@sjcrh/proteinpaint-shared 2.188.1 → 2.190.0

package/README.md

@@ -8,26 +8,30 @@ code. Do NOT put utility/helper code here that are specific to only one
 workspace, those files should be saved in that workspace.
 
 IMPORTANT: 
-- code must work in browser and nodejs: do not import libs, deps, or globals that
-are specific to `nodejs` or `browser` environments, like `fs` or `DOM` elements
+- Shared code must work in browser and nodejs: do not import libs, deps, or globals that
+are specific to `nodejs` or `browser` environments, like `fs` or `DOM` elements.
+- Except for contants, do not import from this workspace (aka `@sjcrh/proteinpaint-shared/` 
+or `#shared`) into `shared/types` as that will cause cyclical imports that break bundler 
+startup or `tsc` compilation.
 
 ## Develop
 
-It is much simpler to import *runtime* code directly from `@sjcrh/proteinpaint-shared`, 
-or static code from `@sjcrh/proteinpaint-shared/devTs`, instead of specifying a code 
-filename.
+It is much simpler to import directly from `@sjcrh/proteinpaint-shared`. Avoid file-specific 
+imports unless tree-shaking performance is a concern. If a specific shared file must be imported,
+prefer an alias such as `#shared/someFile.js`, which shields importers from shared code
+file renames or reorganizations.
 
 For server dev, the `tsx` library will accept imports with or without file extension.
 Server (consumer) code should use `@sjcrh/proteinpaint-shared`, or if for some reason
 a shared file must be specific, it MUST use the `.js` file extension (e.g., 
 `#shared/someFile.js`).
 
-For client dev, the esbuild config will bundle the #shared imports correctly, even
-when `.js` extension is used to import what is actually a `.ts` file, by using
-custom plugins like dirname. 
+For client dev, the esbuild config will bundle the `#shared` imports correctly, even
+when `.js` extension is used to import what is actually a `.ts` file.
 
-When importing types that are defined in `shared/utils` to `shared/types` dev, 
-always use `@sjcrh/proteinpaint-shared/devTs` (or an alias such as `#shared/devTs`).
+Do not import from `#shared/utils` to `#shared/types` - it may cause `tsc` compilation or `esbuild`
+build errors. Only imports in the opposite direction, from `shared/types` to `shared/utils`, is allowed
+to to ensure that there are no cyclical imports that breaks type checks or bundling.
 
 ## Build
 

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"],
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+  "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"],
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+  "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"],
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   "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"],
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+  "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"],
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   "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"],
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+  "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"],
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   "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"],
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+  "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"],
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   "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) {

