@sjcrh/proteinpaint-shared 2.188.1 → 2.189.0

package/constants/AiHisto.ts

@@ -1,16 +1,20 @@
-export enum FlagStatus {
-	Normal = 0,
-	Skipped = 1,
-	Flagged = 2,
-	Deleted = 3
-}
+export const FlagStatus = {
+	Normal: 0,
+	Skipped: 1,
+	Flagged: 2,
+	Deleted: 3
+} as const
 
-export enum FeaturePrefixes {
-	Star = 'annotation-star-',
-	Square = 'annotation-square-',
-	Border = 'annotation-border-',
-	PredBorder = 'prediction-border-'
-}
+export type FlagStatusValues = (typeof FlagStatus)[keyof typeof FlagStatus]
+
+export const FeaturePrefixes = {
+	Star: 'annotation-star-',
+	Square: 'annotation-square-',
+	Border: 'annotation-border-',
+	PredBorder: 'prediction-border-'
+} as const
+
+export type FeaturePrefixValues = (typeof FeaturePrefixes)[keyof typeof FeaturePrefixes]
 
 export const SelectionPrefixes = {
 	TileSelection: 'ts_',
@@ -19,7 +23,7 @@ export const SelectionPrefixes = {
 } as const
 
 export type SelectionPrefixValues = (typeof SelectionPrefixes)[keyof typeof SelectionPrefixes]
-
+//Didn't add Deleted to FlagStatusMessages because deleted annotations dont exist and deleted predictons are filtered out in /Users/jsimps98/dev/sjpp/proteinpaint/server/routes/aiProjectSelectedWSImages.ts line 119
 export const FlagStatusMessages = {
 	[FlagStatus.Normal]: '',
 	[FlagStatus.Skipped]: '(Skipped)',

package/dist/constants/AiHisto.d.ts

@@ -1,15 +1,17 @@
-export declare enum FlagStatus {
-    Normal = 0,
-    Skipped = 1,
-    Flagged = 2,
-    Deleted = 3
-}
-export declare enum FeaturePrefixes {
-    Star = "annotation-star-",
-    Square = "annotation-square-",
-    Border = "annotation-border-",
-    PredBorder = "prediction-border-"
-}
+export declare const FlagStatus: {
+    readonly Normal: 0;
+    readonly Skipped: 1;
+    readonly Flagged: 2;
+    readonly Deleted: 3;
+};
+export type FlagStatusValues = (typeof FlagStatus)[keyof typeof FlagStatus];
+export declare const FeaturePrefixes: {
+    readonly Star: "annotation-star-";
+    readonly Square: "annotation-square-";
+    readonly Border: "annotation-border-";
+    readonly PredBorder: "prediction-border-";
+};
+export type FeaturePrefixValues = (typeof FeaturePrefixes)[keyof typeof FeaturePrefixes];
 export declare const SelectionPrefixes: {
     readonly TileSelection: "ts_";
     readonly Prediction: "pred_";

package/dist/constants/AiHisto.js

@@ -1,26 +1,24 @@
-var FlagStatus = /* @__PURE__ */ ((FlagStatus2) => {
-  FlagStatus2[FlagStatus2["Normal"] = 0] = "Normal";
-  FlagStatus2[FlagStatus2["Skipped"] = 1] = "Skipped";
-  FlagStatus2[FlagStatus2["Flagged"] = 2] = "Flagged";
-  FlagStatus2[FlagStatus2["Deleted"] = 3] = "Deleted";
-  return FlagStatus2;
-})(FlagStatus || {});
-var FeaturePrefixes = /* @__PURE__ */ ((FeaturePrefixes2) => {
-  FeaturePrefixes2["Star"] = "annotation-star-";
-  FeaturePrefixes2["Square"] = "annotation-square-";
-  FeaturePrefixes2["Border"] = "annotation-border-";
-  FeaturePrefixes2["PredBorder"] = "prediction-border-";
-  return FeaturePrefixes2;
-})(FeaturePrefixes || {});
+const FlagStatus = {
+  Normal: 0,
+  Skipped: 1,
+  Flagged: 2,
+  Deleted: 3
+};
+const FeaturePrefixes = {
+  Star: "annotation-star-",
+  Square: "annotation-square-",
+  Border: "annotation-border-",
+  PredBorder: "prediction-border-"
+};
 const SelectionPrefixes = {
   TileSelection: "ts_",
   Prediction: "pred_",
   Annotation: "anno_"
 };
 const FlagStatusMessages = {
-  [0 /* Normal */]: "",
-  [1 /* Skipped */]: "(Skipped)",
-  [2 /* Flagged */]: "(Flagged)"
+  [FlagStatus.Normal]: "",
+  [FlagStatus.Skipped]: "(Skipped)",
+  [FlagStatus.Flagged]: "(Flagged)"
 };
 export {
   FeaturePrefixes,

package/dist/constants/AiHisto.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../constants/AiHisto.ts"],
-  "sourcesContent": ["export enum FlagStatus {\n\tNormal = 0,\n\tSkipped = 1,\n\tFlagged = 2,\n\tDeleted = 3\n}\n\nexport enum FeaturePrefixes {\n\tStar = 'annotation-star-',\n\tSquare = 'annotation-square-',\n\tBorder = 'annotation-border-',\n\tPredBorder = 'prediction-border-'\n}\n\nexport const SelectionPrefixes = {\n\tTileSelection: 'ts_',\n\tPrediction: 'pred_',\n\tAnnotation: 'anno_'\n} as const\n\nexport type SelectionPrefixValues = (typeof SelectionPrefixes)[keyof typeof SelectionPrefixes]\n\nexport const FlagStatusMessages = {\n\t[FlagStatus.Normal]: '',\n\t[FlagStatus.Skipped]: '(Skipped)',\n\t[FlagStatus.Flagged]: '(Flagged)'\n}\n"],
-  "mappings": "AAAO,IAAK,aAAL,kBAAKA,gBAAL;AACN,EAAAA,wBAAA,YAAS,KAAT;AACA,EAAAA,wBAAA,aAAU,KAAV;AACA,EAAAA,wBAAA,aAAU,KAAV;AACA,EAAAA,wBAAA,aAAU,KAAV;AAJW,SAAAA;AAAA,GAAA;AAOL,IAAK,kBAAL,kBAAKC,qBAAL;AACN,EAAAA,iBAAA,UAAO;AACP,EAAAA,iBAAA,YAAS;AACT,EAAAA,iBAAA,YAAS;AACT,EAAAA,iBAAA,gBAAa;AAJF,SAAAA;AAAA,GAAA;AAOL,MAAM,oBAAoB;AAAA,EAChC,eAAe;AAAA,EACf,YAAY;AAAA,EACZ,YAAY;AACb;AAIO,MAAM,qBAAqB;AAAA,EACjC,CAAC,cAAiB,GAAG;AAAA,EACrB,CAAC,eAAkB,GAAG;AAAA,EACtB,CAAC,eAAkB,GAAG;AACvB;",
-  "names": ["FlagStatus", "FeaturePrefixes"]
+  "sourcesContent": ["export const FlagStatus = {\n\tNormal: 0,\n\tSkipped: 1,\n\tFlagged: 2,\n\tDeleted: 3\n} as const\n\nexport type FlagStatusValues = (typeof FlagStatus)[keyof typeof FlagStatus]\n\nexport const FeaturePrefixes = {\n\tStar: 'annotation-star-',\n\tSquare: 'annotation-square-',\n\tBorder: 'annotation-border-',\n\tPredBorder: 'prediction-border-'\n} as const\n\nexport type FeaturePrefixValues = (typeof FeaturePrefixes)[keyof typeof FeaturePrefixes]\n\nexport const SelectionPrefixes = {\n\tTileSelection: 'ts_',\n\tPrediction: 'pred_',\n\tAnnotation: 'anno_'\n} as const\n\nexport type SelectionPrefixValues = (typeof SelectionPrefixes)[keyof typeof SelectionPrefixes]\n//Didn't add Deleted to FlagStatusMessages because deleted annotations dont exist and deleted predictons are filtered out in /Users/jsimps98/dev/sjpp/proteinpaint/server/routes/aiProjectSelectedWSImages.ts line 119\nexport const FlagStatusMessages = {\n\t[FlagStatus.Normal]: '',\n\t[FlagStatus.Skipped]: '(Skipped)',\n\t[FlagStatus.Flagged]: '(Flagged)'\n}\n"],
+  "mappings": "AAAO,MAAM,aAAa;AAAA,EACzB,QAAQ;AAAA,EACR,SAAS;AAAA,EACT,SAAS;AAAA,EACT,SAAS;AACV;AAIO,MAAM,kBAAkB;AAAA,EAC9B,MAAM;AAAA,EACN,QAAQ;AAAA,EACR,QAAQ;AAAA,EACR,YAAY;AACb;AAIO,MAAM,oBAAoB;AAAA,EAChC,eAAe;AAAA,EACf,YAAY;AAAA,EACZ,YAAY;AACb;AAIO,MAAM,qBAAqB;AAAA,EACjC,CAAC,WAAW,MAAM,GAAG;AAAA,EACrB,CAAC,WAAW,OAAO,GAAG;AAAA,EACtB,CAAC,WAAW,OAAO,GAAG;AACvB;",
+  "names": []
 }

package/dist/src/aiHisto.d.ts

@@ -1,5 +1,5 @@
 import { type TileSelection } from '@sjcrh/proteinpaint-types';
-import type { FeaturePrefixes, SelectionPrefixValues } from '../constants/AiHisto.js';
+import type { FeaturePrefixValues, SelectionPrefixValues } from '../constants/AiHisto.js';
 export declare function createSelectionID(prefix: SelectionPrefixValues, coordinates: [number, number]): string;
 export declare function checkSelectionType(tileSelection: TileSelection, suspectedPrefix: SelectionPrefixValues): boolean;
-export declare function createFeatureID(featurePrefix: FeaturePrefixes, coords: [number, number]): string;
+export declare function createFeatureID(featurePrefix: FeaturePrefixValues, coords: [number, number]): string;

package/dist/src/aiHisto.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/aiHisto.ts"],
-  "sourcesContent": ["import { type TileSelection } from '@sjcrh/proteinpaint-types'\nimport type { FeaturePrefixes, SelectionPrefixValues } from '../constants/AiHisto.js'\n\nexport function createSelectionID(prefix: SelectionPrefixValues, coordinates: [number, number]): string {\n\treturn prefix + JSON.stringify(coordinates)\n}\n\nexport function checkSelectionType(tileSelection: TileSelection, suspectedPrefix: SelectionPrefixValues): boolean {\n\treturn tileSelection.id.startsWith(suspectedPrefix)\n}\n\nexport function createFeatureID(featurePrefix: FeaturePrefixes, coords: [number, number]) {\n\treturn featurePrefix + JSON.stringify(coords)\n}\n"],
-  "mappings": "AAGO,SAAS,kBAAkB,QAA+B,aAAuC;AACvG,SAAO,SAAS,KAAK,UAAU,WAAW;AAC3C;AAEO,SAAS,mBAAmB,eAA8B,iBAAiD;AACjH,SAAO,cAAc,GAAG,WAAW,eAAe;AACnD;AAEO,SAAS,gBAAgB,eAAgC,QAA0B;AACzF,SAAO,gBAAgB,KAAK,UAAU,MAAM;AAC7C;",
+  "sourcesContent": ["import { type TileSelection } from '@sjcrh/proteinpaint-types'\nimport type { FeaturePrefixValues, SelectionPrefixValues } from '../constants/AiHisto.js'\n\nexport function createSelectionID(prefix: SelectionPrefixValues, coordinates: [number, number]): string {\n\treturn prefix + JSON.stringify(coordinates)\n}\n\nexport function checkSelectionType(tileSelection: TileSelection, suspectedPrefix: SelectionPrefixValues): boolean {\n\treturn tileSelection.id.startsWith(suspectedPrefix)\n}\n\nexport function createFeatureID(featurePrefix: FeaturePrefixValues, coords: [number, number]) {\n\treturn featurePrefix + JSON.stringify(coords)\n}\n"],
+  "mappings": "AAGO,SAAS,kBAAkB,QAA+B,aAAuC;AACvG,SAAO,SAAS,KAAK,UAAU,WAAW;AAC3C;AAEO,SAAS,mBAAmB,eAA8B,iBAAiD;AACjH,SAAO,cAAc,GAAG,WAAW,eAAe;AACnD;AAEO,SAAS,gBAAgB,eAAoC,QAA0B;AAC7F,SAAO,gBAAgB,KAAK,UAAU,MAAM;AAC7C;",
   "names": []
 }

package/dist/src/bulk.cnv.d.ts

@@ -0,0 +1,2 @@
+export declare function parseheader(line: any, flag: any): false | "invalid file header for CNV" | "gene missing from header" | "CNV missing from header";
+export declare function parseline(i: any, line: any, flag: any): void;

package/dist/src/bulk.cnv.js

@@ -65,7 +65,7 @@ function parseline(i, line, flag) {
   if (!m.class) {
     return;
   }
-  if (bulk.parsesample(m, flag, i, lst, flag.cnv.badlines)) {
+  if (bulk.parsesample(m, flag, i, lst)) {
     return;
   }
   m.dt = common.dtcnv;

