@sjcrh/proteinpaint-shared 2.188.1 → 2.189.0

package/dist/src/terms.d.ts

@@ -34,34 +34,34 @@ export declare const TermTypes: {
 export declare const dtTermTypes: Set<string>;
 export declare const NUMERIC_DICTIONARY_TERM = "numericDictTerm";
 export declare const TermTypes2Dt: {
-    geneExpression: any;
-    ssGSEA: any;
-    dnaMethylation: any;
-    metaboliteIntensity: any;
-    proteomeAbundance: any;
+    geneExpression: number;
+    ssGSEA: number;
+    dnaMethylation: number;
+    metaboliteIntensity: number;
+    proteomeAbundance: number;
 };
 export declare const typeGroup: {
-    categorical: any;
-    condition: any;
-    float: any;
-    integer: any;
-    samplelst: any;
-    survival: any;
-    date: any;
-    multivalue: any;
-    geneVariant: any;
-    snp: any;
-    snplst: any;
-    snplocus: any;
-    geneExpression: any;
-    isoformExpression: any;
-    ssGSEA: any;
-    dnaMethylation: any;
-    metaboliteIntensity: any;
-    proteomeAbundance: any;
-    termCollection: any;
-    singleCellCellType: any;
-    singleCellGeneExpression: any;
+    categorical: string;
+    condition: string;
+    float: string;
+    integer: string;
+    samplelst: string;
+    survival: string;
+    date: string;
+    multivalue: string;
+    geneVariant: string;
+    snp: string;
+    snplst: string;
+    snplocus: string;
+    geneExpression: string;
+    isoformExpression: string;
+    ssGSEA: string;
+    dnaMethylation: string;
+    metaboliteIntensity: string;
+    proteomeAbundance: string;
+    termCollection: string;
+    singleCellCellType: string;
+    singleCellGeneExpression: string;
 };
 export declare const numericTypes: Set<string>;
 export declare const annoNumericTypes: Set<string>;

package/dist/src/tree.d.ts

@@ -0,0 +1 @@
+export declare function stratinput(lst: any, levels: any): any[];

