
     const tlen = Math.abs(f1.tlen || 0);
     if (sameRef && tlen > ((stats === null || stats === void 0 ? void 0 : stats.upper) || 0)) {
-        return 'red';
+        return [exports.fillColor.color_longinsert, exports.strokeColor.color_longinsert];
     }
     else if (sameRef && tlen < ((stats === null || stats === void 0 ? void 0 : stats.lower) || 0)) {
-        return '#f0f';
+        return [exports.fillColor.color_shortinsert, exports.strokeColor.color_shortinsert];
     }
     else if (!sameRef) {
-        return 'purple';
+        return [exports.fillColor.color_interchrom, exports.strokeColor.color_interchrom];
     }
-    return '';
+    return undefined;
 }
-exports.getInsertSizeColor = getInsertSizeColor;
-function getInsertSizeAndOrientationColor(f1, f2, stats) {
-    return getInsertSizeColor(f1, f2, stats) || getOrientationColor(f1);
+exports.getPairedInsertSizeColor = getPairedInsertSizeColor;
+function getPairedInsertSizeAndOrientationColor(f1, f2, stats) {
+    return (getPairedInsertSizeColor(f1, f2, stats) || getPairedOrientationColor(f1));
 }
-exports.getInsertSizeAndOrientationColor = getInsertSizeAndOrientationColor;
-function getOrientationColor(f) {
-    const type = util_1.orientationTypes['fr'];
-    const orientation = type[f.pair_orientation || ''];
-    const map = {
-        LR: 'color_pair_lr',
-        RR: 'color_pair_rr',
-        RL: 'color_pair_rl',
-        LL: 'color_pair_ll',
-    };
-    const val = map[orientation];
-    return alignmentColoring[val] || 'grey';
+exports.getPairedInsertSizeAndOrientationColor = getPairedInsertSizeAndOrientationColor;
+function getPairedOrientationColor(f) {
+    const type = util_1.orientationTypes.fr;
+    const type2 = util_1.pairMap[type[f.pair_orientation || '']];
+    return [
+        exports.fillColor[type2] || exports.fillColor.color_unknown,
+        exports.strokeColor[type2] || exports.strokeColor.color_unknown,
+    ];
 }
-exports.getOrientationColor = getOrientationColor;
+exports.getPairedOrientationColor = getPairedOrientationColor;
 //# sourceMappingURL=color.js.map