package/dist/src/bulk.cnv.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../src/bulk.cnv.js"],
-  "sourcesContent": ["////////////////////////////////////\n//\n//  shared between client and server\n//\n////////////////////////////////////\n\nimport * as common from './common.js'\nimport * as bulk from './bulk.js'\n\nexport function parseheader(line, flag) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid file header for CNV'\n\tconst htry = (...lst) => {\n\t\tfor (const i of lst) {\n\t\t\tconst j = header.indexOf(i)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('gene')\n\tif (i == -1) return 'gene missing from header'\n\theader[i] = 'gene'\n\ti = htry('cnv')\n\tif (i == -1) return 'CNV missing from header'\n\theader[i] = 'cnv'\n\ti = htry('sample', 'sample_name', 'tumor_sample_barcode')\n\tif (i != -1) header[i] = 'sample'\n\ti = htry('patient', 'donor', 'target_case_id')\n\tif (i != -1) header[i] = 'patient'\n\ti = htry('disease')\n\tif (i != -1) header[i] = 'disease'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\ti = htry('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\tflag.cnv.header = header\n\tflag.cnv.loaded = true\n\treturn false\n}\n\nexport function parseline(i, line, flag) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m = {}\n\tfor (let j = 0; j < flag.cnv.header.length; j++) {\n\t\tm[flag.cnv.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.cnv.badlines.push([i, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (!m.cnv) {\n\t\tflag.cnv.badlines.push([i, 'missing cnv value', lst])\n\t\treturn\n\t}\n\tconst value = m.cnv.toLowerCase()\n\tswitch (value) {\n\t\tcase 'amplification':\n\t\tcase 'gain':\n\t\t\tm.class = common.mclasscnvgain\n\t\t\tbreak\n\t\tcase 'deletion':\n\t\tcase 'loss':\n\t\t\tm.class = common.mclasscnvloss\n\t\t\tbreak\n\t\tcase 'loh':\n\t\t\tm.class = common.mclasscnvloh\n\t\t\tbreak\n\t\tdefault:\n\t\t\tflag.cnv.badlines.push([i, 'invalid cnv value: ' + m.cnv, lst])\n\t\t\tm.class = null\n\t}\n\tif (!m.class) {\n\t\treturn\n\t}\n\tif (bulk.parsesample(m, flag, i, lst, flag.cnv.badlines)) {\n\t\treturn\n\t}\n\tm.dt = common.dtcnv\n\tflag.good++\n\tconst n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene\n\tif (!(n in flag.data)) {\n\t\tflag.data[n] = []\n\t}\n\tflag.data[n].push(m)\n}\n"],
-  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAEf,SAAS,YAAY,MAAM,MAAM;AACvC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAWA,MAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQA,EAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,MAAM;AACnB,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,KAAK;AACd,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,OAAK,IAAI,SAAS;AAClB,OAAK,IAAI,SAAS;AAClB,SAAO;AACR;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM;AACxC,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAI,CAAC;AACX,WAAS,IAAI,GAAG,IAAI,KAAK,IAAI,OAAO,QAAQ,KAAK;AAChD,MAAE,KAAK,IAAI,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EAC9B;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,SAAK,IAAI,SAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AAC/C;AAAA,EACD;AACA,MAAI,CAAC,EAAE,KAAK;AACX,SAAK,IAAI,SAAS,KAAK,CAAC,GAAG,qBAAqB,GAAG,CAAC;AACpD;AAAA,EACD;AACA,QAAM,QAAQ,EAAE,IAAI,YAAY;AAChC,UAAQ,OAAO;AAAA,IACd,KAAK;AAAA,IACL,KAAK;AACJ,QAAE,QAAQ,OAAO;AACjB;AAAA,IACD,KAAK;AAAA,IACL,KAAK;AACJ,QAAE,QAAQ,OAAO;AACjB;AAAA,IACD,KAAK;AACJ,QAAE,QAAQ,OAAO;AACjB;AAAA,IACD;AACC,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,wBAAwB,EAAE,KAAK,GAAG,CAAC;AAC9D,QAAE,QAAQ;AAAA,EACZ;AACA,MAAI,CAAC,EAAE,OAAO;AACb;AAAA,EACD;AACA,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,KAAK,KAAK,IAAI,QAAQ,GAAG;AACzD;AAAA,EACD;AACA,IAAE,KAAK,OAAO;AACd,OAAK;AACL,QAAM,IAAI,KAAK,cAAc,EAAE,KAAK,YAAY,IAAI,EAAE;AACtD,MAAI,EAAE,KAAK,KAAK,OAAO;AACtB,SAAK,KAAK,CAAC,IAAI,CAAC;AAAA,EACjB;AACA,OAAK,KAAK,CAAC,EAAE,KAAK,CAAC;AACpB;",
+  "sources": ["../../src/bulk.cnv.ts"],
+  "sourcesContent": ["////////////////////////////////////\n//\n//  shared between client and server\n//\n////////////////////////////////////\n\nimport * as common from './common.js'\nimport * as bulk from './bulk.js'\n\nexport function parseheader(line, flag) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid file header for CNV'\n\tconst htry = (...lst) => {\n\t\tfor (const i of lst) {\n\t\t\tconst j = header.indexOf(i)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('gene')\n\tif (i == -1) return 'gene missing from header'\n\theader[i] = 'gene'\n\ti = htry('cnv')\n\tif (i == -1) return 'CNV missing from header'\n\theader[i] = 'cnv'\n\ti = htry('sample', 'sample_name', 'tumor_sample_barcode')\n\tif (i != -1) header[i] = 'sample'\n\ti = htry('patient', 'donor', 'target_case_id')\n\tif (i != -1) header[i] = 'patient'\n\ti = htry('disease')\n\tif (i != -1) header[i] = 'disease'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\ti = htry('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\tflag.cnv.header = header\n\tflag.cnv.loaded = true\n\treturn false\n}\n\nexport function parseline(i, line, flag) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m: Record<string, any> = {}\n\tfor (let j = 0; j < flag.cnv.header.length; j++) {\n\t\tm[flag.cnv.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.cnv.badlines.push([i, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (!m.cnv) {\n\t\tflag.cnv.badlines.push([i, 'missing cnv value', lst])\n\t\treturn\n\t}\n\tconst value = m.cnv.toLowerCase()\n\tswitch (value) {\n\t\tcase 'amplification':\n\t\tcase 'gain':\n\t\t\tm.class = common.mclasscnvgain\n\t\t\tbreak\n\t\tcase 'deletion':\n\t\tcase 'loss':\n\t\t\tm.class = common.mclasscnvloss\n\t\t\tbreak\n\t\tcase 'loh':\n\t\t\tm.class = common.mclasscnvloh\n\t\t\tbreak\n\t\tdefault:\n\t\t\tflag.cnv.badlines.push([i, 'invalid cnv value: ' + m.cnv, lst])\n\t\t\tm.class = null\n\t}\n\tif (!m.class) {\n\t\treturn\n\t}\n\tif (bulk.parsesample(m, flag, i, lst)) {\n\t\treturn\n\t}\n\tm.dt = common.dtcnv\n\tflag.good++\n\tconst n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene\n\tif (!(n in flag.data)) {\n\t\tflag.data[n] = []\n\t}\n\tflag.data[n].push(m)\n}\n"],
+  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAEf,SAAS,YAAY,MAAM,MAAM;AACvC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAWA,MAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQA,EAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,MAAM;AACnB,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,KAAK;AACd,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,OAAK,IAAI,SAAS;AAClB,OAAK,IAAI,SAAS;AAClB,SAAO;AACR;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM;AACxC,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAyB,CAAC;AAChC,WAAS,IAAI,GAAG,IAAI,KAAK,IAAI,OAAO,QAAQ,KAAK;AAChD,MAAE,KAAK,IAAI,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EAC9B;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,SAAK,IAAI,SAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AAC/C;AAAA,EACD;AACA,MAAI,CAAC,EAAE,KAAK;AACX,SAAK,IAAI,SAAS,KAAK,CAAC,GAAG,qBAAqB,GAAG,CAAC;AACpD;AAAA,EACD;AACA,QAAM,QAAQ,EAAE,IAAI,YAAY;AAChC,UAAQ,OAAO;AAAA,IACd,KAAK;AAAA,IACL,KAAK;AACJ,QAAE,QAAQ,OAAO;AACjB;AAAA,IACD,KAAK;AAAA,IACL,KAAK;AACJ,QAAE,QAAQ,OAAO;AACjB;AAAA,IACD,KAAK;AACJ,QAAE,QAAQ,OAAO;AACjB;AAAA,IACD;AACC,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,wBAAwB,EAAE,KAAK,GAAG,CAAC;AAC9D,QAAE,QAAQ;AAAA,EACZ;AACA,MAAI,CAAC,EAAE,OAAO;AACb;AAAA,EACD;AACA,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,GAAG,GAAG;AACtC;AAAA,EACD;AACA,IAAE,KAAK,OAAO;AACd,OAAK;AACL,QAAM,IAAI,KAAK,cAAc,EAAE,KAAK,YAAY,IAAI,EAAE;AACtD,MAAI,EAAE,KAAK,KAAK,OAAO;AACtB,SAAK,KAAK,CAAC,IAAI,CAAC;AAAA,EACjB;AACA,OAAK,KAAK,CAAC,EAAE,KAAK,CAAC;AACpB;",
   "names": ["i"]
 }

package/dist/src/bulk.d.ts

@@ -0,0 +1,56 @@
+declare const _default: {};
+export default _default;
+export declare function init_bulk_flag(genome: any): {
+    genome: any;
+    mclasslabel2key: {};
+    data: {};
+    sample2disease: {};
+    patient2st: {};
+    good: number;
+    geneToUpper: boolean;
+    snv: {
+        loaded: boolean;
+        header: null;
+        badlines: never[];
+        missense: number;
+        silent: number;
+    };
+    svjson: {
+        loaded: boolean;
+        header: null;
+        badlines: never[];
+    };
+    fusion: {
+        loaded: boolean;
+        header: null;
+        badlines: never[];
+        original: never[];
+    };
+    sv: {
+        loaded: boolean;
+        header: null;
+        badlines: never[];
+        original: never[];
+    };
+    cnv: {
+        loaded: boolean;
+        header: null;
+        badlines: never[];
+    };
+    itd: {
+        loaded: boolean;
+        header: null;
+        badlines: never[];
+    };
+    del: {
+        loaded: boolean;
+        header: null;
+        badlines: never[];
+    };
+    truncation: {
+        loaded: boolean;
+        header: null;
+        badlines: never[];
+    };
+} | null;
+export declare function parsesample(m: any, flag: any, i: any, lst: any): boolean | undefined;

package/dist/src/bulk.del.d.ts

@@ -0,0 +1,2 @@
+export declare function parseheader(line: any, flag: any): false | "gene missing from header" | "invalid header line for intragenic deletion" | "isoform missing from header" | "rnadellength is required when rnaPosition is used" | "chr_start is required when chr is used" | "chr_stop is required when chr is used";
+export declare function parseline(i: any, line: any, flag: any): void;

package/dist/src/bulk.del.js

@@ -99,14 +99,14 @@ function parseline(i, line, flag) {
     }
     m.chrpos2 = v;
   }
-  if (bulk.parsesample(m, flag, i, lst, flag.del.badlines)) {
+  if (bulk.parsesample(m, flag, i, lst)) {
     return;
   }
   m.dt = common.dtdel;
   m.class = common.mclassdel;
   m.mname = "DEL";
   flag.good++;
-  var n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene;
+  const n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene;
   if (!(n in flag.data)) {
     flag.data[n] = [];
   }