package/dist/src/tree.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../src/tree.js"],
-  "sourcesContent": ["/*\ninput:\n1. list of leaf nodes, e.g. mutation cases, each with a set of key-value pairs\n2. levels of hierarchy in an ordered list\n   each item: { k, full }\n   \"k\" and \"full\" are two attribute keys\n\noutput:\na list of items, as input for d3-hierarchy.stratify\none item for each child-parent relationship in the hierarchy\n{\n\tid:\n\tparentId:\n\tlst:\n\tvalue:\n\tname:\n\tfull:\n\tid0:\n\tv0:\n\tid1:\n\tv1:\n\tid2:\n\tv2:\n}\n\nstrange issue: https://github.com/stjude/proteinpaint/commit/c36004d47d4374d2ade719c6ef9e2b848f0850dc\nusing Map for lp, nodes etc will cause memory issue, thus the use of simple objects\n\nto-do: verify this works after a reorg\n*/\n\nconst hardcode_root = 'root'\nconst hierarchy_spacer = '...'\n\nexport function stratinput(lst, levels) {\n\tconst lp = Object.create(null)\n\t// leaf to parent\n\t// k: HM...BALL...sub\n\t// v: HM...BALL\n\n\tconst nodes = Object.create(null)\n\t/*\n\tk: string id of node, e.g. HM...BALL\n\tv: node\n\t\t.full\n\t\t.lst[]\n\t\t\titems from input\n\t*/\n\n\tconst size = Object.create(null)\n\t// only increment size to leaf nodes, so that root.sum() will work\n\t// k: string id of a node, e.g. HM...BALL\n\t// v: number of items\n\n\tfor (const m of lst) {\n\t\tfor (const [i, lev] of levels.entries()) {\n\t\t\tconst thisv = getkey(m, i, levels)\n\t\t\tconst pav = getkey(m, i - 1, levels)\n\n\t\t\t// as mutations can come as {\"subtype\":\"\"}\n\t\t\t// in the sunburst chart at the subtype level, this mutation should not be counted\n\t\t\t// thus the test with !m[lev.k] rather than !(lev.k in m)\n\t\t\tif (!m[lev.k]) {\n\t\t\t\t// stop at this level\n\t\t\t\t// add count to prev level\n\t\t\t\tif (i > 0) {\n\t\t\t\t\tsize[pav] += 1\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\n\t\t\tlp[thisv] = pav\n\t\t\tif (!(thisv in size)) {\n\t\t\t\tsize[thisv] = 0\n\t\t\t}\n\t\t\tif (!(thisv in nodes)) {\n\t\t\t\tconst n = {\n\t\t\t\t\tlst: []\n\t\t\t\t}\n\t\t\t\tif (lev.full) {\n\t\t\t\t\tn.full = m[lev.full]\n\t\t\t\t}\n\n\t\t\t\tn.id0 = levels[0].k\n\t\t\t\tn.v0 = m[levels[0].k]\n\t\t\t\tif (i == 1) {\n\t\t\t\t\tn.id1 = levels[1].k\n\t\t\t\t\tn.v1 = m[levels[1].k]\n\t\t\t\t}\n\t\t\t\tif (i == 2) {\n\t\t\t\t\tn.id2 = levels[2].k\n\t\t\t\t\tn.v1 = m[levels[2].k]\n\t\t\t\t}\n\n\t\t\t\tnodes[thisv] = n\n\t\t\t}\n\t\t\tnodes[thisv].lst.push(m)\n\t\t\tif (i == levels.length - 1) {\n\t\t\t\tsize[thisv] += 1\n\t\t\t}\n\t\t}\n\t}\n\n\tconst nlst = [{ id: hardcode_root, name: hardcode_root }]\n\n\tfor (const chid in lp) {\n\t\tconst paid = lp[chid]\n\t\tconst n = nodes[chid]\n\t\tconst fields = chid.split(hierarchy_spacer)\n\t\tnlst.push({\n\t\t\tid: chid,\n\t\t\tparentId: paid,\n\t\t\tlst: n.lst,\n\t\t\tvalue: size[chid],\n\t\t\tname: fields[fields.length - 1], // show this instead of chid\n\t\t\tfull: n.full,\n\t\t\tid0: n.id0,\n\t\t\tv0: n.v0,\n\t\t\tid1: n.id1,\n\t\t\tv1: n.v1,\n\t\t\tid2: n.id2,\n\t\t\tv2: n.v2\n\t\t})\n\t}\n\treturn nlst\n}\n\nfunction getkey(m, i, levels) {\n\t// if i is 0, return 'root'\n\tconst klst = [hardcode_root]\n\tfor (let j = 0; j < i; j++) {\n\t\tklst.push(m[levels[j].k])\n\t}\n\tif (i >= 0) {\n\t\tklst.push(m[levels[i].k])\n\t}\n\treturn klst.join(hierarchy_spacer)\n}\n"],
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+  "sources": ["../../src/tree.ts"],
+  "sourcesContent": ["/*\ninput:\n1. list of leaf nodes, e.g. mutation cases, each with a set of key-value pairs\n2. levels of hierarchy in an ordered list\n   each item: { k, full }\n   \"k\" and \"full\" are two attribute keys\n\noutput:\na list of items, as input for d3-hierarchy.stratify\none item for each child-parent relationship in the hierarchy\n{\n\tid:\n\tparentId:\n\tlst:\n\tvalue:\n\tname:\n\tfull:\n\tid0:\n\tv0:\n\tid1:\n\tv1:\n\tid2:\n\tv2:\n}\n\nstrange issue: https://github.com/stjude/proteinpaint/commit/c36004d47d4374d2ade719c6ef9e2b848f0850dc\nusing Map for lp, nodes etc will cause memory issue, thus the use of simple objects\n\nto-do: verify this works after a reorg\n*/\n\nconst hardcode_root = 'root'\nconst hierarchy_spacer = '...'\n\nexport function stratinput(lst, levels) {\n\tconst lp = Object.create(null)\n\t// leaf to parent\n\t// k: HM...BALL...sub\n\t// v: HM...BALL\n\n\tconst nodes = Object.create(null)\n\t/*\n\tk: string id of node, e.g. HM...BALL\n\tv: node\n\t\t.full\n\t\t.lst[]\n\t\t\titems from input\n\t*/\n\n\tconst size = Object.create(null)\n\t// only increment size to leaf nodes, so that root.sum() will work\n\t// k: string id of a node, e.g. HM...BALL\n\t// v: number of items\n\n\tfor (const m of lst) {\n\t\tfor (const [i, lev] of levels.entries()) {\n\t\t\tconst thisv = getkey(m, i, levels)\n\t\t\tconst pav = getkey(m, i - 1, levels)\n\n\t\t\t// as mutations can come as {\"subtype\":\"\"}\n\t\t\t// in the sunburst chart at the subtype level, this mutation should not be counted\n\t\t\t// thus the test with !m[lev.k] rather than !(lev.k in m)\n\t\t\tif (!m[lev.k]) {\n\t\t\t\t// stop at this level\n\t\t\t\t// add count to prev level\n\t\t\t\tif (i > 0) {\n\t\t\t\t\tsize[pav] += 1\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\n\t\t\tlp[thisv] = pav\n\t\t\tif (!(thisv in size)) {\n\t\t\t\tsize[thisv] = 0\n\t\t\t}\n\t\t\tif (!(thisv in nodes)) {\n\t\t\t\tconst n: Record<string, any> = {\n\t\t\t\t\tlst: []\n\t\t\t\t}\n\t\t\t\tif (lev.full) {\n\t\t\t\t\tn.full = m[lev.full]\n\t\t\t\t}\n\n\t\t\t\tn.id0 = levels[0].k\n\t\t\t\tn.v0 = m[levels[0].k]\n\t\t\t\tif (i == 1) {\n\t\t\t\t\tn.id1 = levels[1].k\n\t\t\t\t\tn.v1 = m[levels[1].k]\n\t\t\t\t}\n\t\t\t\tif (i == 2) {\n\t\t\t\t\tn.id2 = levels[2].k\n\t\t\t\t\tn.v1 = m[levels[2].k]\n\t\t\t\t}\n\n\t\t\t\tnodes[thisv] = n\n\t\t\t}\n\t\t\tnodes[thisv].lst.push(m)\n\t\t\tif (i == levels.length - 1) {\n\t\t\t\tsize[thisv] += 1\n\t\t\t}\n\t\t}\n\t}\n\n\tconst nlst: any[] = [{ id: hardcode_root, name: hardcode_root }]\n\n\tfor (const chid in lp) {\n\t\tconst paid = lp[chid]\n\t\tconst n = nodes[chid]\n\t\tconst fields = chid.split(hierarchy_spacer)\n\t\tnlst.push({\n\t\t\tid: chid,\n\t\t\tparentId: paid,\n\t\t\tlst: n.lst,\n\t\t\tvalue: size[chid],\n\t\t\tname: fields[fields.length - 1], // show this instead of chid\n\t\t\tfull: n.full,\n\t\t\tid0: n.id0,\n\t\t\tv0: n.v0,\n\t\t\tid1: n.id1,\n\t\t\tv1: n.v1,\n\t\t\tid2: n.id2,\n\t\t\tv2: n.v2\n\t\t})\n\t}\n\treturn nlst\n}\n\nfunction getkey(m, i, levels) {\n\t// if i is 0, return 'root'\n\tconst klst = [hardcode_root]\n\tfor (let j = 0; j < i; j++) {\n\t\tklst.push(m[levels[j].k])\n\t}\n\tif (i >= 0) {\n\t\tklst.push(m[levels[i].k])\n\t}\n\treturn klst.join(hierarchy_spacer)\n}\n"],
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   "names": []
 }

