@sjcrh/proteinpaint-shared 2.187.0 → 2.188.1

package/README.md

@@ -13,14 +13,22 @@ are specific to `nodejs` or `browser` environments, like `fs` or `DOM` elements
 
 ## 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.
+
 For server dev, the `tsx` library will accept imports with or without file extension.
-Server (consumer) code MUST use the `.js` file extension even when importing 
-`#shared/*.ts` files.
+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. 
 
+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`).
+
 ## Build
 
 This package will be bundled as part of the client dependencies. 

package/constants/AiHisto.ts

@@ -0,0 +1,27 @@
+export enum FlagStatus {
+	Normal = 0,
+	Skipped = 1,
+	Flagged = 2,
+	Deleted = 3
+}
+
+export enum FeaturePrefixes {
+	Star = 'annotation-star-',
+	Square = 'annotation-square-',
+	Border = 'annotation-border-',
+	PredBorder = 'prediction-border-'
+}
+
+export const SelectionPrefixes = {
+	TileSelection: 'ts_',
+	Prediction: 'pred_',
+	Annotation: 'anno_'
+} as const
+
+export type SelectionPrefixValues = (typeof SelectionPrefixes)[keyof typeof SelectionPrefixes]
+
+export const FlagStatusMessages = {
+	[FlagStatus.Normal]: '',
+	[FlagStatus.Skipped]: '(Skipped)',
+	[FlagStatus.Flagged]: '(Flagged)'
+}

package/constants/README.md

@@ -0,0 +1,11 @@
+# Shared Constants
+
+The goal of the `constants` code is to allow shared/types code to be able to import type definitions 
+from shared/utils with no bundling or tsc compilation issues. Ideally, there would be a separate
+`shared/constants` workspace. However, due to time constraints and effort required to set up a 
+new workspace, this `shared/utils/constants` directory was created instead.
+
+The code files in proteinpaint/shared/utils/constants:
+- typescript files
+- must have no imports from outside this folder, to prevent cyclical references/imports that crash bundling and/or tsc compilation
+- must export constants that can be transitively exported to devTs.ts file and shared/utils/src/index.js

package/devTs.ts

@@ -0,0 +1,3 @@
+// please list in alphanumeric order for readability
+// use .ts file extension for all code files below
+export * from './constants/AiHisto.ts'

package/dist/constants/AiHisto.d.ts

@@ -0,0 +1,23 @@
+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 SelectionPrefixes: {
+    readonly TileSelection: "ts_";
+    readonly Prediction: "pred_";
+    readonly Annotation: "anno_";
+};
+export type SelectionPrefixValues = (typeof SelectionPrefixes)[keyof typeof SelectionPrefixes];
+export declare const FlagStatusMessages: {
+    0: string;
+    1: string;
+    2: string;
+};

package/dist/constants/AiHisto.js

@@ -0,0 +1,31 @@
+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 SelectionPrefixes = {
+  TileSelection: "ts_",
+  Prediction: "pred_",
+  Annotation: "anno_"
+};
+const FlagStatusMessages = {
+  [0 /* Normal */]: "",
+  [1 /* Skipped */]: "(Skipped)",
+  [2 /* Flagged */]: "(Flagged)"
+};
+export {
+  FeaturePrefixes,
+  FlagStatus,
+  FlagStatusMessages,
+  SelectionPrefixes
+};
+//# sourceMappingURL=AiHisto.js.map

package/dist/constants/AiHisto.js.map

@@ -0,0 +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"]
+}

package/dist/src/aiHisto.d.ts

@@ -0,0 +1,5 @@
+import { type TileSelection } from '@sjcrh/proteinpaint-types';
+import type { FeaturePrefixes, 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;

package/dist/src/aiHisto.js

@@ -0,0 +1,15 @@
+function createSelectionID(prefix, coordinates) {
+  return prefix + JSON.stringify(coordinates);
+}
+function checkSelectionType(tileSelection, suspectedPrefix) {
+  return tileSelection.id.startsWith(suspectedPrefix);
+}
+function createFeatureID(featurePrefix, coords) {
+  return featurePrefix + JSON.stringify(coords);
+}
+export {
+  checkSelectionType,
+  createFeatureID,
+  createSelectionID
+};
+//# sourceMappingURL=aiHisto.js.map

package/dist/src/aiHisto.js.map

@@ -0,0 +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"],
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+  "names": []
+}