package/dist/src/bulk.del.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../src/bulk.del.js"],
-  "sourcesContent": ["////////////////////////////////////\n//\n//  shared between client and server\n//\n////////////////////////////////////\n\nimport * as common from './common.js'\nimport * as bulk from './bulk.js'\n\nexport function parseheader(line, flag) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid header line for intragenic deletion'\n\tconst htry = (...lst) => {\n\t\tfor (const i of lst) {\n\t\t\tconst j = header.indexOf(i)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('gene')\n\tif (i == -1) return 'gene missing from header'\n\theader[i] = 'gene'\n\ti = htry(\n\t\t'annovar_isoform',\n\t\t'mrna_accession',\n\t\t'mrna accession',\n\t\t'refseq_mrna_id',\n\t\t'annovar_sj_filter_isoform',\n\t\t'refseq',\n\t\t'isoform'\n\t)\n\tif (i == -1) return 'isoform missing from header'\n\theader[i] = 'isoform'\n\ti = htry('rnaposition')\n\tif (i != -1) {\n\t\theader[i] = 'rnaposition'\n\t\ti = htry('rnadellength')\n\t\tif (i == -1) return 'rnadellength is required when rnaPosition is used'\n\t\theader[i] = 'rnadellength'\n\t}\n\ti = htry('chromosome', 'chr')\n\tif (i != -1) {\n\t\theader[i] = 'chr'\n\t\ti = htry('chr_start')\n\t\tif (i == -1) return 'chr_start is required when chr is used'\n\t\theader[i] = 'chrpos1'\n\t\ti = htry('chr_stop')\n\t\tif (i == -1) return 'chr_stop is required when chr is used'\n\t\theader[i] = 'chrpos2'\n\t}\n\n\ti = htry('sample', 'sample_name', 'tumor_sample_barcode')\n\tif (i != -1) header[i] = 'sample'\n\ti = htry('patient', 'donor', 'target_case_id')\n\tif (i != -1) header[i] = 'patient'\n\ti = htry('disease')\n\tif (i != -1) header[i] = 'disease'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\ti = htry('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\tflag.del.header = header\n\tflag.del.loaded = true\n\treturn false\n}\n\nexport function parseline(i, line, flag) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m = {}\n\tfor (let j = 0; j < flag.del.header.length; j++) {\n\t\tif (lst[j] == undefined) break\n\t\tm[flag.del.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.del.badlines.push([i, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (m.rnaposition) {\n\t\tlet v = Number.parseInt(m.rnaposition)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid rnaPosition value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnaposition = v\n\t\tif (!m.rnadellength) {\n\t\t\tflag.del.badlines.push([i, 'missing rnaDellength value', lst])\n\t\t\treturn\n\t\t}\n\t\tv = Number.parseInt(m.rnadellength)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid rnaDellength value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnadellength = v\n\t}\n\tif (m.chr) {\n\t\tlet v = Number.parseInt(m.chrpos1)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid chr_start value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos1 = v\n\t\tv = Number.parseInt(m.chrpos2)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid chr_stop value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos2 = v\n\t}\n\n\tif (bulk.parsesample(m, flag, i, lst, flag.del.badlines)) {\n\t\treturn\n\t}\n\tm.dt = common.dtdel\n\tm.class = common.mclassdel\n\tm.mname = 'DEL'\n\tflag.good++\n\tvar n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene\n\tif (!(n in flag.data)) {\n\t\tflag.data[n] = []\n\t}\n\tflag.data[n].push(m)\n}\n"],
-  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAEf,SAAS,YAAY,MAAM,MAAM;AACvC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAWA,MAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQA,EAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,MAAM;AACnB,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI;AAAA,IACH;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EACD;AACA,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,aAAa;AACtB,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,cAAc;AACvB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AAAA,EACb;AACA,MAAI,KAAK,cAAc,KAAK;AAC5B,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,WAAW;AACpB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,UAAU;AACnB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AAAA,EACb;AAEA,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,OAAK,IAAI,SAAS;AAClB,OAAK,IAAI,SAAS;AAClB,SAAO;AACR;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM;AACxC,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAI,CAAC;AACX,WAAS,IAAI,GAAG,IAAI,KAAK,IAAI,OAAO,QAAQ,KAAK;AAChD,QAAI,IAAI,CAAC,KAAK,OAAW;AACzB,MAAE,KAAK,IAAI,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EAC9B;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,SAAK,IAAI,SAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AAC/C;AAAA,EACD;AACA,MAAI,EAAE,aAAa;AAClB,QAAI,IAAI,OAAO,SAAS,EAAE,WAAW;AACrC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,6BAA6B,GAAG,CAAC;AAC5D;AAAA,IACD;AACA,MAAE,cAAc;AAChB,QAAI,CAAC,EAAE,cAAc;AACpB,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,8BAA8B,GAAG,CAAC;AAC7D;AAAA,IACD;AACA,QAAI,OAAO,SAAS,EAAE,YAAY;AAClC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,8BAA8B,GAAG,CAAC;AAC7D;AAAA,IACD;AACA,MAAE,eAAe;AAAA,EAClB;AACA,MAAI,EAAE,KAAK;AACV,QAAI,IAAI,OAAO,SAAS,EAAE,OAAO;AACjC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,2BAA2B,GAAG,CAAC;AAC1D;AAAA,IACD;AACA,MAAE,UAAU;AACZ,QAAI,OAAO,SAAS,EAAE,OAAO;AAC7B,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,0BAA0B,GAAG,CAAC;AACzD;AAAA,IACD;AACA,MAAE,UAAU;AAAA,EACb;AAEA,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,KAAK,KAAK,IAAI,QAAQ,GAAG;AACzD;AAAA,EACD;AACA,IAAE,KAAK,OAAO;AACd,IAAE,QAAQ,OAAO;AACjB,IAAE,QAAQ;AACV,OAAK;AACL,MAAI,IAAI,KAAK,cAAc,EAAE,KAAK,YAAY,IAAI,EAAE;AACpD,MAAI,EAAE,KAAK,KAAK,OAAO;AACtB,SAAK,KAAK,CAAC,IAAI,CAAC;AAAA,EACjB;AACA,OAAK,KAAK,CAAC,EAAE,KAAK,CAAC;AACpB;",
+  "sources": ["../../src/bulk.del.ts"],
+  "sourcesContent": ["////////////////////////////////////\n//\n//  shared between client and server\n//\n////////////////////////////////////\n\nimport * as common from './common.js'\nimport * as bulk from './bulk.js'\n\nexport function parseheader(line, flag) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid header line for intragenic deletion'\n\tconst htry = (...lst) => {\n\t\tfor (const i of lst) {\n\t\t\tconst j = header.indexOf(i)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('gene')\n\tif (i == -1) return 'gene missing from header'\n\theader[i] = 'gene'\n\ti = htry(\n\t\t'annovar_isoform',\n\t\t'mrna_accession',\n\t\t'mrna accession',\n\t\t'refseq_mrna_id',\n\t\t'annovar_sj_filter_isoform',\n\t\t'refseq',\n\t\t'isoform'\n\t)\n\tif (i == -1) return 'isoform missing from header'\n\theader[i] = 'isoform'\n\ti = htry('rnaposition')\n\tif (i != -1) {\n\t\theader[i] = 'rnaposition'\n\t\ti = htry('rnadellength')\n\t\tif (i == -1) return 'rnadellength is required when rnaPosition is used'\n\t\theader[i] = 'rnadellength'\n\t}\n\ti = htry('chromosome', 'chr')\n\tif (i != -1) {\n\t\theader[i] = 'chr'\n\t\ti = htry('chr_start')\n\t\tif (i == -1) return 'chr_start is required when chr is used'\n\t\theader[i] = 'chrpos1'\n\t\ti = htry('chr_stop')\n\t\tif (i == -1) return 'chr_stop is required when chr is used'\n\t\theader[i] = 'chrpos2'\n\t}\n\n\ti = htry('sample', 'sample_name', 'tumor_sample_barcode')\n\tif (i != -1) header[i] = 'sample'\n\ti = htry('patient', 'donor', 'target_case_id')\n\tif (i != -1) header[i] = 'patient'\n\ti = htry('disease')\n\tif (i != -1) header[i] = 'disease'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\ti = htry('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\tflag.del.header = header\n\tflag.del.loaded = true\n\treturn false\n}\n\nexport function parseline(i, line, flag) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m: Record<string, any> = {}\n\tfor (let j = 0; j < flag.del.header.length; j++) {\n\t\tif (lst[j] == undefined) break\n\t\tm[flag.del.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.del.badlines.push([i, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (m.rnaposition) {\n\t\tlet v = Number.parseInt(m.rnaposition)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid rnaPosition value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnaposition = v\n\t\tif (!m.rnadellength) {\n\t\t\tflag.del.badlines.push([i, 'missing rnaDellength value', lst])\n\t\t\treturn\n\t\t}\n\t\tv = Number.parseInt(m.rnadellength)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid rnaDellength value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnadellength = v\n\t}\n\tif (m.chr) {\n\t\tlet v = Number.parseInt(m.chrpos1)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid chr_start value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos1 = v\n\t\tv = Number.parseInt(m.chrpos2)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid chr_stop value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos2 = v\n\t}\n\n\tif (bulk.parsesample(m, flag, i, lst)) {\n\t\treturn\n\t}\n\tm.dt = common.dtdel\n\tm.class = common.mclassdel\n\tm.mname = 'DEL'\n\tflag.good++\n\tconst n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene\n\tif (!(n in flag.data)) {\n\t\tflag.data[n] = []\n\t}\n\tflag.data[n].push(m)\n}\n"],
+  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAEf,SAAS,YAAY,MAAM,MAAM;AACvC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAWA,MAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQA,EAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,MAAM;AACnB,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI;AAAA,IACH;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EACD;AACA,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,aAAa;AACtB,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,cAAc;AACvB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AAAA,EACb;AACA,MAAI,KAAK,cAAc,KAAK;AAC5B,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,WAAW;AACpB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,UAAU;AACnB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AAAA,EACb;AAEA,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,OAAK,IAAI,SAAS;AAClB,OAAK,IAAI,SAAS;AAClB,SAAO;AACR;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM;AACxC,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAyB,CAAC;AAChC,WAAS,IAAI,GAAG,IAAI,KAAK,IAAI,OAAO,QAAQ,KAAK;AAChD,QAAI,IAAI,CAAC,KAAK,OAAW;AACzB,MAAE,KAAK,IAAI,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EAC9B;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,SAAK,IAAI,SAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AAC/C;AAAA,EACD;AACA,MAAI,EAAE,aAAa;AAClB,QAAI,IAAI,OAAO,SAAS,EAAE,WAAW;AACrC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,6BAA6B,GAAG,CAAC;AAC5D;AAAA,IACD;AACA,MAAE,cAAc;AAChB,QAAI,CAAC,EAAE,cAAc;AACpB,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,8BAA8B,GAAG,CAAC;AAC7D;AAAA,IACD;AACA,QAAI,OAAO,SAAS,EAAE,YAAY;AAClC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,8BAA8B,GAAG,CAAC;AAC7D;AAAA,IACD;AACA,MAAE,eAAe;AAAA,EAClB;AACA,MAAI,EAAE,KAAK;AACV,QAAI,IAAI,OAAO,SAAS,EAAE,OAAO;AACjC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,2BAA2B,GAAG,CAAC;AAC1D;AAAA,IACD;AACA,MAAE,UAAU;AACZ,QAAI,OAAO,SAAS,EAAE,OAAO;AAC7B,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,0BAA0B,GAAG,CAAC;AACzD;AAAA,IACD;AACA,MAAE,UAAU;AAAA,EACb;AAEA,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,GAAG,GAAG;AACtC;AAAA,EACD;AACA,IAAE,KAAK,OAAO;AACd,IAAE,QAAQ,OAAO;AACjB,IAAE,QAAQ;AACV,OAAK;AACL,QAAM,IAAI,KAAK,cAAc,EAAE,KAAK,YAAY,IAAI,EAAE;AACtD,MAAI,EAAE,KAAK,KAAK,OAAO;AACtB,SAAK,KAAK,CAAC,IAAI,CAAC;AAAA,EACjB;AACA,OAAK,KAAK,CAAC,EAAE,KAAK,CAAC;AACpB;",
   "names": ["i"]
 }

package/dist/src/bulk.itd.d.ts

@@ -0,0 +1,2 @@
+export declare function parseheader(line: any, flag: any): false | "gene missing from header" | "isoform missing from header" | "invalid header line for ITD" | "rnaduplength is required when rnaposition is present" | "chr_start is required when chr is present" | "chr_stop is required when chr is present";
+export declare function parseline(i: any, line: any, flag: any): void;

package/dist/src/bulk.itd.js

@@ -99,14 +99,14 @@ function parseline(i, line, flag) {
     }
     m.chrpos2 = v;
   }
-  if (bulk.parsesample(m, flag, i, lst, flag.itd.badlines)) {
+  if (bulk.parsesample(m, flag, i, lst)) {
     return;
   }
   m.dt = common.dtitd;
   m.class = common.mclassitd;
   m.mname = "ITD";
   flag.good++;
-  var n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene;
+  const n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene;
   if (!(n in flag.data)) {
     flag.data[n] = [];
   }