package/dist/src/vcf.ann.d.ts

@@ -0,0 +1 @@
+export declare function parse_ANN(str: any, header: any, m: any): true | null;

package/dist/src/vcf.ann.js

@@ -1,4 +1,4 @@
-import { vepinfo } from "./common.js";
+import { vepinfo, dtsnvindel, mclassnonstandard } from "./common.js";
 function parse_ANN(str, header, m) {
   if (!header) {
     return null;
@@ -45,7 +45,6 @@ function parse_ANN(str, header, m) {
       o._mname = o["HGVS.p"];
     } else if (o["HGVS.c"]) {
       o._mname = o["HGVS.c"];
-    } else {
     }
   }
   return true;

package/dist/src/vcf.ann.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../src/vcf.ann.js"],
-  "sourcesContent": ["import { vepinfo } from './common.js'\n\nexport function parse_ANN(str, header, m) {\n\t// snpEff\n\tif (!header) {\n\t\treturn null\n\t}\n\tfor (const thisannotation of str.split(',')) {\n\t\tconst lst = thisannotation.replace(/&/g, ',').split('|')\n\n\t\tconst o = {}\n\n\t\tfor (let i = 0; i < header.length; i++) {\n\t\t\tif (lst[i]) {\n\t\t\t\to[header[i].name] = lst[i]\n\t\t\t}\n\t\t}\n\t\tif (!o.Allele) {\n\t\t\tcontinue\n\t\t}\n\t\tlet allele = null\n\t\tfor (const a of m.alleles) {\n\t\t\tif (a.allele == o.Allele) {\n\t\t\t\tallele = a\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tif (!allele) {\n\t\t\t// cannot match to allele!!!\n\t\t\tcontinue\n\t\t}\n\t\tif (!allele.ann) {\n\t\t\tallele.ann = []\n\t\t}\n\t\tallele.ann.push(o)\n\t\to._gene = o.Gene_Name\n\t\t// isoform\n\t\tif (o.Feature_Type && o.Feature_Type == 'transcript' && o.Feature_ID) {\n\t\t\to._isoform = o.Feature_ID.split('.')[0]\n\t\t}\n\t\t// class\n\t\tif (o.Annotation) {\n\t\t\tconst [dt, cls, rank] = vepinfo(o.Annotation)\n\t\t\to._dt = dt\n\t\t\to._class = cls\n\t\t\to._csqrank = rank\n\t\t} else {\n\t\t\t// FIXME\n\t\t\to._dt = dtsnvindel\n\t\t\to._class = mclassnonstandard\n\t\t}\n\t\t// mname\n\t\tif (o['HGVS.p']) {\n\t\t\t//o._mname=decodeURIComponent(o.HGVSp.substr(o.HGVSp.indexOf(':')+1))\n\t\t\to._mname = o['HGVS.p']\n\t\t} else if (o['HGVS.c']) {\n\t\t\to._mname = o['HGVS.c']\n\t\t} else {\n\t\t}\n\t}\n\treturn true\n}\n"],
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+  "sources": ["../../src/vcf.ann.ts"],
+  "sourcesContent": ["import { vepinfo, dtsnvindel, mclassnonstandard } from './common.js'\n\nexport function parse_ANN(str, header, m) {\n\t// snpEff\n\tif (!header) {\n\t\treturn null\n\t}\n\tfor (const thisannotation of str.split(',')) {\n\t\tconst lst = thisannotation.replace(/&/g, ',').split('|')\n\n\t\tconst o: Record<string, any> = {}\n\n\t\tfor (let i = 0; i < header.length; i++) {\n\t\t\tif (lst[i]) {\n\t\t\t\to[header[i].name] = lst[i]\n\t\t\t}\n\t\t}\n\t\tif (!o.Allele) {\n\t\t\tcontinue\n\t\t}\n\t\tlet allele: any = null\n\t\tfor (const a of m.alleles) {\n\t\t\tif (a.allele == o.Allele) {\n\t\t\t\tallele = a\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tif (!allele) {\n\t\t\t// cannot match to allele!!!\n\t\t\tcontinue\n\t\t}\n\t\tif (!allele.ann) {\n\t\t\tallele.ann = []\n\t\t}\n\t\tallele.ann.push(o)\n\t\to._gene = o.Gene_Name\n\t\t// isoform\n\t\tif (o.Feature_Type && o.Feature_Type == 'transcript' && o.Feature_ID) {\n\t\t\to._isoform = o.Feature_ID.split('.')[0]\n\t\t}\n\t\t// class\n\t\tif (o.Annotation) {\n\t\t\tconst [dt, cls, rank] = vepinfo(o.Annotation)\n\t\t\to._dt = dt\n\t\t\to._class = cls\n\t\t\to._csqrank = rank\n\t\t} else {\n\t\t\t// FIXME\n\t\t\to._dt = dtsnvindel\n\t\t\to._class = mclassnonstandard\n\t\t}\n\t\t// mname\n\t\tif (o['HGVS.p']) {\n\t\t\t//o._mname=decodeURIComponent(o.HGVSp.substr(o.HGVSp.indexOf(':')+1))\n\t\t\to._mname = o['HGVS.p']\n\t\t} else if (o['HGVS.c']) {\n\t\t\to._mname = o['HGVS.c']\n\t\t}\n\t}\n\treturn true\n}\n"],
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   "names": []
 }