package/dist/shared/color.js.map

@@ -1 +1 @@
-{"version":3,"file":"color.js","sourceRoot":"","sources":["../../src/shared/color.ts"],"names":[],"mappings":";;;AAAA,kCAA0C;AAG1C,MAAM,iBAAiB,GAA8B;IACnD,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,MAAM;IACrB,aAAa,EAAE,MAAM;IACrB,aAAa,EAAE,OAAO;CACvB,CAAA;AAED,SAAgB,kBAAkB,CAChC,EAAsC,EACtC,EAAuB,EACvB,KAAkB;IAElB,MAAM,OAAO,GAAG,EAAE,CAAC,OAAO,KAAK,EAAE,CAAC,OAAO,CAAA;IACzC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,IAAI,CAAC,CAAC,CAAA;IACnC,IAAI,OAAO,IAAI,IAAI,GAAG,CAAC,CAAA,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,KAAK,KAAI,CAAC,CAAC,EAAE;QACzC,OAAO,KAAK,CAAA;KACb;SAAM,IAAI,OAAO,IAAI,IAAI,GAAG,CAAC,CAAA,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,KAAK,KAAI,CAAC,CAAC,EAAE;QAChD,OAAO,MAAM,CAAA;KACd;SAAM,IAAI,CAAC,OAAO,EAAE;QACnB,OAAO,QAAQ,CAAA;KAChB;IACD,OAAO,EAAE,CAAA;AACX,CAAC;AAfD,gDAeC;AAED,SAAgB,gCAAgC,CAC9C,EAAiE,EACjE,EAAuB,EACvB,KAAkB;IAElB,OAAO,kBAAkB,CAAC,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,mBAAmB,CAAC,EAAE,CAAC,CAAA;AACrE,CAAC;AAND,4EAMC;AAED,SAAgB,mBAAmB,CAAC,CAAgC;IAClE,MAAM,IAAI,GAAG,uBAAgB,CAAC,IAAI,CAAC,CAAA;IACnC,MAAM,WAAW,GAAG,IAAI,CAAC,CAAC,CAAC,gBAAgB,IAAI,EAAE,CAAC,CAAA;IAClD,MAAM,GAAG,GAAG;QACV,EAAE,EAAE,eAAe;QACnB,EAAE,EAAE,eAAe;QACnB,EAAE,EAAE,eAAe;QACnB,EAAE,EAAE,eAAe;KACpB,CAAA;IACD,MAAM,GAAG,GAAG,GAAG,CAAC,WAA+B,CAAC,CAAA;IAChD,OAAO,iBAAiB,CAAC,GAAG,CAAC,IAAI,MAAM,CAAA;AACzC,CAAC;AAXD,kDAWC"}
+{"version":3,"file":"color.js","sourceRoot":"","sources":["../../src/shared/color.ts"],"names":[],"mappings":";;;AAAA,kCAAmD;AAGtC,QAAA,SAAS,GAAG;IACvB,2BAA2B,EAAE,SAAS;IACtC,2BAA2B,EAAE,SAAS;IACtC,gBAAgB,EAAE,SAAS;IAC3B,gBAAgB,EAAE,SAAS;IAC3B,sBAAsB,EAAE,SAAS;IACjC,sBAAsB,EAAE,SAAS;IACjC,kBAAkB,EAAE,MAAM;IAC1B,kBAAkB,EAAE,SAAS;IAC7B,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,MAAM;IACrB,aAAa,EAAE,MAAM;IACrB,aAAa,EAAE,OAAO;IACtB,cAAc,EAAE,SAAS;IACzB,gBAAgB,EAAE,QAAQ;IAC1B,gBAAgB,EAAE,KAAK;IACvB,iBAAiB,EAAE,MAAM;IACzB,aAAa,EAAE,MAAM;CACtB,CAAA;AAED,iCAAiC;AACjC,iCAAiC;AACjC,kEAAkE;AAClE,iDAAiD;AACjD,MAAM;AACN,yDAAyD;AAC5C,QAAA,WAAW,GAAG;IACzB,2BAA2B,EAAE,SAAS;IACtC,2BAA2B,EAAE,SAAS;IACtC,gBAAgB,EAAE,SAAS;IAC3B,gBAAgB,EAAE,SAAS;IAC3B,sBAAsB,EAAE,SAAS;IACjC,sBAAsB,EAAE,SAAS;IACjC,kBAAkB,EAAE,SAAS;IAC7B,kBAAkB,EAAE,SAAS;IAC7B,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,SAAS;IACxB,cAAc,EAAE,SAAS;IACzB,gBAAgB,EAAE,SAAS;IAC3B,gBAAgB,EAAE,SAAS;IAC3B,iBAAiB,EAAE,SAAS;IAC5B,aAAa,EAAE,MAAM;CACtB,CAAA;AAED,SAAgB,wBAAwB,CACtC,EAAsC,EACtC,EAAuB,EACvB,KAAkB;IAElB,MAAM,OAAO,GAAG,EAAE,CAAC,OAAO,KAAK,EAAE,CAAC,OAAO,CAAA;IACzC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,IAAI,CAAC,CAAC,CAAA;IACnC,IAAI,OAAO,IAAI,IAAI,GAAG,CAAC,CAAA,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,KAAK,KAAI,CAAC,CAAC,EAAE;QACzC,OAAO,CAAC,iBAAS,CAAC,gBAAgB,EAAE,mBAAW,CAAC,gBAAgB,CAAU,CAAA;KAC3E;SAAM,IAAI,OAAO,IAAI,IAAI,GAAG,CAAC,CAAA,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,KAAK,KAAI,CAAC,CAAC,EAAE;QAChD,OAAO,CAAC,iBAAS,CAAC,iBAAiB,EAAE,mBAAW,CAAC,iBAAiB,CAAU,CAAA;KAC7E;SAAM,IAAI,CAAC,OAAO,EAAE;QACnB,OAAO,CAAC,iBAAS,CAAC,gBAAgB,EAAE,mBAAW,CAAC,gBAAgB,CAAU,CAAA;KAC3E;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAfD,4DAeC;AAED,SAAgB,sCAAsC,CACpD,EAAiE,EACjE,EAAuB,EACvB,KAAkB;IAElB,OAAO,CACL,wBAAwB,CAAC,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,yBAAyB,CAAC,EAAE,CAAC,CACzE,CAAA;AACH,CAAC;AARD,wFAQC;AAED,SAAgB,yBAAyB,CAAC,CAAgC;IACxE,MAAM,IAAI,GAAG,uBAAgB,CAAC,EAAE,CAAA;IAChC,MAAM,KAAK,GAAG,cAAO,CACnB,IAAI,CAAC,CAAC,CAAC,gBAAgB,IAAI,EAAE,CAAyB,CAC7B,CAAA;IAC3B,OAAO;QACL,iBAAS,CAAC,KAAK,CAAC,IAAI,iBAAS,CAAC,aAAa;QAC3C,mBAAW,CAAC,KAAK,CAAC,IAAI,mBAAW,CAAC,aAAa;KACvC,CAAA;AACZ,CAAC;AATD,8DASC"}