package/dist/src/bulk.itd.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../src/bulk.itd.js"],
-  "sourcesContent": ["////////////////////////////////////\n//\n//  shared between client and server\n//\n////////////////////////////////////\n\nimport * as common from './common.js'\nimport * as bulk from './bulk.js'\n\nexport function parseheader(line, flag) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid header line for ITD'\n\tconst htry = (...lst) => {\n\t\tfor (const i of lst) {\n\t\t\tconst j = header.indexOf(i)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('gene')\n\tif (i == -1) return 'gene missing from header'\n\theader[i] = 'gene'\n\ti = htry(\n\t\t'annovar_isoform',\n\t\t'mrna_accession',\n\t\t'mrna accession',\n\t\t'refseq_mrna_id',\n\t\t'annovar_sj_filter_isoform',\n\t\t'refseq',\n\t\t'isoform'\n\t)\n\tif (i == -1) return 'isoform missing from header'\n\theader[i] = 'isoform'\n\ti = htry('rnaposition')\n\tif (i != -1) {\n\t\theader[i] = 'rnaposition'\n\t\ti = htry('rnaduplength')\n\t\tif (i == -1) return 'rnaduplength is required when rnaposition is present'\n\t\theader[i] = 'rnaduplength'\n\t}\n\ti = htry('chromosome', 'chr')\n\tif (i != -1) {\n\t\theader[i] = 'chr'\n\t\ti = htry('chr_start')\n\t\tif (i == -1) return 'chr_start is required when chr is present'\n\t\theader[i] = 'chrpos1'\n\t\ti = htry('chr_stop')\n\t\tif (i == -1) return 'chr_stop is required when chr is present'\n\t\theader[i] = 'chrpos2'\n\t}\n\n\ti = htry('sample', 'sample_name', 'tumor_sample_barcode')\n\tif (i != -1) header[i] = 'sample'\n\ti = htry('patient', 'donor', 'target_case_id')\n\tif (i != -1) header[i] = 'patient'\n\ti = htry('disease')\n\tif (i != -1) header[i] = 'disease'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\ti = htry('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\tflag.itd.header = header\n\tflag.itd.loaded = true\n\treturn false\n}\n\nexport function parseline(i, line, flag) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m = {}\n\tfor (let j = 0; j < flag.itd.header.length; j++) {\n\t\tif (lst[j] == undefined) break\n\t\tm[flag.itd.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.itd.badlines.push([i, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (m.rnaposition) {\n\t\tlet v = Number.parseInt(m.rnaposition)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid rnaPosition value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnaposition = v\n\t\tif (!m.rnaduplength) {\n\t\t\tflag.itd.badlines.push([i, 'missing rnaDuplength value', lst])\n\t\t\treturn\n\t\t}\n\t\tv = Number.parseInt(m.rnaduplength)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid rnaDuplength value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnaduplength = v\n\t}\n\tif (m.chr) {\n\t\tlet v = Number.parseInt(m.chrpos1)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid chr_start value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos1 = v\n\t\tv = Number.parseInt(m.chrpos2)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid chr_stop value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos2 = v\n\t}\n\tif (bulk.parsesample(m, flag, i, lst, flag.itd.badlines)) {\n\t\treturn\n\t}\n\tm.dt = common.dtitd\n\tm.class = common.mclassitd\n\tm.mname = 'ITD'\n\tflag.good++\n\tvar n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene\n\tif (!(n in flag.data)) {\n\t\tflag.data[n] = []\n\t}\n\tflag.data[n].push(m)\n}\n"],
-  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAEf,SAAS,YAAY,MAAM,MAAM;AACvC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAWA,MAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQA,EAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,MAAM;AACnB,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI;AAAA,IACH;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EACD;AACA,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,aAAa;AACtB,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,cAAc;AACvB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AAAA,EACb;AACA,MAAI,KAAK,cAAc,KAAK;AAC5B,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,WAAW;AACpB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,UAAU;AACnB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AAAA,EACb;AAEA,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,OAAK,IAAI,SAAS;AAClB,OAAK,IAAI,SAAS;AAClB,SAAO;AACR;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM;AACxC,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAI,CAAC;AACX,WAAS,IAAI,GAAG,IAAI,KAAK,IAAI,OAAO,QAAQ,KAAK;AAChD,QAAI,IAAI,CAAC,KAAK,OAAW;AACzB,MAAE,KAAK,IAAI,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EAC9B;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,SAAK,IAAI,SAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AAC/C;AAAA,EACD;AACA,MAAI,EAAE,aAAa;AAClB,QAAI,IAAI,OAAO,SAAS,EAAE,WAAW;AACrC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,6BAA6B,GAAG,CAAC;AAC5D;AAAA,IACD;AACA,MAAE,cAAc;AAChB,QAAI,CAAC,EAAE,cAAc;AACpB,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,8BAA8B,GAAG,CAAC;AAC7D;AAAA,IACD;AACA,QAAI,OAAO,SAAS,EAAE,YAAY;AAClC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,8BAA8B,GAAG,CAAC;AAC7D;AAAA,IACD;AACA,MAAE,eAAe;AAAA,EAClB;AACA,MAAI,EAAE,KAAK;AACV,QAAI,IAAI,OAAO,SAAS,EAAE,OAAO;AACjC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,2BAA2B,GAAG,CAAC;AAC1D;AAAA,IACD;AACA,MAAE,UAAU;AACZ,QAAI,OAAO,SAAS,EAAE,OAAO;AAC7B,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,0BAA0B,GAAG,CAAC;AACzD;AAAA,IACD;AACA,MAAE,UAAU;AAAA,EACb;AACA,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,KAAK,KAAK,IAAI,QAAQ,GAAG;AACzD;AAAA,EACD;AACA,IAAE,KAAK,OAAO;AACd,IAAE,QAAQ,OAAO;AACjB,IAAE,QAAQ;AACV,OAAK;AACL,MAAI,IAAI,KAAK,cAAc,EAAE,KAAK,YAAY,IAAI,EAAE;AACpD,MAAI,EAAE,KAAK,KAAK,OAAO;AACtB,SAAK,KAAK,CAAC,IAAI,CAAC;AAAA,EACjB;AACA,OAAK,KAAK,CAAC,EAAE,KAAK,CAAC;AACpB;",
+  "sources": ["../../src/bulk.itd.ts"],
+  "sourcesContent": ["////////////////////////////////////\n//\n//  shared between client and server\n//\n////////////////////////////////////\n\nimport * as common from './common.js'\nimport * as bulk from './bulk.js'\n\nexport function parseheader(line, flag) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid header line for ITD'\n\tconst htry = (...lst) => {\n\t\tfor (const i of lst) {\n\t\t\tconst j = header.indexOf(i)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('gene')\n\tif (i == -1) return 'gene missing from header'\n\theader[i] = 'gene'\n\ti = htry(\n\t\t'annovar_isoform',\n\t\t'mrna_accession',\n\t\t'mrna accession',\n\t\t'refseq_mrna_id',\n\t\t'annovar_sj_filter_isoform',\n\t\t'refseq',\n\t\t'isoform'\n\t)\n\tif (i == -1) return 'isoform missing from header'\n\theader[i] = 'isoform'\n\ti = htry('rnaposition')\n\tif (i != -1) {\n\t\theader[i] = 'rnaposition'\n\t\ti = htry('rnaduplength')\n\t\tif (i == -1) return 'rnaduplength is required when rnaposition is present'\n\t\theader[i] = 'rnaduplength'\n\t}\n\ti = htry('chromosome', 'chr')\n\tif (i != -1) {\n\t\theader[i] = 'chr'\n\t\ti = htry('chr_start')\n\t\tif (i == -1) return 'chr_start is required when chr is present'\n\t\theader[i] = 'chrpos1'\n\t\ti = htry('chr_stop')\n\t\tif (i == -1) return 'chr_stop is required when chr is present'\n\t\theader[i] = 'chrpos2'\n\t}\n\n\ti = htry('sample', 'sample_name', 'tumor_sample_barcode')\n\tif (i != -1) header[i] = 'sample'\n\ti = htry('patient', 'donor', 'target_case_id')\n\tif (i != -1) header[i] = 'patient'\n\ti = htry('disease')\n\tif (i != -1) header[i] = 'disease'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\ti = htry('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\tflag.itd.header = header\n\tflag.itd.loaded = true\n\treturn false\n}\n\nexport function parseline(i, line, flag) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m: Record<string, any> = {}\n\tfor (let j = 0; j < flag.itd.header.length; j++) {\n\t\tif (lst[j] == undefined) break\n\t\tm[flag.itd.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.itd.badlines.push([i, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (m.rnaposition) {\n\t\tlet v = Number.parseInt(m.rnaposition)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid rnaPosition value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnaposition = v\n\t\tif (!m.rnaduplength) {\n\t\t\tflag.itd.badlines.push([i, 'missing rnaDuplength value', lst])\n\t\t\treturn\n\t\t}\n\t\tv = Number.parseInt(m.rnaduplength)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid rnaDuplength value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnaduplength = v\n\t}\n\tif (m.chr) {\n\t\tlet v = Number.parseInt(m.chrpos1)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid chr_start value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos1 = v\n\t\tv = Number.parseInt(m.chrpos2)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid chr_stop value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos2 = v\n\t}\n\tif (bulk.parsesample(m, flag, i, lst)) {\n\t\treturn\n\t}\n\tm.dt = common.dtitd\n\tm.class = common.mclassitd\n\tm.mname = 'ITD'\n\tflag.good++\n\tconst n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene\n\tif (!(n in flag.data)) {\n\t\tflag.data[n] = []\n\t}\n\tflag.data[n].push(m)\n}\n"],
+  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAEf,SAAS,YAAY,MAAM,MAAM;AACvC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAWA,MAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQA,EAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,MAAM;AACnB,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI;AAAA,IACH;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EACD;AACA,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,aAAa;AACtB,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,cAAc;AACvB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AAAA,EACb;AACA,MAAI,KAAK,cAAc,KAAK;AAC5B,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,WAAW;AACpB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,UAAU;AACnB,QAAI,KAAK,GAAI,QAAO;AACpB,WAAO,CAAC,IAAI;AAAA,EACb;AAEA,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,OAAK,IAAI,SAAS;AAClB,OAAK,IAAI,SAAS;AAClB,SAAO;AACR;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM;AACxC,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAyB,CAAC;AAChC,WAAS,IAAI,GAAG,IAAI,KAAK,IAAI,OAAO,QAAQ,KAAK;AAChD,QAAI,IAAI,CAAC,KAAK,OAAW;AACzB,MAAE,KAAK,IAAI,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EAC9B;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,SAAK,IAAI,SAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AAC/C;AAAA,EACD;AACA,MAAI,EAAE,aAAa;AAClB,QAAI,IAAI,OAAO,SAAS,EAAE,WAAW;AACrC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,6BAA6B,GAAG,CAAC;AAC5D;AAAA,IACD;AACA,MAAE,cAAc;AAChB,QAAI,CAAC,EAAE,cAAc;AACpB,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,8BAA8B,GAAG,CAAC;AAC7D;AAAA,IACD;AACA,QAAI,OAAO,SAAS,EAAE,YAAY;AAClC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,8BAA8B,GAAG,CAAC;AAC7D;AAAA,IACD;AACA,MAAE,eAAe;AAAA,EAClB;AACA,MAAI,EAAE,KAAK;AACV,QAAI,IAAI,OAAO,SAAS,EAAE,OAAO;AACjC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,2BAA2B,GAAG,CAAC;AAC1D;AAAA,IACD;AACA,MAAE,UAAU;AACZ,QAAI,OAAO,SAAS,EAAE,OAAO;AAC7B,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,IAAI,SAAS,KAAK,CAAC,GAAG,0BAA0B,GAAG,CAAC;AACzD;AAAA,IACD;AACA,MAAE,UAAU;AAAA,EACb;AACA,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,GAAG,GAAG;AACtC;AAAA,EACD;AACA,IAAE,KAAK,OAAO;AACd,IAAE,QAAQ,OAAO;AACjB,IAAE,QAAQ;AACV,OAAK;AACL,QAAM,IAAI,KAAK,cAAc,EAAE,KAAK,YAAY,IAAI,EAAE;AACtD,MAAI,EAAE,KAAK,KAAK,OAAO;AACtB,SAAK,KAAK,CAAC,IAAI,CAAC;AAAA,EACjB;AACA,OAAK,KAAK,CAAC,EAAE,KAAK,CAAC;AACpB;",
   "names": ["i"]
 }

package/dist/src/bulk.js

@@ -69,7 +69,7 @@ function init_bulk_flag(genome) {
     }
   };
 }
-function parsesample(m, flag, i, lst, badline) {
+function parsesample(m, flag, i, lst) {
   let variantorigin = common.moriginsomatic;
   if (m.sampletype) {
     const s = m.sampletype.toLowerCase();
@@ -145,7 +145,6 @@ function parsesample(m, flag, i, lst, badline) {
     return;
   }
   const nopatientname = "no patient/individual name";
-  let p;
   if (m.patient) {
     if (!flag.patient2st[m.patient]) {
       flag.patient2st[m.patient] = {};