package/dist/src/vcf.csq.d.ts

@@ -0,0 +1 @@
+export declare function parse_CSQ(str: any, header: any, m: any): true | null;

package/dist/src/vcf.csq.js

@@ -1,4 +1,4 @@
-import { vepinfo } from "./common.js";
+import { vepinfo, dtsnvindel, mclassnonstandard } from "./common.js";
 function parse_CSQ(str, header, m) {
   if (!header) {
     return null;
@@ -71,7 +71,6 @@ function parse_CSQ(str, header, m) {
       o._mname = o.HGVSc.substr(o.HGVSc.indexOf(":") + 1);
     } else if (o.Existing_variation) {
       o._name = o.Existing_variation;
-    } else {
     }
   }
   return true;

package/dist/src/vcf.csq.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../src/vcf.csq.js"],
-  "sourcesContent": ["import { vepinfo } from './common.js'\n/*\nparse csq field from a variant line, not header\nCSQ header must have already been parsed\n\nstr: the csq value for a vcf line\nheader: [ // something like this\n  { name: 'Allele' },\n  { name: 'Consequence' },\n  { name: 'IMPACT' },\n  { name: 'SYMBOL' },\n  { name: 'Gene' },\n  { name: 'Feature_type' },\n  { name: 'Feature' },\n  { name: 'BIOTYPE' },\n  { name: 'EXON' },\n  { name: 'INTRON' },\n  { name: 'HGVSc' },\n  { name: 'HGVSp' },\n  { name: 'cDNA_position' },\n  { name: 'CDS_position' },\n  { name: 'Protein_position' },\n  { name: 'Amino_acids' },\n  { name: 'Codons' },\n  { name: 'Existing_variation' },\n  { name: 'DISTANCE' },\n  { name: 'STRAND' },\n  { name: 'FLAGS' },\n  { name: 'SYMBOL_SOURCE' },\n  { name: 'HGNC_ID' },\n  { name: 'CANONICAL' },\n  { name: 'REFSEQ_MATCH' },\n  { name: 'GIVEN_REF' },\n  { name: 'USED_REF' },\n  { name: 'BAM_EDIT' },\n  { name: 'HGVS_OFFSET' },\n  { name: 'CLIN_SIG' },\n  { name: 'SOMATIC' },\n  { name: 'PHENO' }\n]\n\nm: {\n\tmlst[ {} ]\n\t\t.allele_original\n\t\t.csq[ {} ] // parse_CSQ will add this array to this allele\n\t\t\t._class\n\t\t\t._csqrank\n\t\t\t._dt\n\t\t\t._gene\n\t\t\t._isoform\n\t\t\t._mname\n}\n\n*/\n\nexport function parse_CSQ(str, header, m) {\n\tif (!header) {\n\t\treturn null\n\t}\n\tfor (const thisannotation of str.split(',')) {\n\t\tconst lst = thisannotation.replace(/&/g, ',').split('|')\n\n\t\tconst o = {}\n\n\t\tfor (let i = 0; i < header.length; i++) {\n\t\t\tif (lst[i]) {\n\t\t\t\to[header[i].name] = lst[i]\n\t\t\t}\n\t\t}\n\t\tif (!o.Allele) {\n\t\t\tcontinue\n\t\t}\n\t\tlet allele = null\n\n\t\t//////////////////////////////////////\n\t\t// NOTE\n\t\t// mds2delete\n\t\t// m.alleles[] is based on old vcf parsing and may delete?\n\t\t// latest spec is m.mlst[]\n\t\t//////////////////////////////////////\n\n\t\tfor (const a of m.mlst || m.alleles) {\n\t\t\tif (a.allele_original == o.Allele) {\n\t\t\t\tallele = a\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tif (!allele) {\n\t\t\tif (o.Allele == '-') {\n\t\t\t\t// deletion\n\t\t\t\tif (m.mlst) {\n\t\t\t\t\tif (m.mlst.length == 1) {\n\t\t\t\t\t\tallele = m.mlst[0]\n\t\t\t\t\t}\n\t\t\t\t} else if (m.alleles) {\n\t\t\t\t\tif (m.alleles.length == 1) {\n\t\t\t\t\t\tallele = m.alleles[0]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tfor (const a of m.mlst || m.alleles) {\n\t\t\t\t\tif (a.allele_original.substr(1) == o.Allele) {\n\t\t\t\t\t\t// insertion, without first padding base\n\t\t\t\t\t\tallele = a\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!allele) {\n\t\t\t\t// cannot match to allele!!!\n\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\t\tif (!allele.csq) {\n\t\t\tallele.csq = []\n\t\t}\n\t\tallele.csq.push(o)\n\n\t\t// gene\n\t\to._gene = o.SYMBOL || o.Gene\n\n\t\t// isoform\n\t\tif (o.Feature_type && o.Feature_type == 'Transcript') {\n\t\t\to._isoform = o.Feature.split('.')[0] // remove version\n\t\t} else {\n\t\t\to._isoform = o._gene\n\t\t}\n\n\t\t// class\n\t\tif (o.Consequence) {\n\t\t\tconst [dt, cls, rank] = vepinfo(o.Consequence)\n\t\t\to._dt = dt\n\t\t\to._class = cls\n\t\t\to._csqrank = rank\n\t\t} else {\n\t\t\t// FIXME\n\t\t\to._dt = dtsnvindel\n\t\t\to._class = mclassnonstandard\n\t\t}\n\t\t// mname\n\t\tif (o.HGVSp) {\n\t\t\to._mname = decodeURIComponent(o.HGVSp.substr(o.HGVSp.indexOf(':') + 1))\n\t\t} else if (o.Protein_position && o.Amino_acids) {\n\t\t\to._mname = decodeURIComponent(o.Protein_position + o.Amino_acids)\n\t\t} else if (o.HGVSc) {\n\t\t\to._mname = o.HGVSc.substr(o.HGVSc.indexOf(':') + 1)\n\t\t} else if (o.Existing_variation) {\n\t\t\to._name = o.Existing_variation\n\t\t} else {\n\t\t}\n\t}\n\treturn true\n}\n"],