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

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../src/bulk.sv.js"],
-  "sourcesContent": ["import * as bulk from './bulk.js'\nimport * as common from './common.js'\n\n/////////////////////////////////\n//\n// client/server shared\n//\n/////////////////////////////////\n\n// work for both sv/fusion\n// must tell if the data is fusion or sv\n\nexport function parseheader(line, flag, issv) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid file header for fusions'\n\tconst htry = (...lst) => {\n\t\tfor (const a of lst) {\n\t\t\tconst j = header.indexOf(a)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('gene_a', 'gene1', 'genea')\n\tif (i == -1) return 'gene_a missing from header'\n\theader[i] = 'gene1'\n\ti = htry('gene_b', 'gene2', 'geneb')\n\tif (i == -1) return 'gene_b missing from header'\n\theader[i] = 'gene2'\n\ti = htry('chr_a', 'chr1', 'chra')\n\tif (i == -1) return 'chr_a missing from header'\n\theader[i] = 'chr1'\n\ti = htry('chr_b', 'chr2', 'chrb')\n\tif (i == -1) return 'chr_b missing from header'\n\theader[i] = 'chr2'\n\ti = htry('pos_a', 'position_a', 'position1', 'posa')\n\tif (i == -1) return 'pos_a missing from header'\n\theader[i] = 'position1'\n\ti = htry('pos_b', 'position_b', 'position2', 'posb')\n\tif (i == -1) return 'pos_b missing from header'\n\theader[i] = 'position2'\n\ti = htry('isoform_a', 'refseq_a', 'refseq1', 'isoform1', 'sv_refseqa')\n\tif (i == -1) return 'isoform_a missing from header'\n\theader[i] = 'isoform1'\n\ti = htry('isoform_b', 'refseq_b', 'refseq2', 'isoform2', 'sv_refseqb')\n\tif (i == -1) return 'isoform_b missing from header'\n\theader[i] = 'isoform2'\n\ti = htry('strand_a', 'orta')\n\tif (i == -1) return 'strand_a missing from header'\n\theader[i] = 'strand1'\n\ti = htry('strand_b', 'ortb')\n\tif (i == -1) return 'strand_b missing from header'\n\theader[i] = 'strand2'\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('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\ti = htry('disease')\n\tif (i != -1) header[i] = 'disease'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\tif (issv) {\n\t\tflag.sv.loaded = true\n\t\tflag.sv.header = header\n\t} else {\n\t\tflag.fusion.loaded = true\n\t\tflag.fusion.header = header\n\t}\n\treturn false\n}\n\nexport function parseline(i, line, flag, issv) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m = {}\n\tconst header = issv ? flag.sv.header : flag.fusion.header\n\tconst badlines = issv ? flag.sv.badlines : flag.fusion.badlines\n\n\tfor (let j = 0; j < header.length; j++) {\n\t\tm[header[j]] = lst[j]\n\t}\n\tif (!m.chr1) {\n\t\tbadlines.push([i, 'missing chr1', lst])\n\t\treturn\n\t}\n\tif (m.chr1.toLowerCase().indexOf('chr') != 0) {\n\t\tm.chr1 = 'chr' + m.chr1\n\t}\n\tif (!m.chr2) {\n\t\tbadlines.push([i, 'missing chr2', lst])\n\t\treturn\n\t}\n\tif (m.chr2.toLowerCase().indexOf('chr') != 0) {\n\t\tm.chr2 = 'chr' + m.chr2\n\t}\n\tlet v = m.position1\n\tif (!v) {\n\t\tbadlines.push([i, 'missing position1', lst])\n\t\treturn\n\t}\n\tlet v2 = Number.parseInt(v)\n\tif (Number.isNaN(v2) || v2 <= 0) {\n\t\tbadlines.push([i, 'invalid value for position1', lst])\n\t\treturn\n\t}\n\tm.position1 = v2\n\tv = m.position2\n\tif (!v) {\n\t\tbadlines.push([i, 'missing position2', lst])\n\t\treturn\n\t}\n\tv2 = Number.parseInt(v)\n\tif (Number.isNaN(v2) || v2 <= 0) {\n\t\tbadlines.push([i, 'invalid value for position2', lst])\n\t\treturn\n\t}\n\tm.position2 = v2\n\tif (bulk.parsesample(m, flag, i, lst, badlines)) {\n\t\treturn\n\t}\n\tif (m.isoform1 && m.isoform1.indexOf(',') != -1) {\n\t\tconst lst2 = m.isoform1.split(',')\n\t\tm.isoform1 = undefined\n\t\tfor (const t of lst2) {\n\t\t\tif (t != '') m.isoform1 = t\n\t\t}\n\t}\n\tif (m.isoform2 && m.isoform2.indexOf(',') != -1) {\n\t\tconst lst2 = m.isoform2.split(',')\n\t\tm.isoform2 = undefined\n\t\tfor (const t of lst2) {\n\t\t\tif (t != '') m.isoform2 = t\n\t\t}\n\t}\n\tif (!m.gene1) {\n\t\tm.isoform1 = undefined\n\t}\n\tif (!m.gene2) {\n\t\tm.isoform2 = undefined\n\t}\n\tif (m.gene1) {\n\t\t// put data under gene1\n\t\tflag.good++\n\t\tconst m2 = {\n\t\t\tdt: issv ? common.dtsv : common.dtfusionrna,\n\t\t\tclass: issv ? common.mclasssv : common.mclassfusionrna,\n\t\t\tisoform: m.isoform1,\n\t\t\tmname: m.gene2 || m.chr2,\n\t\t\tsample: m.sample,\n\t\t\tpatient: m.patient,\n\t\t\tsampletype: m.sampletype,\n\t\t\torigin: m.origin,\n\t\t\tdisease: m.disease,\n\t\t\tpairlst: [\n\t\t\t\t{\n\t\t\t\t\ta: {\n\t\t\t\t\t\tname: m.gene1,\n\t\t\t\t\t\tisoform: m.isoform1,\n\t\t\t\t\t\tstrand: m.strand1,\n\t\t\t\t\t\tchr: m.chr1,\n\t\t\t\t\t\tposition: m.position1\n\t\t\t\t\t},\n\t\t\t\t\tb: {\n\t\t\t\t\t\tname: m.gene2,\n\t\t\t\t\t\tisoform: m.isoform2,\n\t\t\t\t\t\tstrand: m.strand2,\n\t\t\t\t\t\tchr: m.chr2,\n\t\t\t\t\t\tposition: m.position2\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t\tconst n = flag.geneToUpper ? m.gene1.toUpperCase() : m.gene1\n\t\tif (!flag.data[n]) {\n\t\t\tflag.data[n] = []\n\t\t}\n\t\tflag.data[n].push(m2)\n\t}\n\tif (m.gene2 && m.gene2 != m.gene1) {\n\t\t// put data under gene2\n\t\tflag.good++\n\t\tconst m2 = {\n\t\t\tdt: issv ? common.dtsv : common.dtfusionrna,\n\t\t\tclass: issv ? common.mclasssv : common.mclassfusionrna,\n\t\t\tisoform: m.isoform2,\n\t\t\tmname: m.gene1 || m.chr1,\n\t\t\tsample: m.sample,\n\t\t\tpatient: m.patient,\n\t\t\tsampletype: m.sampletype,\n\t\t\torigin: m.origin,\n\t\t\tdisease: m.disease,\n\t\t\tpairlst: [\n\t\t\t\t{\n\t\t\t\t\ta: {\n\t\t\t\t\t\tname: m.gene1,\n\t\t\t\t\t\tisoform: m.isoform1,\n\t\t\t\t\t\tstrand: m.strand1,\n\t\t\t\t\t\tchr: m.chr1,\n\t\t\t\t\t\tposition: m.position1\n\t\t\t\t\t},\n\t\t\t\t\tb: {\n\t\t\t\t\t\tname: m.gene2,\n\t\t\t\t\t\tisoform: m.isoform2,\n\t\t\t\t\t\tstrand: m.strand2,\n\t\t\t\t\t\tchr: m.chr2,\n\t\t\t\t\t\tposition: m.position2\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t\tconst n = flag.geneToUpper ? m.gene2.toUpperCase() : m.gene2\n\t\tif (!flag.data[n]) {\n\t\t\tflag.data[n] = []\n\t\t}\n\t\tflag.data[n].push(m2)\n\t}\n}\n\nexport function duplicate(m) {\n\tconst n = {}\n\tfor (const k in m) {\n\t\tif (k == 'pairlst') continue\n\t\tconst v = m[k]\n\t\tconst type = typeof v\n\t\tif (type == 'object') {\n\t\t\tcontinue\n\t\t}\n\t\tn[k] = v\n\t}\n\tif (m.pairlst) {\n\t\tn.pairlst = []\n\t\tfor (const pair of m.pairlst) {\n\t\t\tconst p = {}\n\t\t\tfor (const k in pair) {\n\t\t\t\tif (k == 'a' || k == 'b' || k == 'interstitial') {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tp[k] = pair[k]\n\t\t\t}\n\t\t\tif (pair.a) {\n\t\t\t\tp.a = {}\n\t\t\t\tfor (const k in pair.a) {\n\t\t\t\t\tconst v = pair.a[k]\n\t\t\t\t\tif (typeof v == 'object') {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tp.a[k] = v\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (pair.b) {\n\t\t\t\tp.b = {}\n\t\t\t\tfor (const k in pair.b) {\n\t\t\t\t\tconst v = pair.b[k]\n\t\t\t\t\tif (typeof v == 'object') {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tp.b[k] = v\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (pair.interstitial) {\n\t\t\t\tp.interstitial = {}\n\t\t\t\tfor (const k in pair.interstitial) {\n\t\t\t\t\tconst v = pair.interstitial[k]\n\t\t\t\t\tif (typeof v == 'object') {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tp.interstitial[k] = v\n\t\t\t\t}\n\t\t\t}\n\t\t\tn.pairlst.push(p)\n\t\t}\n\t}\n\treturn n\n}\n"],
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+  "sources": ["../../src/bulk.sv.ts"],
+  "sourcesContent": ["import * as bulk from './bulk.js'\nimport * as common from './common.js'\n\n/////////////////////////////////\n//\n// client/server shared\n//\n/////////////////////////////////\n\n// work for both sv/fusion\n// must tell if the data is fusion or sv\n\nexport function parseheader(line, flag, issv) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid file header for fusions'\n\tconst htry = (...lst) => {\n\t\tfor (const a of lst) {\n\t\t\tconst j = header.indexOf(a)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('gene_a', 'gene1', 'genea')\n\tif (i == -1) return 'gene_a missing from header'\n\theader[i] = 'gene1'\n\ti = htry('gene_b', 'gene2', 'geneb')\n\tif (i == -1) return 'gene_b missing from header'\n\theader[i] = 'gene2'\n\ti = htry('chr_a', 'chr1', 'chra')\n\tif (i == -1) return 'chr_a missing from header'\n\theader[i] = 'chr1'\n\ti = htry('chr_b', 'chr2', 