package/dist/src/bulk.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../src/bulk.js"],
-  "sourcesContent": ["////////////////////////////////////\n//\n//  shared between client and server\n//\n////////////////////////////////////\n\nimport * as common from './common.js'\n\nexport default {}\n\nexport function init_bulk_flag(genome) {\n\tif (!genome) {\n\t\treturn null\n\t}\n\tconst mclasslabel2key = {}\n\tfor (const n in common.mclass) {\n\t\tmclasslabel2key[common.mclass[n].label.toUpperCase()] = n\n\t}\n\treturn {\n\t\tgenome: genome,\n\t\tmclasslabel2key: mclasslabel2key,\n\t\tdata: {},\n\t\tsample2disease: {}, // (proof) k: sample, v: disease\n\t\t// will only record this when origin is used\n\t\tpatient2st: {},\n\t\t// k: patient, v: { k: sampletype, v: sample }\n\t\t// new sample names always override old\n\t\tgood: 0,\n\t\tgeneToUpper: true, // option to not force uppercase on gene names\n\t\tsnv: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: [],\n\t\t\t// jinghui: based on missense/silent ratio of entire dataset to decide whether to include silent when importing...\n\t\t\t// hard-coded class codes\n\t\t\tmissense: 0,\n\t\t\tsilent: 0\n\t\t},\n\t\tsvjson: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\tfusion: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: [],\n\t\t\toriginal: []\n\t\t},\n\t\tsv: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: [],\n\t\t\toriginal: []\n\t\t},\n\t\tcnv: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\titd: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\tdel: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\ttruncation: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t}\n\t}\n}\n\nexport function parsesample(m, flag, i, lst, badline) {\n\tlet variantorigin = common.moriginsomatic\n\tif (m.sampletype) {\n\t\tconst s = m.sampletype.toLowerCase()\n\t\tswitch (s) {\n\t\t\tcase 'relapse':\n\t\t\t\tvariantorigin = common.moriginrelapse\n\t\t\t\tbreak\n\t\t\tcase 'germline':\n\t\t\t\tvariantorigin = common.morigingermline\n\t\t\t\tbreak\n\t\t\tcase 'somatic':\n\t\t\tcase 'diagnosis':\n\t\t\t\tbreak\n\t\t}\n\t\tif (m.sample) {\n\t\t\tif (m.patient) {\n\t\t\t\t// good\n\t\t\t} else {\n\t\t\t\tm.patient = m.sample + ' ' + m.sampletype\n\t\t\t}\n\t\t} else {\n\t\t\tif (m.patient) {\n\t\t\t\tm.sample = m.patient + ' ' + m.sampletype\n\t\t\t} else {\n\t\t\t\t// neither sample or patient, will quit later\n\t\t\t}\n\t\t}\n\t} else {\n\t\tif (m.patient) {\n\t\t\tif (m.sample) {\n\t\t\t\tm.sampletype = m.sample\n\t\t\t} else {\n\t\t\t\tm.sample = m.sampletype = m.patient\n\t\t\t}\n\t\t} else {\n\t\t\tif (m.sample) {\n\t\t\t\tm.sampletype = m.sample\n\t\t\t} else {\n\t\t\t\t// no patient/sample, will quit later\n\t\t\t}\n\t\t}\n\t}\n\tif (m.origin) {\n\t\t// override existing variantorigin\n\t\tconst s = m.origin.toLowerCase()\n\t\tswitch (s) {\n\t\t\tcase 'r':\n\t\t\tcase 'relapse':\n\t\t\t\tvariantorigin = common.moriginrelapse\n\t\t\t\tm.isrim2 = true\n\t\t\t\tbreak\n\t\t\tcase 'g':\n\t\t\tcase 'germline':\n\t\t\t\tvariantorigin = common.morigingermline\n\t\t\t\tm.isrim1 = true\n\t\t\t\tbreak\n\t\t\tcase 'gp':\n\t\t\tcase 'germline pathogenic':\n\t\t\t\tvariantorigin = common.morigingermlinepathogenic\n\t\t\t\tm.isrim1 = true\n\t\t\t\tbreak\n\t\t\tcase 'gnp':\n\t\t\tcase 'germline nonpathogenic':\n\t\t\tcase 'germline non-pathogenic':\n\t\t\t\tvariantorigin = common.morigingermlinenonpathogenic\n\t\t\t\tm.isrim1 = true\n\t\t\t\tbreak\n\t\t\tcase 's':\n\t\t\tcase 'somatic':\n\t\t\tcase 'diagnosis':\n\t\t\t\tvariantorigin = common.moriginsomatic\n\t\t\t\tbreak\n\t\t}\n\t}\n\tm.origin = variantorigin\n\n\tif (!m.sample && !m.patient) {\n\t\t// will not go into sample table\n\t\treturn\n\t}\n\n\tconst nopatientname = 'no patient/individual name'\n\tlet p\n\tif (m.patient) {\n\t\tif (!flag.patient2st[m.patient]) {\n\t\t\tflag.patient2st[m.patient] = {}\n\t\t}\n\t\tflag.patient2st[m.patient][m.sampletype] = m.sample\n\t} else {\n\t\tif (!flag.patient2st[nopatientname]) {\n\t\t\tflag.patient2st[nopatientname] = {}\n\t\t}\n\t\tflag.patient2st[nopatientname][m.sampletype] = m.sample\n\t}\n\n\tif (m.sample) {\n\t\tif (m.disease) {\n\t\t\tif (m.sample in flag.sample2disease) {\n\t\t\t\tif (m.disease != flag.sample2disease[m.sample]) {\n\t\t\t\t\tflag.snv.badlines.push([\n\t\t\t\t\t\ti,\n\t\t\t\t\t\t'conflict of disease types for sample \"' +\n\t\t\t\t\t\t\tm.sample +\n\t\t\t\t\t\t\t'\": ' +\n\t\t\t\t\t\t\tm.disease +\n\t\t\t\t\t\t\t', ' +\n\t\t\t\t\t\t\tflag.sample2disease[m.sample],\n\t\t\t\t\t\tlst\n\t\t\t\t\t])\n\t\t\t\t\treturn true\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tflag.sample2disease[m.sample] = m.disease\n\t\t\t}\n\t\t}\n\t}\n\treturn false\n}\n"],
-  "mappings": "AAMA,YAAY,YAAY;AAExB,IAAO,eAAQ,CAAC;AAET,SAAS,eAAe,QAAQ;AACtC,MAAI,CAAC,QAAQ;AACZ,WAAO;AAAA,EACR;AACA,QAAM,kBAAkB,CAAC;AACzB,aAAW,KAAK,OAAO,QAAQ;AAC9B,oBAAgB,OAAO,OAAO,CAAC,EAAE,MAAM,YAAY,CAAC,IAAI;AAAA,EACzD;AACA,SAAO;AAAA,IACN;AAAA,IACA;AAAA,IACA,MAAM,CAAC;AAAA,IACP,gBAAgB,CAAC;AAAA;AAAA;AAAA,IAEjB,YAAY,CAAC;AAAA;AAAA;AAAA,IAGb,MAAM;AAAA,IACN,aAAa;AAAA;AAAA,IACb,KAAK;AAAA,MACJ,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA;AAAA;AAAA,MAGX,UAAU;AAAA,MACV,QAAQ;AAAA,IACT;AAAA,IACA,QAAQ;AAAA,MACP,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,QAAQ;AAAA,MACP,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,MACX,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,IAAI;AAAA,MACH,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,MACX,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,KAAK;AAAA,MACJ,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,KAAK;AAAA,MACJ,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,KAAK;AAAA,MACJ,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,YAAY;AAAA,MACX,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,IACZ;AAAA,EACD;AACD;AAEO,SAAS,YAAY,GAAG,MAAM,GAAG,KAAK,SAAS;AACrD,MAAI,gBAAgB,OAAO;AAC3B,MAAI,EAAE,YAAY;AACjB,UAAM,IAAI,EAAE,WAAW,YAAY;AACnC,YAAQ,GAAG;AAAA,MACV,KAAK;AACJ,wBAAgB,OAAO;AACvB;AAAA,MACD,KAAK;AACJ,wBAAgB,OAAO;AACvB;AAAA,MACD,KAAK;AAAA,MACL,KAAK;AACJ;AAAA,IACF;AACA,QAAI,EAAE,QAAQ;AACb,UAAI,EAAE,SAAS;AAAA,MAEf,OAAO;AACN,UAAE,UAAU,EAAE,SAAS,MAAM,EAAE;AAAA,MAChC;AAAA,IACD,OAAO;AACN,UAAI,EAAE,SAAS;AACd,UAAE,SAAS,EAAE,UAAU,MAAM,EAAE;AAAA,MAChC,OAAO;AAAA,MAEP;AAAA,IACD;AAAA,EACD,OAAO;AACN,QAAI,EAAE,SAAS;AACd,UAAI,EAAE,QAAQ;AACb,UAAE,aAAa,EAAE;AAAA,MAClB,OAAO;AACN,UAAE,SAAS,EAAE,aAAa,EAAE;AAAA,MAC7B;AAAA,IACD,OAAO;AACN,UAAI,EAAE,QAAQ;AACb,UAAE,aAAa,EAAE;AAAA,MAClB,OAAO;AAAA,MAEP;AAAA,IACD;AAAA,EACD;AACA,MAAI,EAAE,QAAQ;AAEb,UAAM,IAAI,EAAE,OAAO,YAAY;AAC/B,YAAQ,GAAG;AAAA,MACV,KAAK;AAAA,MACL,KAAK;AACJ,wBAAgB,OAAO;AACvB,UAAE,SAAS;AACX;AAAA,MACD,KAAK;AAAA,MACL,KAAK;AACJ,wBAAgB,OAAO;AACvB,UAAE,SAAS;AACX;AAAA,MACD,KAAK;AAAA,MACL,KAAK;AACJ,wBAAgB,OAAO;AACvB,UAAE,SAAS;AACX;AAAA,MACD,KAAK;AAAA,MACL,KAAK;AAAA,MACL,KAAK;AACJ,wBAAgB,OAAO;AACvB,UAAE,SAAS;AACX;AAAA,MACD,KAAK;AAAA,MACL,KAAK;AAAA,MACL,KAAK;AACJ,wBAAgB,OAAO;AACvB;AAAA,IACF;AAAA,EACD;AACA,IAAE,SAAS;AAEX,MAAI,CAAC,EAAE,UAAU,CAAC,EAAE,SAAS;AAE5B;AAAA,EACD;AAEA,QAAM,gBAAgB;AACtB,MAAI;AACJ,MAAI,EAAE,SAAS;AACd,QAAI,CAAC,KAAK,WAAW,EAAE,OAAO,GAAG;AAChC,WAAK,WAAW,EAAE,OAAO,IAAI,CAAC;AAAA,IAC/B;AACA,SAAK,WAAW,EAAE,OAAO,EAAE,EAAE,UAAU,IAAI,EAAE;AAAA,EAC9C,OAAO;AACN,QAAI,CAAC,KAAK,WAAW,aAAa,GAAG;AACpC,WAAK,WAAW,aAAa,IAAI,CAAC;AAAA,IACnC;AACA,SAAK,WAAW,aAAa,EAAE,EAAE,UAAU,IAAI,EAAE;AAAA,EAClD;AAEA,MAAI,EAAE,QAAQ;AACb,QAAI,EAAE,SAAS;AACd,UAAI,EAAE,UAAU,KAAK,gBAAgB;AACpC,YAAI,EAAE,WAAW,KAAK,eAAe,EAAE,MAAM,GAAG;AAC/C,eAAK,IAAI,SAAS,KAAK;AAAA,YACtB;AAAA,YACA,2CACC,EAAE,SACF,QACA,EAAE,UACF,OACA,KAAK,eAAe,EAAE,MAAM;AAAA,YAC7B;AAAA,UACD,CAAC;AACD,iBAAO;AAAA,QACR;AAAA,MACD,OAAO;AACN,aAAK,eAAe,EAAE,MAAM,IAAI,EAAE;AAAA,MACnC;AAAA,IACD;AAAA,EACD;AACA,SAAO;AACR;",
+  "sources": ["../../src/bulk.ts"],
+  "sourcesContent": ["////////////////////////////////////\n//\n//  shared between client and server\n//\n////////////////////////////////////\n\nimport * as common from './common.js'\n\nexport default {}\n\nexport function init_bulk_flag(genome) {\n\tif (!genome) {\n\t\treturn null\n\t}\n\tconst mclasslabel2key = {}\n\tfor (const n in common.mclass) {\n\t\tmclasslabel2key[common.mclass[n].label.toUpperCase()] = n\n\t}\n\treturn {\n\t\tgenome: genome,\n\t\tmclasslabel2key: mclasslabel2key,\n\t\tdata: {},\n\t\tsample2disease: {}, // (proof) k: sample, v: disease\n\t\t// will only record this when origin is used\n\t\tpatient2st: {},\n\t\t// k: patient, v: { k: sampletype, v: sample }\n\t\t// new sample names always override old\n\t\tgood: 0,\n\t\tgeneToUpper: true, // option to not force uppercase on gene names\n\t\tsnv: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: [],\n\t\t\t// jinghui: based on missense/silent ratio of entire dataset to decide whether to include silent when importing...\n\t\t\t// hard-coded class codes\n\t\t\tmissense: 0,\n\t\t\tsilent: 0\n\t\t},\n\t\tsvjson: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\tfusion: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: [],\n\t\t\toriginal: []\n\t\t},\n\t\tsv: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: [],\n\t\t\toriginal: []\n\t\t},\n\t\tcnv: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\titd: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\tdel: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\ttruncation: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t}\n\t}\n}\n\nexport function parsesample(m, flag, i, lst) {\n\tlet variantorigin = common.moriginsomatic\n\tif (m.sampletype) {\n\t\tconst s = m.sampletype.toLowerCase()\n\t\tswitch (s) {\n\t\t\tcase 'relapse':\n\t\t\t\tvariantorigin = common.moriginrelapse\n\t\t\t\tbreak\n\t\t\tcase 'germline':\n\t\t\t\tvariantorigin = common.morigingermline\n\t\t\t\tbreak\n\t\t\tcase 'somatic':\n\t\t\tcase 'diagnosis':\n\t\t\t\tbreak\n\t\t}\n\t\tif (m.sample) {\n\t\t\tif (m.patient) {\n\t\t\t\t// good\n\t\t\t} else {\n\t\t\t\tm.patient = m.sample + ' ' + m.sampletype\n\t\t\t}\n\t\t} else {\n\t\t\tif (m.patient) {\n\t\t\t\tm.sample = m.patient + ' ' + m.sampletype\n\t\t\t} else {\n\t\t\t\t// neither sample or patient, will quit later\n\t\t\t}\n\t\t}\n\t} else {\n\t\tif (m.patient) {\n\t\t\tif (m.sample) {\n\t\t\t\tm.sampletype = m.sample\n\t\t\t} else {\n\t\t\t\tm.sample = m.sampletype = m.patient\n\t\t\t}\n\t\t} else {\n\t\t\tif (m.sample) {\n\t\t\t\tm.sampletype = m.sample\n\t\t\t} else {\n\t\t\t\t// no patient/sample, will quit later\n\t\t\t}\n\t\t}\n\t}\n\tif (m.origin) {\n\t\t// override existing variantorigin\n\t\tconst s = m.origin.toLowerCase()\n\t\tswitch (s) {\n\t\t\tcase 'r':\n\t\t\tcase 'relapse':\n\t\t\t\tvariantorigin = common.moriginrelapse\n\t\t\t\tm.isrim2 = true\n\t\t\t\tbreak\n\t\t\tcase 'g':\n\t\t\tcase 'germline':\n\t\t\t\tvariantorigin = common.morigingermline\n\t\t\t\tm.isrim1 = true\n\t\t\t\tbreak\n\t\t\tcase 'gp':\n\t\t\tcase 'germline pathogenic':\n\t\t\t\tvariantorigin = common.morigingermlinepathogenic\n\t\t\t\tm.isrim1 = true\n\t\t\t\tbreak\n\t\t\tcase 'gnp':\n\t\t\tcase 'germline nonpathogenic':\n\t\t\tcase 'germline non-pathogenic':\n\t\t\t\tvariantorigin = common.morigingermlinenonpathogenic\n\t\t\t\tm.isrim1 = true\n\t\t\t\tbreak\n\t\t\tcase 's':\n\t\t\tcase 'somatic':\n\t\t\tcase 'diagnosis':\n\t\t\t\tvariantorigin = common.moriginsomatic\n\t\t\t\tbreak\n\t\t}\n\t}\n\tm.origin = variantorigin\n\n\tif (!m.sample && !m.patient) {\n\t\t// will not go into sample table\n\t\treturn\n\t}\n\n\tconst nopatientname = 'no patient/individual name'\n\n\tif (m.patient) {\n\t\tif (!flag.patient2st[m.patient]) {\n\t\t\tflag.patient2st[m.patient] = {}\n\t\t}\n\t\tflag.patient2st[m.patient][m.sampletype] = m.sample\n\t} else {\n\t\tif (!flag.patient2st[nopatientname]) {\n\t\t\tflag.patient2st[nopatientname] = {}\n\t\t}\n\t\tflag.patient2st[nopatientname][m.sampletype] = m.sample\n\t}\n\n\tif (m.sample) {\n\t\tif (m.disease) {\n\t\t\tif (m.sample in flag.sample2disease) {\n\t\t\t\tif (m.disease != flag.sample2disease[m.sample]) {\n\t\t\t\t\tflag.snv.badlines.push([\n\t\t\t\t\t\ti,\n\t\t\t\t\t\t'conflict of disease types for sample \"' +\n\t\t\t\t\t\t\tm.sample +\n\t\t\t\t\t\t\t'\": ' +\n\t\t\t\t\t\t\tm.disease +\n\t\t\t\t\t\t\t', ' +\n\t\t\t\t\t\t\tflag.sample2disease[m.sample],\n\t\t\t\t\t\tlst\n\t\t\t\t\t])\n\t\t\t\t\treturn true\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tflag.sample2disease[m.sample] = m.disease\n\t\t\t}\n\t\t}\n\t}\n\treturn false\n}\n"],
+  "mappings": "AAMA,YAAY,YAAY;AAExB,IAAO,eAAQ,CAAC;AAET,SAAS,eAAe,QAAQ;AACtC,MAAI,CAAC,QAAQ;AACZ,WAAO;AAAA,EACR;AACA,QAAM,kBAAkB,CAAC;AACzB,aAAW,KAAK,OAAO,QAAQ;AAC9B,oBAAgB,OAAO,OAAO,CAAC,EAAE,MAAM,YAAY,CAAC,IAAI;AAAA,EACzD;AACA,SAAO;AAAA,IACN;AAAA,IACA;AAAA,IACA,MAAM,CAAC;AAAA,IACP,gBAAgB,CAAC;AAAA;AAAA;AAAA,IAEjB,YAAY,CAAC;AAAA;AAAA;AAAA,IAGb,MAAM;AAAA,IACN,aAAa;AAAA;AAAA,IACb,KAAK;AAAA,MACJ,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA;AAAA;AAAA,MAGX,UAAU;AAAA,MACV,QAAQ;AAAA,IACT;AAAA,IACA,QAAQ;AAAA,MACP,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,QAAQ;AAAA,MACP,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,MACX,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,IAAI;AAAA,MACH,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,MACX,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,KAAK;AAAA,MACJ,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,KAAK;AAAA,MACJ,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,KAAK;AAAA,MACJ,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,IACZ;AAAA,IACA,YAAY;AAAA,MACX,QAAQ;AAAA,MACR,QAAQ;AAAA,MACR,UAAU,CAAC;AAAA,IACZ;AAAA,EACD;AACD;AAEO,SAAS,YAAY,GAAG,MAAM,GAAG,KAAK;AAC5C,MAAI,gBAAgB,OAAO;AAC3B,MAAI,EAAE,YAAY;AACjB,UAAM,IAAI,EAAE,WAAW,YAAY;AACnC,YAAQ,GAAG;AAAA,MACV,KAAK;AACJ,wBAAgB,OAAO;AACvB;AAAA,MACD,KAAK;AACJ,wBAAgB,OAAO;AACvB;AAAA,MACD,KAAK;AAAA,MACL,KAAK;AACJ;AAAA,IACF;AACA,QAAI,EAAE,QAAQ;AACb,UAAI,EAAE,SAAS;AAAA,MAEf,OAAO;AACN,UAAE,UAAU,EAAE,SAAS,MAAM,EAAE;AAAA,MAChC;AAAA,IACD,OAAO;AACN,UAAI,EAAE,SAAS;AACd,UAAE,SAAS,EAAE,UAAU,MAAM,EAAE;AAAA,MAChC,OAAO;AAAA,MAEP;AAAA,IACD;AAAA,EACD,OAAO;AACN,QAAI,EAAE,SAAS;AACd,UAAI,EAAE,QAAQ;AACb,UAAE,aAAa,EAAE;AAAA,MAClB,OAAO;AACN,UAAE,SAAS,EAAE,aAAa,EAAE;AAAA,MAC7B;AAAA,IACD,OAAO;AACN,UAAI,EAAE,QAAQ;AACb,UAAE,aAAa,EAAE;AAAA,MAClB,OAAO;AAAA,MAEP;AAAA,IACD;AAAA,EACD;AACA,MAAI,EAAE,QAAQ;AAEb,UAAM,IAAI,EAAE,OAAO,YAAY;AAC/B,YAAQ,GAAG;AAAA,MACV,KAAK;AAAA,MACL,KAAK;AACJ,wBAAgB,OAAO;AACvB,UAAE,SAAS;AACX;AAAA,MACD,KAAK;AAAA,MACL,KAAK;AACJ,wBAAgB,OAAO;AACvB,UAAE,SAAS;AACX;AAAA,MACD,KAAK;AAAA,MACL,KAAK;AACJ,wBAAgB,OAAO;AACvB,UAAE,SAAS;AACX;AAAA,MACD,KAAK;AAAA,MACL,KAAK;AAAA,MACL,KAAK;AACJ,wBAAgB,OAAO;AACvB,UAAE,SAAS;AACX;AAAA,MACD,KAAK;AAAA,MACL,KAAK;AAAA,MACL,KAAK;AACJ,wBAAgB,OAAO;AACvB;AAAA,IACF;AAAA,EACD;AACA,IAAE,SAAS;AAEX,MAAI,CAAC,EAAE,UAAU,CAAC,EAAE,SAAS;AAE5B;AAAA,EACD;AAEA,QAAM,gBAAgB;AAEtB,MAAI,EAAE,SAAS;AACd,QAAI,CAAC,KAAK,WAAW,EAAE,OAAO,GAAG;AAChC,WAAK,WAAW,EAAE,OAAO,IAAI,CAAC;AAAA,IAC/B;AACA,SAAK,WAAW,EAAE,OAAO,EAAE,EAAE,UAAU,IAAI,EAAE;AAAA,EAC9C,OAAO;AACN,QAAI,CAAC,KAAK,WAAW,aAAa,GAAG;AACpC,WAAK,WAAW,aAAa,IAAI,CAAC;AAAA,IACnC;AACA,SAAK,WAAW,aAAa,EAAE,EAAE,UAAU,IAAI,EAAE;AAAA,EAClD;AAEA,MAAI,EAAE,QAAQ;AACb,QAAI,EAAE,SAAS;AACd,UAAI,EAAE,UAAU,KAAK,gBAAgB;AACpC,YAAI,EAAE,WAAW,KAAK,eAAe,EAAE,MAAM,GAAG;AAC/C,eAAK,IAAI,SAAS,KAAK;AAAA,YACtB;AAAA,YACA,2CACC,EAAE,SACF,QACA,EAAE,UACF,OACA,KAAK,eAAe,EAAE,MAAM;AAAA,YAC7B;AAAA,UACD,CAAC;AACD,iBAAO;AAAA,QACR;AAAA,MACD,OAAO;AACN,aAAK,eAAe,EAAE,MAAM,IAAI,EAAE;AAAA,MACnC;AAAA,IACD;AAAA,EACD;AACA,SAAO;AACR;",
   "names": []
 }