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+  "sources": ["../../src/vcf.csq.ts"],
+  "sourcesContent": ["import { vepinfo, dtsnvindel, mclassnonstandard } from './common.js'\n/*\nparse csq field from a variant line, not header\nCSQ header must have already been parsed\n\nstr: the csq value for a vcf line\nheader: [ // something like this\n  { name: 'Allele' },\n  { name: 'Consequence' },\n  { name: 'IMPACT' },\n  { name: 'SYMBOL' },\n  { name: 'Gene' },\n  { name: 'Feature_type' },\n  { name: 'Feature' },\n  { name: 'BIOTYPE' },\n  { name: 'EXON' },\n  { name: 'INTRON' },\n  { name: 'HGVSc' },\n  { name: 'HGVSp' },\n  { name: 'cDNA_position' },\n  { name: 'CDS_position' },\n  { name: 'Protein_position' },\n  { name: 'Amino_acids' },\n  { name: 'Codons' },\n  { name: 'Existing_variation' },\n  { name: 'DISTANCE' },\n  { name: 'STRAND' },\n  { name: 'FLAGS' },\n  { name: 'SYMBOL_SOURCE' },\n  { name: 'HGNC_ID' },\n  { name: 'CANONICAL' },\n  { name: 'REFSEQ_MATCH' },\n  { name: 'GIVEN_REF' },\n  { name: 'USED_REF' },\n  { name: 'BAM_EDIT' },\n  { name: 'HGVS_OFFSET' },\n  { name: 'CLIN_SIG' },\n  { name: 'SOMATIC' },\n  { name: 'PHENO' }\n]\n\nm: {\n\tmlst[ {} ]\n\t\t.allele_original\n\t\t.csq[ {} ] // parse_CSQ will add this array to this allele\n\t\t\t._class\n\t\t\t._csqrank\n\t\t\t._dt\n\t\t\t._gene\n\t\t\t._isoform\n\t\t\t._mname\n}\n\n*/\n\nexport function parse_CSQ(str, header, m) {\n\tif (!header) {\n\t\treturn null\n\t}\n\tfor (const thisannotation of str.split(',')) {\n\t\tconst lst = thisannotation.replace(/&/g, ',').split('|')\n\n\t\tconst o: Record<string, any> = {}\n\n\t\tfor (let i = 0; i < header.length; i++) {\n\t\t\tif (lst[i]) {\n\t\t\t\to[header[i].name] = lst[i]\n\t\t\t}\n\t\t}\n\t\tif (!o.Allele) {\n\t\t\tcontinue\n\t\t}\n\t\tlet allele: any = null\n\n\t\t//////////////////////////////////////\n\t\t// NOTE\n\t\t// mds2delete\n\t\t// m.alleles[] is based on old vcf parsing and may delete?\n\t\t// latest spec is m.mlst[]\n\t\t//////////////////////////////////////\n\n\t\tfor (const a of m.mlst || m.alleles) {\n\t\t\tif (a.allele_original == o.Allele) {\n\t\t\t\tallele = a\n\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tif (!allele) {\n\t\t\tif (o.Allele == '-') {\n\t\t\t\t// deletion\n\t\t\t\tif (m.mlst) {\n\t\t\t\t\tif (m.mlst.length == 1) {\n\t\t\t\t\t\tallele = m.mlst[0]\n\t\t\t\t\t}\n\t\t\t\t} else if (m.alleles) {\n\t\t\t\t\tif (m.alleles.length == 1) {\n\t\t\t\t\t\tallele = m.alleles[0]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tfor (const a of m.mlst || m.alleles) {\n\t\t\t\t\tif (a.allele_original.substr(1) == o.Allele) {\n\t\t\t\t\t\t// insertion, without first padding base\n\t\t\t\t\t\tallele = a\n\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!allele) {\n\t\t\t\t// cannot match to allele!!!\n\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\t\tif (!allele.csq) {\n\t\t\tallele.csq = []\n\t\t}\n\t\tallele.csq.push(o)\n\n\t\t// gene\n\t\to._gene = o.SYMBOL || o.Gene\n\n\t\t// isoform\n\t\tif (o.Feature_type && o.Feature_type == 'Transcript') {\n\t\t\to._isoform = o.Feature.split('.')[0] // remove version\n\t\t} else {\n\t\t\to._isoform = o._gene\n\t\t}\n\n\t\t// class\n\t\tif (o.Consequence) {\n\t\t\tconst [dt, cls, rank] = vepinfo(o.Consequence)\n\t\t\to._dt = dt\n\t\t\to._class = cls\n\t\t\to._csqrank = rank\n\t\t} else {\n\t\t\t// FIXME\n\t\t\to._dt = dtsnvindel\n\t\t\to._class = mclassnonstandard\n\t\t}\n\t\t// mname\n\t\tif (o.HGVSp) {\n\t\t\to._mname = decodeURIComponent(o.HGVSp.substr(o.HGVSp.indexOf(':') + 1))\n\t\t} else if (o.Protein_position && o.Amino_acids) {\n\t\t\to._mname = decodeURIComponent(o.Protein_position + o.Amino_acids)\n\t\t} else if (o.HGVSc) {\n\t\t\to._mname = o.HGVSc.substr(o.HGVSc.indexOf(':') + 1)\n\t\t} else if (o.Existing_variation) {\n\t\t\to._name = o.Existing_variation\n\t\t}\n\t}\n\treturn true\n}\n"],
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   "names": []
 }