package/dist/src/bulk.cnv.js

@@ -0,0 +1,83 @@
+import * as common from "./common.js";
+import * as bulk from "./bulk.js";
+function parseheader(line, flag) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid file header for CNV";
+  const htry = (...lst) => {
+    for (const i2 of lst) {
+      const j = header.indexOf(i2);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("gene");
+  if (i == -1) return "gene missing from header";
+  header[i] = "gene";
+  i = htry("cnv");
+  if (i == -1) return "CNV missing from header";
+  header[i] = "cnv";
+  i = htry("sample", "sample_name", "tumor_sample_barcode");
+  if (i != -1) header[i] = "sample";
+  i = htry("patient", "donor", "target_case_id");
+  if (i != -1) header[i] = "patient";
+  i = htry("disease");
+  if (i != -1) header[i] = "disease";
+  i = htry("origin");
+  if (i != -1) header[i] = "origin";
+  i = htry("sampletype", "sample type", "sample_type");
+  if (i != -1) header[i] = "sampletype";
+  flag.cnv.header = header;
+  flag.cnv.loaded = true;
+  return false;
+}
+function parseline(i, line, flag) {
+  if (line == "" || line[0] == "#") return;
+  const lst = line.split("	");
+  const m = {};
+  for (let j = 0; j < flag.cnv.header.length; j++) {
+    m[flag.cnv.header[j]] = lst[j];
+  }
+  if (!m.gene) {
+    flag.cnv.badlines.push([i, "missing gene", lst]);
+    return;
+  }
+  if (!m.cnv) {
+    flag.cnv.badlines.push([i, "missing cnv value", lst]);
+    return;
+  }
+  const value = m.cnv.toLowerCase();
+  switch (value) {
+    case "amplification":
+    case "gain":
+      m.class = common.mclasscnvgain;
+      break;
+    case "deletion":
+    case "loss":
+      m.class = common.mclasscnvloss;
+      break;
+    case "loh":
+      m.class = common.mclasscnvloh;
+      break;
+    default:
+      flag.cnv.badlines.push([i, "invalid cnv value: " + m.cnv, lst]);
+      m.class = null;
+  }
+  if (!m.class) {
+    return;
+  }
+  if (bulk.parsesample(m, flag, i, lst, flag.cnv.badlines)) {
+    return;
+  }
+  m.dt = common.dtcnv;
+  flag.good++;
+  const n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene;
+  if (!(n in flag.data)) {
+    flag.data[n] = [];
+  }
+  flag.data[n].push(m);
+}
+export {
+  parseheader,
+  parseline
+};
+//# sourceMappingURL=bulk.cnv.js.map

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

@@ -0,0 +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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+  "names": ["i"]
+}

package/dist/src/bulk.del.js

@@ -0,0 +1,119 @@
+import * as common from "./common.js";
+import * as bulk from "./bulk.js";
+function parseheader(line, flag) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid header line for intragenic deletion";
+  const htry = (...lst) => {
+    for (const i2 of lst) {
+      const j = header.indexOf(i2);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("gene");
+  if (i == -1) return "gene missing from header";
+  header[i] = "gene";
+  i = htry(
+    "annovar_isoform",
+    "mrna_accession",
+    "mrna accession",
+    "refseq_mrna_id",
+    "annovar_sj_filter_isoform",
+    "refseq",
+    "isoform"
+  );
+  if (i == -1) return "isoform missing from header";
+  header[i] = "isoform";
+  i = htry("rnaposition");
+  if (i != -1) {
+    header[i] = "rnaposition";
+    i = htry("rnadellength");
+    if (i == -1) return "rnadellength is required when rnaPosition is used";
+    header[i] = "rnadellength";
+  }
+  i = htry("chromosome", "chr");
+  if (i != -1) {
+    header[i] = "chr";
+    i = htry("chr_start");
+    if (i == -1) return "chr_start is required when chr is used";
+    header[i] = "chrpos1";
+    i = htry("chr_stop");
+    if (i == -1) return "chr_stop is required when chr is used";
+    header[i] = "chrpos2";
+  }
+  i = htry("sample", "sample_name", "tumor_sample_barcode");
+  if (i != -1) header[i] = "sample";
+  i = htry("patient", "donor", "target_case_id");
+  if (i != -1) header[i] = "patient";
+  i = htry("disease");
+  if (i != -1) header[i] = "disease";
+  i = htry("origin");
+  if (i != -1) header[i] = "origin";
+  i = htry("sampletype", "sample type", "sample_type");
+  if (i != -1) header[i] = "sampletype";
+  flag.del.header = header;
+  flag.del.loaded = true;
+  return false;
+}
+function parseline(i, line, flag) {
+  if (line == "" || line[0] == "#") return;
+  const lst = line.split("	");
+  const m = {};
+  for (let j = 0; j < flag.del.header.length; j++) {
+    if (lst[j] == void 0) break;
+    m[flag.del.header[j]] = lst[j];
+  }
+  if (!m.gene) {
+    flag.del.badlines.push([i, "missing gene", lst]);
+    return;
+  }
+  if (m.rnaposition) {
+    let v = Number.parseInt(m.rnaposition);
+    if (Number.isNaN(v) || v < 0) {
+      flag.del.badlines.push([i, "invalid rnaPosition value", lst]);
+      return;
+    }
+    m.rnaposition = v;
+    if (!m.rnadellength) {
+      flag.del.badlines.push([i, "missing rnaDellength value", lst]);
+      return;
+    }
+    v = Number.parseInt(m.rnadellength);
+    if (Number.isNaN(v) || v < 0) {
+      flag.del.badlines.push([i, "invalid rnaDellength value", lst]);
+      return;
+    }
+    m.rnadellength = v;
+  }
+  if (m.chr) {
+    let v = Number.parseInt(m.chrpos1);
+    if (Number.isNaN(v) || v < 0) {
+      flag.del.badlines.push([i, "invalid chr_start value", lst]);
+      return;
+    }
+    m.chrpos1 = v;
+    v = Number.parseInt(m.chrpos2);
+    if (Number.isNaN(v) || v < 0) {
+      flag.del.badlines.push([i, "invalid chr_stop value", lst]);
+      return;
+    }
+    m.chrpos2 = v;
+  }
+  if (bulk.parsesample(m, flag, i, lst, flag.del.badlines)) {
+    return;
+  }
+  m.dt = common.dtdel;
+  m.class = common.mclassdel;
+  m.mname = "DEL";
+  flag.good++;
+  var n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene;
+  if (!(n in flag.data)) {
+    flag.data[n] = [];
+  }
+  flag.data[n].push(m);
+}
+export {
+  parseheader,
+  parseline
+};
+//# sourceMappingURL=bulk.del.js.map