package/dist/src/bulk.snv.d.ts

@@ -0,0 +1,2 @@
+export declare function parseheader(line: any, flag: any): false | "gene missing from header" | "isoform missing from header" | "invalid file header for snv/indel" | "amino_acid_change missing from header" | "variant_class missing from header" | "chromosome missing from header" | "start missing from header";
+export declare function parseline(linei: any, line: any, flag: any): void;

package/dist/src/bulk.snv.js

@@ -109,7 +109,7 @@ function parseline(linei, line, flag) {
       return;
     }
   }
-  if (bulk.parsesample(m, flag, linei, lst, flag.snv.badlines)) {
+  if (bulk.parsesample(m, flag, linei, lst)) {
     return;
   }
   if (!m.chr) {
@@ -132,7 +132,7 @@ function parseline(linei, line, flag) {
   if (m.maf_tumor_v2 != void 0 && m.maf_tumor_v1 != void 0) {
     if (m.maf_tumor_v2 == "") {
     } else {
-      let v1 = Number.parseInt(m.maf_tumor_v1), v2 = Number.parseInt(m.maf_tumor_v2);
+      const v1 = Number.parseInt(m.maf_tumor_v1), v2 = Number.parseInt(m.maf_tumor_v2);
       if (Number.isNaN(v1) || Number.isNaN(v2)) {
         flag.snv.badlines.push([linei, "invalid maf_tumor mutant and/or total read count", lst]);
         return;
@@ -145,7 +145,7 @@ function parseline(linei, line, flag) {
   if (m.maf_normal_v1 != void 0 && m.maf_normal_v2 != void 0) {
     if (m.maf_normal_v2 == "") {
     } else {
-      let v1 = Number.parseInt(m.maf_normal_v1), v2 = Number.parseInt(m.maf_normal_v2);
+      const v1 = Number.parseInt(m.maf_normal_v1), v2 = Number.parseInt(m.maf_normal_v2);
       if (Number.isNaN(v1) || Number.isNaN(v2)) {
         flag.snv.badlines.push([linei, "invalid maf_normal mutant and/or total read count", lst]);
         return;