package/dist/src/vcf.d.ts

@@ -0,0 +1,2 @@
+export declare function vcfparsemeta(lines: any): (any[] | Record<string, any> | null)[];
+export declare function vcfparseline(line: any, vcf: any): (string | any[] | null)[];

package/dist/src/vcf.info.d.ts

@@ -0,0 +1 @@
+export declare function dissect_INFO(str: any): {};

package/dist/src/vcf.info.js.map

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../src/vcf.info.js"],
+  "sources": ["../../src/vcf.info.ts"],
   "sourcesContent": ["/*\nto parse a variant line, not header\n\ncannot simply slice by /[;=]/, but read char by char\ncase  CLNVI=Breast_Cancer_Information_Core__(BRCA2):745-4&base_change=C_to_G;\ncase  k1=v1;DB;k2=v2;\n*/\nexport function dissect_INFO(str) {\n\t//let findequal=true\n\tlet findsemicolon = false\n\tlet findequalorsemicolon = true\n\n\tlet i = 0\n\tlet idx = 0\n\n\tconst k2v = {}\n\tlet lastkey\n\n\twhile (i < str.length) {\n\t\tconst c = str[i]\n\t\tif (findequalorsemicolon) {\n\t\t\tif (c == '=') {\n\t\t\t\tfindsemicolon = true\n\t\t\t\tfindequalorsemicolon = false\n\t\t\t\tlastkey = str.substring(idx, i)\n\t\t\t\tidx = i + 1\n\t\t\t} else if (c == ';') {\n\t\t\t\t// should be a flag\n\t\t\t\tk2v[str.substring(idx, i)] = 1\n\t\t\t\tidx = i + 1\n\t\t\t}\n\t\t} else if (findsemicolon && c == ';') {\n\t\t\tfindequalorsemicolon = true\n\t\t\tfindsemicolon = false\n\t\t\tk2v[lastkey] = str.substring(idx, i)\n\t\t\tlastkey = null\n\t\t\tidx = i + 1\n\t\t}\n\t\ti++\n\t}\n\n\tconst remainstr = str.substr(idx, i)\n\tif (lastkey) {\n\t\tk2v[lastkey] = remainstr\n\t} else {\n\t\tk2v[remainstr] = 1\n\t}\n\n\treturn k2v\n}\n"],
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   "names": []