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

@@ -0,0 +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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+  "names": ["i"]
+}

package/dist/src/bulk.itd.js

@@ -0,0 +1,119 @@
+import * as common from "./common.js";
+import * as bulk from "./bulk.js";
+function parseheader(line, flag) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid header line for ITD";
+  const htry = (...lst) => {
+    for (const i2 of lst) {
+      const j = header.indexOf(i2);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("gene");
+  if (i == -1) return "gene missing from header";
+  header[i] = "gene";
+  i = htry(
+    "annovar_isoform",
+    "mrna_accession",
+    "mrna accession",
+    "refseq_mrna_id",
+    "annovar_sj_filter_isoform",
+    "refseq",
+    "isoform"
+  );
+  if (i == -1) return "isoform missing from header";
+  header[i] = "isoform";
+  i = htry("rnaposition");
+  if (i != -1) {
+    header[i] = "rnaposition";
+    i = htry("rnaduplength");
+    if (i == -1) return "rnaduplength is required when rnaposition is present";
+    header[i] = "rnaduplength";
+  }
+  i = htry("chromosome", "chr");
+  if (i != -1) {
+    header[i] = "chr";
+    i = htry("chr_start");
+    if (i == -1) return "chr_start is required when chr is present";
+    header[i] = "chrpos1";
+    i = htry("chr_stop");
+    if (i == -1) return "chr_stop is required when chr is present";
+    header[i] = "chrpos2";
+  }
+  i = htry("sample", "sample_name", "tumor_sample_barcode");
+  if (i != -1) header[i] = "sample";
+  i = htry("patient", "donor", "target_case_id");
+  if (i != -1) header[i] = "patient";
+  i = htry("disease");
+  if (i != -1) header[i] = "disease";
+  i = htry("origin");
+  if (i != -1) header[i] = "origin";
+  i = htry("sampletype", "sample type", "sample_type");
+  if (i != -1) header[i] = "sampletype";
+  flag.itd.header = header;
+  flag.itd.loaded = true;
+  return false;
+}
+function parseline(i, line, flag) {
+  if (line == "" || line[0] == "#") return;
+  const lst = line.split("	");
+  const m = {};
+  for (let j = 0; j < flag.itd.header.length; j++) {
+    if (lst[j] == void 0) break;
+    m[flag.itd.header[j]] = lst[j];
+  }
+  if (!m.gene) {
+    flag.itd.badlines.push([i, "missing gene", lst]);
+    return;
+  }
+  if (m.rnaposition) {
+    let v = Number.parseInt(m.rnaposition);
+    if (Number.isNaN(v) || v < 0) {
+      flag.itd.badlines.push([i, "invalid rnaPosition value", lst]);
+      return;
+    }
+    m.rnaposition = v;
+    if (!m.rnaduplength) {
+      flag.itd.badlines.push([i, "missing rnaDuplength value", lst]);
+      return;
+    }
+    v = Number.parseInt(m.rnaduplength);
+    if (Number.isNaN(v) || v < 0) {
+      flag.itd.badlines.push([i, "invalid rnaDuplength value", lst]);
+      return;
+    }
+    m.rnaduplength = v;
+  }
+  if (m.chr) {
+    let v = Number.parseInt(m.chrpos1);
+    if (Number.isNaN(v) || v < 0) {
+      flag.itd.badlines.push([i, "invalid chr_start value", lst]);
+      return;
+    }
+    m.chrpos1 = v;
+    v = Number.parseInt(m.chrpos2);
+    if (Number.isNaN(v) || v < 0) {
+      flag.itd.badlines.push([i, "invalid chr_stop value", lst]);
+      return;
+    }
+    m.chrpos2 = v;
+  }
+  if (bulk.parsesample(m, flag, i, lst, flag.itd.badlines)) {
+    return;
+  }
+  m.dt = common.dtitd;
+  m.class = common.mclassitd;
+  m.mname = "ITD";
+  flag.good++;
+  var n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene;
+  if (!(n in flag.data)) {
+    flag.data[n] = [];
+  }
+  flag.data[n].push(m);
+}
+export {
+  parseheader,
+  parseline
+};
+//# sourceMappingURL=bulk.itd.js.map

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

@@ -0,0 +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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+  "names": ["i"]
+}