package/dist/shared/fetchChains.d.ts

@@ -1,4 +1,5 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
+import { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
 export interface ReducedFeature {
     name: string;
     strand: number;
@@ -24,4 +25,4 @@ export interface ChainData {
     chains: ReducedFeature[][];
     stats?: ChainStats;
 }
-export declare function fetchChains(self: IAnyStateTreeNode): Promise<void>;
+export declare function fetchChains(self: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel): Promise<void>;

package/dist/shared/fetchChains.js

@@ -4,27 +4,21 @@ exports.fetchChains = void 0;
 const util_1 = require("@jbrowse/core/util");
 const mobx_state_tree_1 = require("mobx-state-tree");
 async function fetchChains(self) {
-    try {
-        const { rpcSessionId: sessionId } = (0, util_1.getContainingTrack)(self);
-        const { rpcManager } = (0, util_1.getSession)(self);
-        const view = (0, util_1.getContainingView)(self);
-        if (!view.initialized || self.error) {
-            return;
-        }
-        self.setLoading(true);
-        const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
-            sessionId,
-            regions: view.staticBlocks.contentBlocks,
-            filterBy: (0, mobx_state_tree_1.getSnapshot)(self.filterBy),
-            adapterConfig: self.adapterConfig,
-        }));
-        self.setChainData(ret);
-        self.setLoading(false);
-    }
-    catch (e) {
-        console.error(e);
-        self.setError(e);
+    const { rpcSessionId: sessionId } = (0, util_1.getContainingTrack)(self);
+    const { rpcManager } = (0, util_1.getSession)(self);
+    const view = (0, util_1.getContainingView)(self);
+    if (!view.initialized || self.error || self.regionTooLarge) {
+        return;
     }
+    self.setLoading(true);
+    const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
+        sessionId,
+        regions: view.staticBlocks.contentBlocks,
+        filterBy: (0, mobx_state_tree_1.getSnapshot)(self.filterBy),
+        adapterConfig: self.adapterConfig,
+    }));
+    self.setChainData(ret);
+    self.setLoading(false);
 }
 exports.fetchChains = fetchChains;
 //# sourceMappingURL=fetchChains.js.map