package/dist/src/vcf.js

@@ -9,7 +9,12 @@ for (const k in mclass) {
   mclasslabel2key[mclass[k].label.toUpperCase()] = k;
 }
 function vcfparsemeta(lines) {
-  let sample = [], errlst = [], info = {}, hasinfo = false, format = {}, hasformat = false;
+  let sample = [];
+  const errlst = [];
+  const info = {};
+  let hasinfo = false;
+  const format = {};
+  let hasformat = false;
   for (const line of lines) {
     if (!line.startsWith("#")) {
       continue;
@@ -207,7 +212,7 @@ function parse_FORMAT2(lst, m, vcf) {
       }
     }
     const sampleidx = _sampleidx - 9;
-    for (let i2 = 1; i2 < m.alleles.length; i2++) {
+    for (let i = 1; i < m.alleles.length; i++) {
       const sobj = {};
       if (vcf.samples && vcf.samples[sampleidx]) {
         for (const k in vcf.samples[sampleidx]) {
@@ -216,7 +221,7 @@ function parse_FORMAT2(lst, m, vcf) {
       } else {
         sobj.name = "missing_samplename_from_vcf_header";
       }
-      m.alleles[i2].sampledata.push({
+      m.alleles[i].sampledata.push({
         sampleobj: sobj
       });
     }
@@ -231,12 +236,12 @@ function parse_FORMAT2(lst, m, vcf) {
         let gtsum = 0;
         let unknowngt = false;
         const gtalleles = [];
-        for (const i2 of value.split(splitter)) {
-          if (i2 == ".") {
+        for (const i of value.split(splitter)) {
+          if (i == ".") {
             unknowngt = true;
             continue;
           }
-          const j = Number.parseInt(i2);
+          const j = Number.parseInt(i);
           if (Number.isNaN(j)) {
             unknowngt = true;
             continue;
@@ -252,8 +257,8 @@ function parse_FORMAT2(lst, m, vcf) {
           gtallref = gtsum == 0;
         }
         const genotype = gtalleles.join(splitter);
-        for (let i2 = 1; i2 < m.alleles.length; i2++) {
-          const ms = m.alleles[i2].sampledata[m.alleles[i2].sampledata.length - 1];
+        for (let i = 1; i < m.alleles.length; i++) {
+          const ms = m.alleles[i].sampledata[m.alleles[i].sampledata.length - 1];
           ms.GT = value;
           ms.genotype = genotype;
           if (gtallref) {
@@ -265,48 +270,48 @@ function parse_FORMAT2(lst, m, vcf) {
       }
       const formatdesc = vcf.format ? vcf.format[field] : null;
       if (!formatdesc) {
-        for (let i2 = 1; i2 < m.alleles.length; i2++) {
-          m.alleles[i2].sampledata[m.alleles[i2].sampledata.length - 1][field] = value;
+        for (let i = 1; i < m.alleles.length; i++) {
+          m.alleles[i].sampledata[m.alleles[i].sampledata.length - 1][field] = value;
         }
         continue;
       }
       const isinteger = formatdesc.Type == "Integer";
       const isfloat = formatdesc.Type == "Float";
       if (formatdesc.Number && formatdesc.Number == "R" || field == "AD") {
-        const fvlst = value.split(",").map((i2) => {
-          if (isinteger) return Number.parseInt(i2);
-          if (isfloat) return Number.parseFloat(i2);
-          return i2;
+        const fvlst = value.split(",").map((i) => {
+          if (isinteger) return Number.parseInt(i);
+          if (isfloat) return Number.parseFloat(i);
+          return i;
         });
-        for (let i2 = 1; i2 < m.alleles.length; i2++) {
-          if (fvlst[i2] != void 0) {
-            const m2 = m.alleles[i2];
+        for (let i = 1; i < m.alleles.length; i++) {
+          if (fvlst[i] != void 0) {
+            const m2 = m.alleles[i];
             const m2s = m2.sampledata[m2.sampledata.length - 1];
             m2s[field] = {};
             m2s[field][m2.ref] = fvlst[0];
-            m2s[field][m2.allele] = fvlst[i2];
+            m2s[field][m2.allele] = fvlst[i];
           }
         }
         continue;
       }
       if (formatdesc.Number && formatdesc.Number == "A") {
-        const fvlst = value.split(",").map((i2) => {
-          if (isinteger) return Number.parseInt(i2);
-          if (isfloat) return Number.parseFloat(i2);
-          return i2;
+        const fvlst = value.split(",").map((i) => {
+          if (isinteger) return Number.parseInt(i);
+          if (isfloat) return Number.parseFloat(i);
+          return i;
         });
-        for (let i2 = 1; i2 < m.alleles.length; i2++) {
-          if (fvlst[i2 - 1] != void 0) {
-            const m2 = m.alleles[i2];
+        for (let i = 1; i < m.alleles.length; i++) {
+          if (fvlst[i - 1] != void 0) {
+            const m2 = m.alleles[i];
             const m2s = m2.sampledata[m2.sampledata.length - 1];
             m2s[field] = {};
-            m2s[field][m2.allele] = fvlst[i2 - 1];
+            m2s[field][m2.allele] = fvlst[i - 1];
           }
         }
         continue;
       }
-      for (let i2 = 1; i2 < m.alleles.length; i2++) {
-        m.alleles[i2].sampledata[m.alleles[i2].sampledata.length - 1][field] = value;
+      for (let i = 1; i < m.alleles.length; i++) {
+        m.alleles[i].sampledata[m.alleles[i].sampledata.length - 1][field] = value;
       }
     }
   }
@@ -324,15 +329,15 @@ function parse_FORMAT2(lst, m, vcf) {
 function tohash(s, hash) {
   const h = {}, err = [];
   let prev = 0, prevdoublequote = false, k = null;
-  for (let i2 = 0; i2 < s.length; i2++) {
-    if (s[i2] == '"') {
-      i2++;
-      const thisstart = i2;
-      while (s[i2] != '"') {
-        i2++;
+  for (let i = 0; i < s.length; i++) {
+    if (s[i] == '"') {
+      i++;
+      const thisstart = i;
+      while (s[i] != '"') {
+        i++;
       }
       if (k) {
-        h[k] = s.substring(thisstart, i2);
+        h[k] = s.substring(thisstart, i);
         k = null;
       } else {
         err.push("k undefined before double quotes");
@@ -340,28 +345,28 @@ function tohash(s, hash) {
       prevdoublequote = true;
       continue;
     }
-    if (s[i2] == "=") {
-      k = s.substring(prev, i2);
-      prev = i2 + 1;
+    if (s[i] == "=") {
+      k = s.substring(prev, i);
+      prev = i + 1;
       continue;
     }
-    if (s[i2] == ",") {
+    if (s[i] == ",") {
       if (prevdoublequote) {
         prevdoublequote = false;
       } else {
         if (k) {
-          h[k] = s.substring(prev, i2);
+          h[k] = s.substring(prev, i);
           k = null;
         } else {
           err.push("k undefined");
         }
       }
-      prev = i2 + 1;
+      prev = i + 1;
       continue;
     }
   }
   if (k) {
-    h[k] = s.substring(prev, i);
+    h[k] = s.substring(prev);
   }
   if (h.ID) {
     hash[h.ID] = h;