package/dist/src/bulk.snv.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../src/bulk.snv.js"],
-  "sourcesContent": ["///////////////////////////////\n//\n//  shared between client and server\n//\n///////////////////////////////\n\nimport * as common from './common.js'\nimport * as bulk from './bulk.js'\n\nexport function parseheader(line, flag) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid file header for snv/indel'\n\tconst htry = (...args) => {\n\t\tfor (const s of args) {\n\t\t\tconst i = header.indexOf(s)\n\t\t\tif (i != -1) return i\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('annovar_gene', 'annovar_sj_gene', 'gene', 'genename', 'gene_symbol', 'hugo_symbol')\n\tif (i == -1) return 'gene missing from header'\n\theader[i] = 'gene'\n\ti = htry('annovar_aachange', 'amino_acid_change', 'annovar_sj_aachange', 'aachange', 'protein_change', 'variant')\n\tif (i == -1) return 'amino_acid_change missing from header'\n\theader[i] = 'mname'\n\ti = htry('annovar_class', 'class', 'mclass', 'variant_class', 'variant_classification', 'annovar_sj_class')\n\tif (i == -1) return 'variant_class missing from header'\n\theader[i] = 'class'\n\ti = htry('chromosome', 'chr')\n\tif (i == -1) return 'chromosome missing from header'\n\theader[i] = 'chr'\n\ti = htry('wu_hg19_pos', 'start', 'start_position', 'chr_position', 'position')\n\tif (i == -1) return 'start missing from header'\n\theader[i] = 'pos'\n\ti = htry(\n\t\t'annovar_isoform',\n\t\t'mrna_accession',\n\t\t'mrna accession',\n\t\t'refseq_mrna_id',\n\t\t'annovar_sj_filter_isoform',\n\t\t'refseq',\n\t\t'isoform'\n\t)\n\tif (i == -1) return 'isoform missing from header'\n\theader[i] = 'isoform'\n\n\t// optional\n\ti = htry('sample', 'sample_name', 'tumor_sample_barcode')\n\tif (i != -1) header[i] = 'sample'\n\ti = htry('patient', 'donor', 'target_case_id')\n\tif (i != -1) header[i] = 'patient'\n\ti = htry('quantitative_measurements')\n\tif (i != -1) header[i] = 'qmset'\n\t// dna maf tumor\n\ti = htry('mutant_reads_in_case', 'mutant_in_tumor', 'tumor_readcount_alt')\n\tif (i != -1) header[i] = 'maf_tumor_v1'\n\ti = htry('total_reads_in_case', 'total_in_tumor', 'tumor_readcount_total')\n\tif (i != -1) header[i] = 'maf_tumor_v2'\n\t// dna maf normal\n\ti = htry('mutant_reads_in_control', 'mutant_in_normal', 'normal_readcount_alt')\n\tif (i != -1) header[i] = 'maf_normal_v1'\n\ti = htry('total_reads_in_control', 'total_in_normal', 'normal_readcount_total')\n\tif (i != -1) header[i] = 'maf_normal_v2'\n\t// rna maf\n\t// cdna\n\ti = htry('cdna_change')\n\tif (i != -1) header[i] = 'cdna_change'\n\ti = htry('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\ti = htry('cancer', 'disease', 'diagnosis')\n\tif (i != -1) header[i] = 'disease'\n\tflag.snv.header = header\n\tflag.snv.loaded = true\n\treturn false\n}\n\nexport function parseline(linei, line, flag) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m = {}\n\tfor (let j = 0; j < flag.snv.header.length; j++) {\n\t\tif (lst[j] == undefined) break\n\t\tm[flag.snv.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.snv.badlines.push([linei, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (m.gene.toUpperCase() == 'UNKNOWN') {\n\t\tflag.snv.badlines.push([linei, 'gene name is UNKNOWN', lst])\n\t\treturn\n\t}\n\tif (!m.isoform) {\n\t\tflag.snv.badlines.push([linei, 'missing isoform', lst])\n\t\treturn\n\t}\n\tif (!m.mname) {\n\t\tm.mname = m.cdna_change\n\t\tif (!m.mname) {\n\t\t\tflag.snv.badlines.push([linei, 'missing amino acid change', lst])\n\t\t\treturn\n\t\t}\n\t} else {\n\t\tif (m.mname.indexOf('p.') == 0) {\n\t\t\tm.mname = m.mname.replace(/^p\\./, '')\n\t\t}\n\t}\n\tif (!m.class) {\n\t\tflag.snv.badlines.push([linei, 'missing mutation class', lst])\n\t\treturn\n\t}\n\tlet _c = flag.mclasslabel2key[m.class.toUpperCase()]\n\tif (_c) {\n\t\tm.class = _c\n\t} else {\n\t\t_c = common.mclasstester(m.class)\n\t\tif (_c) {\n\t\t\tm.class = _c\n\t\t} else {\n\t\t\tflag.snv.badlines.push([linei, 'wrong mutation class: ' + m.class, lst])\n\t\t\treturn\n\t\t}\n\t}\n\tif (bulk.parsesample(m, flag, linei, lst, flag.snv.badlines)) {\n\t\treturn\n\t}\n\tif (!m.chr) {\n\t\tflag.snv.badlines.push([linei, 'missing chromosome', lst])\n\t\treturn\n\t}\n\tif (m.chr.toLowerCase().indexOf('chr') != 0) {\n\t\tm.chr = 'chr' + m.chr\n\t}\n\tif (!m.pos) {\n\t\tflag.snv.badlines.push([linei, 'missing chromosome position', lst])\n\t\treturn\n\t}\n\tconst v = Number.parseInt(m.pos)\n\tif (Number.isNaN(v)) {\n\t\tflag.snv.badlines.push([linei, 'invalid chromosome position', lst])\n\t\treturn\n\t}\n\tm.pos = v - 1\n\n\tif (m.maf_tumor_v2 != undefined && m.maf_tumor_v1 != undefined) {\n\t\tif (m.maf_tumor_v2 == '') {\n\t\t\t// no value, do not parse\n\t\t} else {\n\t\t\tlet v1 = Number.parseInt(m.maf_tumor_v1),\n\t\t\t\tv2 = Number.parseInt(m.maf_tumor_v2)\n\t\t\tif (Number.isNaN(v1) || Number.isNaN(v2)) {\n\t\t\t\tflag.snv.badlines.push([linei, 'invalid maf_tumor mutant and/or total read count', lst])\n\t\t\t\treturn\n\t\t\t}\n\t\t\tm.maf_tumor = { f: v1 / v2, v1: v1, v2: v2 }\n\t\t}\n\t\tdelete m.maf_tumor_v1\n\t\tdelete m.maf_tumor_v2\n\t}\n\n\tif (m.maf_normal_v1 != undefined && m.maf_normal_v2 != undefined) {\n\t\tif (m.maf_normal_v2 == '') {\n\t\t\t// no value\n\t\t} else {\n\t\t\tlet v1 = Number.parseInt(m.maf_normal_v1),\n\t\t\t\tv2 = Number.parseInt(m.maf_normal_v2)\n\t\t\tif (Number.isNaN(v1) || Number.isNaN(v2)) {\n\t\t\t\tflag.snv.badlines.push([linei, 'invalid maf_normal mutant and/or total read count', lst])\n\t\t\t\treturn\n\t\t\t}\n\t\t\tm.maf_normal = { f: v1 / v2, v1: v1, v2: v2 }\n\t\t}\n\t\tdelete m.maf_normal_v1\n\t\tdelete m.maf_normal_v2\n\t}\n\n\t/*\n\tif(m.qmset) {\n\t\ttry{\n\t\t\tvar v=JSON.parse(m.qmset)\n\t\t} catch(e){\n\t\t\tflag.snv.badlines.push([linei,'invalid JSON for quantitative_measurements',lst])\n\t\t\tv=null\n\t\t} finally {\n\t\t\tif(v) {\n\t\t\t\tif(typeof(v)!='object') {\n\t\t\t\t\tflag.snv.badlines.push([linei,'value of quantitative_measurements must be an object',lst])\n\t\t\t\t\tdelete m.qmset\n\t\t\t\t} else {\n\t\t\t\t\tfor(var n in v) {\n\t\t\t\t\t\tif(!Array.isArray(v[n])) {\n\t\t\t\t\t\t\tflag.snv.badlines.push([linei,'quantitative_measurements: \"'+n+'\" value must be an array',lst])\n\t\t\t\t\t\t\tdelete v[n]\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tvar tmp=[]\n\t\t\t\t\t\t\tv[n].forEach(function(v2){\n\t\t\t\t\t\t\t\tif(typeof(v2)=='number') {\n\t\t\t\t\t\t\t\t\ttmp.push({v:v2})\n\t\t\t\t\t\t\t\t} else if(v2.v && typeof(v2.v)=='number') {\n\t\t\t\t\t\t\t\t\ttmp.push(v2)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\tif(tmp.length) {\n\t\t\t\t\t\t\t\tv[n]=tmp\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tflag.snv.badlines.push([linei,'quantitative_measurements: no valid value for \"'+n+'\"',lst])\n\t\t\t\t\t\t\t\tdelete v[n]\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tm.qmset=v\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tdelete m.qmset\n\t\t\t}\n\t\t}\n\t}\n\t*/\n\tflag.good++\n\t// FIXME hard-coded M and S\n\tif (m.class == 'M') {\n\t\tflag.snv.missense++\n\t} else if (m.class == 'S') {\n\t\tflag.snv.silent++\n\t}\n\tconst n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene\n\tif (!flag.data[n]) {\n\t\tflag.data[n] = []\n\t}\n\tm.dt = common.dtsnvindel\n\tflag.data[n].push(m)\n}\n"],
-  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAEf,SAAS,YAAY,MAAM,MAAM;AACvC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,SAAS;AACzB,eAAW,KAAK,MAAM;AACrB,YAAMA,KAAI,OAAO,QAAQ,CAAC;AAC1B,UAAIA,MAAK,GAAI,QAAOA;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,gBAAgB,mBAAmB,QAAQ,YAAY,eAAe,aAAa;AAChG,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,oBAAoB,qBAAqB,uBAAuB,YAAY,kBAAkB,SAAS;AAChH,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,iBAAiB,SAAS,UAAU,iBAAiB,0BAA0B,kBAAkB;AAC1G,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,cAAc,KAAK;AAC5B,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,eAAe,SAAS,kBAAkB,gBAAgB,UAAU;AAC7E,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI;AAAA,IACH;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EACD;AACA,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AAGZ,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,2BAA2B;AACpC,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AAEzB,MAAI,KAAK,wBAAwB,mBAAmB,qBAAqB;AACzE,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,uBAAuB,kBAAkB,uBAAuB;AACzE,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AAEzB,MAAI,KAAK,2BAA2B,oBAAoB,sBAAsB;AAC9E,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,0BAA0B,mBAAmB,wBAAwB;AAC9E,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AAGzB,MAAI,KAAK,aAAa;AACtB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,UAAU,WAAW,WAAW;AACzC,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,OAAK,IAAI,SAAS;AAClB,OAAK,IAAI,SAAS;AAClB,SAAO;AACR;AAEO,SAAS,UAAU,OAAO,MAAM,MAAM;AAC5C,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAI,CAAC;AACX,WAAS,IAAI,GAAG,IAAI,KAAK,IAAI,OAAO,QAAQ,KAAK;AAChD,QAAI,IAAI,CAAC,KAAK,OAAW;AACzB,MAAE,KAAK,IAAI,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EAC9B;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,gBAAgB,GAAG,CAAC;AACnD;AAAA,EACD;AACA,MAAI,EAAE,KAAK,YAAY,KAAK,WAAW;AACtC,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,wBAAwB,GAAG,CAAC;AAC3D;AAAA,EACD;AACA,MAAI,CAAC,EAAE,SAAS;AACf,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,mBAAmB,GAAG,CAAC;AACtD;AAAA,EACD;AACA,MAAI,CAAC,EAAE,OAAO;AACb,MAAE,QAAQ,EAAE;AACZ,QAAI,CAAC,EAAE,OAAO;AACb,WAAK,IAAI,SAAS,KAAK,CAAC,OAAO,6BAA6B,GAAG,CAAC;AAChE;AAAA,IACD;AAAA,EACD,OAAO;AACN,QAAI,EAAE,MAAM,QAAQ,IAAI,KAAK,GAAG;AAC/B,QAAE,QAAQ,EAAE,MAAM,QAAQ,QAAQ,EAAE;AAAA,IACrC;AAAA,EACD;AACA,MAAI,CAAC,EAAE,OAAO;AACb,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,0BAA0B,GAAG,CAAC;AAC7D;AAAA,EACD;AACA,MAAI,KAAK,KAAK,gBAAgB,EAAE,MAAM,YAAY,CAAC;AACnD,MAAI,IAAI;AACP,MAAE,QAAQ;AAAA,EACX,OAAO;AACN,SAAK,OAAO,aAAa,EAAE,KAAK;AAChC,QAAI,IAAI;AACP,QAAE,QAAQ;AAAA,IACX,OAAO;AACN,WAAK,IAAI,SAAS,KAAK,CAAC,OAAO,2BAA2B,EAAE,OAAO,GAAG,CAAC;AACvE;AAAA,IACD;AAAA,EACD;AACA,MAAI,KAAK,YAAY,GAAG,MAAM,OAAO,KAAK,KAAK,IAAI,QAAQ,GAAG;AAC7D;AAAA,EACD;AACA,MAAI,CAAC,EAAE,KAAK;AACX,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,sBAAsB,GAAG,CAAC;AACzD;AAAA,EACD;AACA,MAAI,EAAE,IAAI,YAAY,EAAE,QAAQ,KAAK,KAAK,GAAG;AAC5C,MAAE,MAAM,QAAQ,EAAE;AAAA,EACnB;AACA,MAAI,CAAC,EAAE,KAAK;AACX,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,+BAA+B,GAAG,CAAC;AAClE;AAAA,EACD;AACA,QAAM,IAAI,OAAO,SAAS,EAAE,GAAG;AAC/B,MAAI,OAAO,MAAM,CAAC,GAAG;AACpB,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,+BAA+B,GAAG,CAAC;AAClE;AAAA,EACD;AACA,IAAE,MAAM,IAAI;AAEZ,MAAI,EAAE,gBAAgB,UAAa,EAAE,gBAAgB,QAAW;AAC/D,QAAI,EAAE,gBAAgB,IAAI;AAAA,IAE1B,OAAO;AACN,UAAI,KAAK,OAAO,SAAS,EAAE,YAAY,GACtC,KAAK,OAAO,SAAS,EAAE,YAAY;AACpC,UAAI,OAAO,MAAM,EAAE,KAAK,OAAO,MAAM,EAAE,GAAG;AACzC,aAAK,IAAI,SAAS,KAAK,CAAC,OAAO,oDAAoD,GAAG,CAAC;AACvF;AAAA,MACD;AACA,QAAE,YAAY,EAAE,GAAG,KAAK,IAAI,IAAQ,GAAO;AAAA,IAC5C;AACA,WAAO,EAAE;AACT,WAAO,EAAE;AAAA,EACV;AAEA,MAAI,EAAE,iBAAiB,UAAa,EAAE,iBAAiB,QAAW;AACjE,QAAI,EAAE,iBAAiB,IAAI;AAAA,IAE3B,OAAO;AACN,UAAI,KAAK,OAAO,SAAS,EAAE,aAAa,GACvC,KAAK,OAAO,SAAS,EAAE,aAAa;AACrC,UAAI,OAAO,MAAM,EAAE,KAAK,OAAO,MAAM,EAAE,GAAG;AACzC,aAAK,IAAI,SAAS,KAAK,CAAC,OAAO,qDAAqD,GAAG,CAAC;AACxF;AAAA,MACD;AACA,QAAE,aAAa,EAAE,GAAG,KAAK,IAAI,IAAQ,GAAO;AAAA,IAC7C;AACA,WAAO,EAAE;AACT,WAAO,EAAE;AAAA,EACV;AA4CA,OAAK;AAEL,MAAI,EAAE,SAAS,KAAK;AACnB,SAAK,IAAI;AAAA,EACV,WAAW,EAAE,SAAS,KAAK;AAC1B,SAAK,IAAI;AAAA,EACV;AACA,QAAM,IAAI,KAAK,cAAc,EAAE,KAAK,YAAY,IAAI,EAAE;AACtD,MAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,SAAK,KAAK,CAAC,IAAI,CAAC;AAAA,EACjB;AACA,IAAE,KAAK,OAAO;AACd,OAAK,KAAK,CAAC,EAAE,KAAK,CAAC;AACpB;",
+  "sources": ["../../src/bulk.snv.ts"],