'chrb')\n\tif (i == -1) return 'chr_b missing from header'\n\theader[i] = 'chr2'\n\ti = htry('pos_a', 'position_a', 'position1', 'posa')\n\tif (i == -1) return 'pos_a missing from header'\n\theader[i] = 'position1'\n\ti = htry('pos_b', 'position_b', 'position2', 'posb')\n\tif (i == -1) return 'pos_b missing from header'\n\theader[i] = 'position2'\n\ti = htry('isoform_a', 'refseq_a', 'refseq1', 'isoform1', 'sv_refseqa')\n\tif (i == -1) return 'isoform_a missing from header'\n\theader[i] = 'isoform1'\n\ti = htry('isoform_b', 'refseq_b', 'refseq2', 'isoform2', 'sv_refseqb')\n\tif (i == -1) return 'isoform_b missing from header'\n\theader[i] = 'isoform2'\n\ti = htry('strand_a', 'orta')\n\tif (i == -1) return 'strand_a missing from header'\n\theader[i] = 'strand1'\n\ti = htry('strand_b', 'ortb')\n\tif (i == -1) return 'strand_b missing from header'\n\theader[i] = 'strand2'\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('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\ti = htry('disease')\n\tif (i != -1) header[i] = 'disease'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\tif (issv) {\n\t\tflag.sv.loaded = true\n\t\tflag.sv.header = header\n\t} else {\n\t\tflag.fusion.loaded = true\n\t\tflag.fusion.header = header\n\t}\n\treturn false\n}\n\nexport function parseline(i, line, flag, issv) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m: Record<string, any> = {}\n\tconst header = issv ? flag.sv.header : flag.fusion.header\n\tconst badlines = issv ? flag.sv.badlines : flag.fusion.badlines\n\n\tfor (let j = 0; j < header.length; j++) {\n\t\tm[header[j]] = lst[j]\n\t}\n\tif (!m.chr1) {\n\t\tbadlines.push([i, 'missing chr1', lst])\n\t\treturn\n\t}\n\tif (m.chr1.toLowerCase().indexOf('chr') != 0) {\n\t\tm.chr1 = 'chr' + m.chr1\n\t}\n\tif (!m.chr2) {\n\t\tbadlines.push([i, 'missing chr2', lst])\n\t\treturn\n\t}\n\tif (m.chr2.toLowerCase().indexOf('chr') != 0) {\n\t\tm.chr2 = 'chr' + m.chr2\n\t}\n\tlet v = m.position1\n\tif (!v) {\n\t\tbadlines.push([i, 'missing position1', lst])\n\t\treturn\n\t}\n\tlet v2 = Number.parseInt(v)\n\tif (Number.isNaN(v2) || v2 <= 0) {\n\t\tbadlines.push([i, 'invalid value for position1', lst])\n\t\treturn\n\t}\n\tm.position1 = v2\n\tv = m.position2\n\tif (!v) {\n\t\tbadlines.push([i, 'missing position2', lst])\n\t\treturn\n\t}\n\tv2 = Number.parseInt(v)\n\tif (Number.isNaN(v2) || v2 <= 0) {\n\t\tbadlines.push([i, 'invalid value for position2', lst])\n\t\treturn\n\t}\n\tm.position2 = v2\n\tif (bulk.parsesample(m, flag, i, lst)) {\n\t\treturn\n\t}\n\tif (m.isoform1 && m.isoform1.indexOf(',') != -1) {\n\t\tconst lst2 = m.isoform1.split(',')\n\t\tm.isoform1 = undefined\n\t\tfor (const t of lst2) {\n\t\t\tif (t != '') m.isoform1 = t\n\t\t}\n\t}\n\tif (m.isoform2 && m.isoform2.indexOf(',') != -1) {\n\t\tconst lst2 = m.isoform2.split(',')\n\t\tm.isoform2 = undefined\n\t\tfor (const t of lst2) {\n\t\t\tif (t != '') m.isoform2 = t\n\t\t}\n\t}\n\tif (!m.gene1) {\n\t\tm.isoform1 = undefined\n\t}\n\tif (!m.gene2) {\n\t\tm.isoform2 = undefined\n\t}\n\tif (m.gene1) {\n\t\t// put data under gene1\n\t\tflag.good++\n\t\tconst m2 = {\n\t\t\tdt: issv ? 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   "names": []
 }

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

@@ -0,0 +1,2 @@
+export declare function parseheader(line: any): any[] | "invalid file header for svjson";
+export declare function parseline(i: any, line: any, flag: any, header: any): void;

package/dist/src/bulk.svjson.js

@@ -1,6 +1,6 @@
 import * as common from "./common.js";
 import * as bulk from "./bulk.js";
-function parseheader(line, flag) {
+function parseheader(line) {
   const header = line.toLowerCase().split("	");
   if (header.length <= 1) return "invalid file header for svjson";
   const htry = (...lst) => {
@@ -33,13 +33,13 @@ function parseline(i, line, flag, header) {
     badlines.push([i, "missing jsontext", lst]);
     return;
   }
-  if (bulk.parsesample(m, flag, i, lst, badlines)) {
+  if (bulk.parsesample(m, flag, i, lst)) {
     return;
   }
   let json;
   try {
     json = JSON.parse(m.jsontext);
-  } catch (e) {
+  } catch (_) {
     badlines.push([i, "invalid JSON text", lst]);
     return;
   }