+  "sourcesContent": ["///////////////////////////////\n//\n//  shared between client and server\n//\n///////////////////////////////\n\nimport * as common from './common.js'\nimport * as bulk from './bulk.js'\n\nexport function parseheader(line, flag) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid file header for snv/indel'\n\tconst htry = (...args) => {\n\t\tfor (const s of args) {\n\t\t\tconst i = header.indexOf(s)\n\t\t\tif (i != -1) return i\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('annovar_gene', 'annovar_sj_gene', 'gene', 'genename', 'gene_symbol', 'hugo_symbol')\n\tif (i == -1) return 'gene missing from header'\n\theader[i] = 'gene'\n\ti = htry('annovar_aachange', 'amino_acid_change', 'annovar_sj_aachange', 'aachange', 'protein_change', 'variant')\n\tif (i == -1) return 'amino_acid_change missing from header'\n\theader[i] = 'mname'\n\ti = htry('annovar_class', 'class', 'mclass', 'variant_class', 'variant_classification', 'annovar_sj_class')\n\tif (i == -1) return 'variant_class missing from header'\n\theader[i] = 'class'\n\ti = htry('chromosome', 'chr')\n\tif (i == -1) return 'chromosome missing from header'\n\theader[i] = 'chr'\n\ti = htry('wu_hg19_pos', 'start', 'start_position', 'chr_position', 'position')\n\tif (i == -1) return 'start missing from header'\n\theader[i] = 'pos'\n\ti = htry(\n\t\t'annovar_isoform',\n\t\t'mrna_accession',\n\t\t'mrna accession',\n\t\t'refseq_mrna_id',\n\t\t'annovar_sj_filter_isoform',\n\t\t'refseq',\n\t\t'isoform'\n\t)\n\tif (i == -1) return 'isoform missing from header'\n\theader[i] = 'isoform'\n\n\t// optional\n\ti = htry('sample', 'sample_name', 'tumor_sample_barcode')\n\tif (i != -1) header[i] = 'sample'\n\ti = htry('patient', 'donor', 'target_case_id')\n\tif (i != -1) header[i] = 'patient'\n\ti = htry('quantitative_measurements')\n\tif (i != -1) header[i] = 'qmset'\n\t// dna maf tumor\n\ti = htry('mutant_reads_in_case', 'mutant_in_tumor', 'tumor_readcount_alt')\n\tif (i != -1) header[i] = 'maf_tumor_v1'\n\ti = htry('total_reads_in_case', 'total_in_tumor', 'tumor_readcount_total')\n\tif (i != -1) header[i] = 'maf_tumor_v2'\n\t// dna maf normal\n\ti = htry('mutant_reads_in_control', 'mutant_in_normal', 'normal_readcount_alt')\n\tif (i != -1) header[i] = 'maf_normal_v1'\n\ti = htry('total_reads_in_control', 'total_in_normal', 'normal_readcount_total')\n\tif (i != -1) header[i] = 'maf_normal_v2'\n\t// rna maf\n\t// cdna\n\ti = htry('cdna_change')\n\tif (i != -1) header[i] = 'cdna_change'\n\ti = htry('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\ti = htry('cancer', 'disease', 'diagnosis')\n\tif (i != -1) header[i] = 'disease'\n\tflag.snv.header = header\n\tflag.snv.loaded = true\n\treturn false\n}\n\nexport function parseline(linei, line, flag) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m: Record<string, any> = {}\n\tfor (let j = 0; j < flag.snv.header.length; j++) {\n\t\tif (lst[j] == undefined) break\n\t\tm[flag.snv.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.snv.badlines.push([linei, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (m.gene.toUpperCase() == 'UNKNOWN') {\n\t\tflag.snv.badlines.push([linei, 'gene name is UNKNOWN', lst])\n\t\treturn\n\t}\n\tif (!m.isoform) {\n\t\tflag.snv.badlines.push([linei, 'missing isoform', lst])\n\t\treturn\n\t}\n\tif (!m.mname) {\n\t\tm.mname = m.cdna_change\n\t\tif (!m.mname) {\n\t\t\tflag.snv.badlines.push([linei, 'missing amino acid change', lst])\n\t\t\treturn\n\t\t}\n\t} else {\n\t\tif (m.mname.indexOf('p.') == 0) {\n\t\t\tm.mname = m.mname.replace(/^p\\./, '')\n\t\t}\n\t}\n\tif (!m.class) {\n\t\tflag.snv.badlines.push([linei, 'missing mutation class', lst])\n\t\treturn\n\t}\n\tlet _c = flag.mclasslabel2key[m.class.toUpperCase()]\n\tif (_c) {\n\t\tm.class = _c\n\t} else {\n\t\t_c = common.mclasstester(m.class)\n\t\tif (_c) {\n\t\t\tm.class = _c\n\t\t} else {\n\t\t\tflag.snv.badlines.push([linei, 'wrong mutation class: ' + m.class, lst])\n\t\t\treturn\n\t\t}\n\t}\n\tif (bulk.parsesample(m, flag, linei, lst)) {\n\t\treturn\n\t}\n\tif (!m.chr) {\n\t\tflag.snv.badlines.push([linei, 'missing chromosome', lst])\n\t\treturn\n\t}\n\tif (m.chr.toLowerCase().indexOf('chr') != 0) {\n\t\tm.chr = 'chr' + m.chr\n\t}\n\tif (!m.pos) {\n\t\tflag.snv.badlines.push([linei, 'missing chromosome position', lst])\n\t\treturn\n\t}\n\tconst v = Number.parseInt(m.pos)\n\tif (Number.isNaN(v)) {\n\t\tflag.snv.badlines.push([linei, 'invalid chromosome position', lst])\n\t\treturn\n\t}\n\tm.pos = v - 1\n\n\tif (m.maf_tumor_v2 != undefined && m.maf_tumor_v1 != undefined) {\n\t\tif (m.maf_tumor_v2 == '') {\n\t\t\t// no value, do not parse\n\t\t} else {\n\t\t\tconst v1 = Number.parseInt(m.maf_tumor_v1),\n\t\t\t\tv2 = Number.parseInt(m.maf_tumor_v2)\n\t\t\tif (Number.isNaN(v1) || Number.isNaN(v2)) {\n\t\t\t\tflag.snv.badlines.push([linei, 'invalid maf_tumor mutant and/or total read count', lst])\n\t\t\t\treturn\n\t\t\t}\n\t\t\tm.maf_tumor = { f: v1 / v2, v1: v1, v2: v2 }\n\t\t}\n\t\tdelete m.maf_tumor_v1\n\t\tdelete m.maf_tumor_v2\n\t}\n\n\tif (m.maf_normal_v1 != undefined && m.maf_normal_v2 != undefined) {\n\t\tif (m.maf_normal_v2 == '') {\n\t\t\t// no value\n\t\t} else {\n\t\t\tconst v1 = Number.parseInt(m.maf_normal_v1),\n\t\t\t\tv2 = Number.parseInt(m.maf_normal_v2)\n\t\t\tif (Number.isNaN(v1) || Number.isNaN(v2)) {\n\t\t\t\tflag.snv.badlines.push([linei, 'invalid maf_normal mutant and/or total read count', lst])\n\t\t\t\treturn\n\t\t\t}\n\t\t\tm.maf_normal = { f: v1 / v2, v1: v1, v2: v2 }\n\t\t}\n\t\tdelete m.maf_normal_v1\n\t\tdelete m.maf_normal_v2\n\t}\n\n\t/*\n\tif(m.qmset) {\n\t\ttry{\n\t\t\tvar v=JSON.parse(m.qmset)\n\t\t} catch(e){\n\t\t\tflag.snv.badlines.push([linei,'invalid JSON for quantitative_measurements',lst])\n\t\t\tv=null\n\t\t} finally {\n\t\t\tif(v) {\n\t\t\t\tif(typeof(v)!='object') {\n\t\t\t\t\tflag.snv.badlines.push([linei,'value of quantitative_measurements must be an object',lst])\n\t\t\t\t\tdelete m.qmset\n\t\t\t\t} else {\n\t\t\t\t\tfor(var n in v) {\n\t\t\t\t\t\tif(!Array.isArray(v[n])) {\n\t\t\t\t\t\t\tflag.snv.badlines.push([linei,'quantitative_measurements: \"'+n+'\" value must be an array',lst])\n\t\t\t\t\t\t\tdelete v[n]\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tvar tmp=[]\n\t\t\t\t\t\t\tv[n].forEach(function(v2){\n\t\t\t\t\t\t\t\tif(typeof(v2)=='number') {\n\t\t\t\t\t\t\t\t\ttmp.push({v:v2})\n\t\t\t\t\t\t\t\t} else if(v2.v && typeof(v2.v)=='number') {\n\t\t\t\t\t\t\t\t\ttmp.push(v2)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\tif(tmp.length) {\n\t\t\t\t\t\t\t\tv[n]=tmp\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tflag.snv.badlines.push([linei,'quantitative_measurements: no valid value for \"'+n+'\"',lst])\n\t\t\t\t\t\t\t\tdelete v[n]\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tm.qmset=v\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tdelete m.qmset\n\t\t\t}\n\t\t}\n\t}\n\t*/\n\tflag.good++\n\t// FIXME hard-coded M and S\n\tif (m.class == 'M') {\n\t\tflag.snv.missense++\n\t} else if (m.class == 'S') {\n\t\tflag.snv.silent++\n\t}\n\tconst n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene\n\tif (!flag.data[n]) {\n\t\tflag.data[n] = []\n\t}\n\tm.dt = common.dtsnvindel\n\tflag.data[n].push(m)\n}\n"],
+  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAEf,SAAS,YAAY,MAAM,MAAM;AACvC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,SAAS;AACzB,eAAW,KAAK,MAAM;AACrB,YAAMA,KAAI,OAAO,QAAQ,CAAC;AAC1B,UAAIA,MAAK,GAAI,QAAOA;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,gBAAgB,mBAAmB,QAAQ,YAAY,eAAe,aAAa;AAChG,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,oBAAoB,qBAAqB,uBAAuB,YAAY,kBAAkB,SAAS;AAChH,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,iBAAiB,SAAS,UAAU,iBAAiB,0BAA0B,kBAAkB;AAC1G,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,cAAc,KAAK;AAC5B,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,eAAe,SAAS,kBAAkB,gBAAgB,UAAU;AAC7E,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI;AAAA,IACH;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EACD;AACA,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AAGZ,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,2BAA2B;AACpC,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AAEzB,MAAI,KAAK,wBAAwB,mBAAmB,qBAAqB;AACzE,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,uBAAuB,kBAAkB,uBAAuB;AACzE,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AAEzB,MAAI,KAAK,2BAA2B,oBAAoB,sBAAsB;AAC9E,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,0BAA0B,mBAAmB,wBAAwB;AAC9E,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AAGzB,MAAI,KAAK,aAAa;AACtB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,UAAU,WAAW,WAAW;AACzC,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,OAAK,IAAI,SAAS;AAClB,OAAK,IAAI,SAAS;AAClB,SAAO;AACR;AAEO,SAAS,UAAU,OAAO,MAAM,MAAM;AAC5C,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAyB,CAAC;AAChC,WAAS,IAAI,GAAG,IAAI,KAAK,IAAI,OAAO,QAAQ,KAAK;AAChD,QAAI,IAAI,CAAC,KAAK,OAAW;AACzB,MAAE,KAAK,IAAI,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EAC9B;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,gBAAgB,GAAG,CAAC;AACnD;AAAA,EACD;AACA,MAAI,EAAE,KAAK,YAAY,KAAK,WAAW;AACtC,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,wBAAwB,GAAG,CAAC;AAC3D;AAAA,EACD;AACA,MAAI,CAAC,EAAE,SAAS;AACf,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,mBAAmB,GAAG,CAAC;AACtD;AAAA,EACD;AACA,MAAI,CAAC,EAAE,OAAO;AACb,MAAE,QAAQ,EAAE;AACZ,QAAI,CAAC,EAAE,OAAO;AACb,WAAK,IAAI,SAAS,KAAK,CAAC,OAAO,6BAA6B,GAAG,CAAC;AAChE;AAAA,IACD;AAAA,EACD,OAAO;AACN,QAAI,EAAE,MAAM,QAAQ,IAAI,KAAK,GAAG;AAC/B,QAAE,QAAQ,EAAE,MAAM,QAAQ,QAAQ,EAAE;AAAA,IACrC;AAAA,EACD;AACA,MAAI,CAAC,EAAE,OAAO;AACb,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,0BAA0B,GAAG,CAAC;AAC7D;AAAA,EACD;AACA,MAAI,KAAK,KAAK,gBAAgB,EAAE,MAAM,YAAY,CAAC;AACnD,MAAI,IAAI;AACP,MAAE,QAAQ;AAAA,EACX,OAAO;AACN,SAAK,OAAO,aAAa,EAAE,KAAK;AAChC,QAAI,IAAI;AACP,QAAE,QAAQ;AAAA,IACX,OAAO;AACN,WAAK,IAAI,SAAS,KAAK,CAAC,OAAO,2BAA2B,EAAE,OAAO,GAAG,CAAC;AACvE;AAAA,IACD;AAAA,EACD;AACA,MAAI,KAAK,YAAY,GAAG,MAAM,OAAO,GAAG,GAAG;AAC1C;AAAA,EACD;AACA,MAAI,CAAC,EAAE,KAAK;AACX,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,sBAAsB,GAAG,CAAC;AACzD;AAAA,EACD;AACA,MAAI,EAAE,IAAI,YAAY,EAAE,QAAQ,KAAK,KAAK,GAAG;AAC5C,MAAE,MAAM,QAAQ,EAAE;AAAA,EACnB;AACA,MAAI,CAAC,EAAE,KAAK;AACX,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,+BAA+B,GAAG,CAAC;AAClE;AAAA,EACD;AACA,QAAM,IAAI,OAAO,SAAS,EAAE,GAAG;AAC/B,MAAI,OAAO,MAAM,CAAC,GAAG;AACpB,SAAK,IAAI,SAAS,KAAK,CAAC,OAAO,+BAA+B,GAAG,CAAC;AAClE;AAAA,EACD;AACA,IAAE,MAAM,IAAI;AAEZ,MAAI,EAAE,gBAAgB,UAAa,EAAE,gBAAgB,QAAW;AAC/D,QAAI,EAAE,gBAAgB,IAAI;AAAA,IAE1B,OAAO;AACN,YAAM,KAAK,OAAO,SAAS,EAAE,YAAY,GACxC,KAAK,OAAO,SAAS,EAAE,YAAY;AACpC,UAAI,OAAO,MAAM,EAAE,KAAK,OAAO,MAAM,EAAE,GAAG;AACzC,aAAK,IAAI,SAAS,KAAK,CAAC,OAAO,oDAAoD,GAAG,CAAC;AACvF;AAAA,MACD;AACA,QAAE,YAAY,EAAE,GAAG,KAAK,IAAI,IAAQ,GAAO;AAAA,IAC5C;AACA,WAAO,EAAE;AACT,WAAO,EAAE;AAAA,EACV;AAEA,MAAI,EAAE,iBAAiB,UAAa,EAAE,iBAAiB,QAAW;AACjE,QAAI,EAAE,iBAAiB,IAAI;AAAA,IAE3B,OAAO;AACN,YAAM,KAAK,OAAO,SAAS,EAAE,aAAa,GACzC,KAAK,OAAO,SAAS,EAAE,aAAa;AACrC,UAAI,OAAO,MAAM,EAAE,KAAK,OAAO,MAAM,EAAE,GAAG;AACzC,aAAK,IAAI,SAAS,KAAK,CAAC,OAAO,qDAAqD,GAAG,CAAC;AACxF;AAAA,MACD;AACA,QAAE,aAAa,EAAE,GAAG,KAAK,IAAI,IAAQ,GAAO;AAAA,IAC7C;AACA,WAAO,EAAE;AACT,WAAO,EAAE;AAAA,EACV;AA4CA,OAAK;AAEL,MAAI,EAAE,SAAS,KAAK;AACnB,SAAK,IAAI;AAAA,EACV,WAAW,EAAE,SAAS,KAAK;AAC1B,SAAK,IAAI;AAAA,EACV;AACA,QAAM,IAAI,KAAK,cAAc,EAAE,KAAK,YAAY,IAAI,EAAE;AACtD,MAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,SAAK,KAAK,CAAC,IAAI,CAAC;AAAA,EACjB;AACA,IAAE,KAAK,OAAO;AACd,OAAK,KAAK,CAAC,EAAE,KAAK,CAAC;AACpB;",
   "names": ["i"]
 }

package/dist/src/bulk.sv.d.ts

@@ -0,0 +1,3 @@
+export declare function parseheader(line: any, flag: any, issv: any): false | "invalid file header for fusions" | "gene_a missing from header" | "gene_b missing from header" | "chr_a missing from header" | "chr_b missing from header" | "pos_a missing from header" | "pos_b missing from header" | "isoform_a missing from header" | "isoform_b missing from header" | "strand_a missing from header" | "strand_b missing from header";
+export declare function parseline(i: any, line: any, flag: any, issv: any): void;
+export declare function duplicate(m: any): Record<string, any>;

package/dist/src/bulk.sv.js

@@ -104,7 +104,7 @@ function parseline(i, line, flag, issv) {
     return;
   }
   m.position2 = v2;
-  if (bulk.parsesample(m, flag, i, lst, badlines)) {
+  if (bulk.parsesample(m, flag, i, lst)) {
     return;
   }
   if (m.isoform1 && m.isoform1.indexOf(",") != -1) {