package/dist/src/vcf.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../src/vcf.js"],
-  "sourcesContent": ["import { mclass } from './common.js'\nimport { dissect_INFO } from './vcf.info.js'\nimport { parse_CSQ } from './vcf.csq.js'\nimport { parse_ANN } from './vcf.ann.js'\nimport { getVariantType } from './vcf.type.js'\n\n/*\nOnly for parsing vcf files\nis not involved in creating vcf tracks\n\nshared between client-server\n*/\n\n// for telling symbolic alleles e.g. <*:DEL>\nconst getallelename = new RegExp(/<(.+)>/)\n\nconst mclasslabel2key = {}\nfor (const k in mclass) {\n\tmclasslabel2key[mclass[k].label.toUpperCase()] = k\n}\n\nexport function vcfparsemeta(lines) {\n\t/*\n\tinput: array of string, as lines separated by linebreak\n\n\t##INFO for meta lines\n\t#CHROM for header, to get samples\n\n\t*/\n\n\tlet sample = [],\n\t\terrlst = [],\n\t\tinfo = {},\n\t\thasinfo = false,\n\t\tformat = {},\n\t\thasformat = false\n\n\tfor (const line of lines) {\n\t\tif (!line.startsWith('#')) {\n\t\t\tcontinue\n\t\t}\n\n\t\tif (line.startsWith('#C')) {\n\t\t\t// header, get samples\n\t\t\tsample = line.split('\\t').slice(9)\n\t\t\tcontinue\n\t\t}\n\n\t\tif (line.startsWith('##INFO')) {\n\t\t\tconst e = tohash(line.substring(8, line.length - 1), info)\n\t\t\tif (e) {\n\t\t\t\terrlst.push('INFO error: ' + e)\n\t\t\t} else {\n\t\t\t\thasinfo = true\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\n\t\tif (line.startsWith('##FORMAT')) {\n\t\t\tconst e = tohash(line.substring(10, line.length - 1), format)\n\t\t\tif (e) {\n\t\t\t\terrlst.push('FORMAT error: ' + e)\n\t\t\t} else {\n\t\t\t\thasformat = true\n\t\t\t}\n\t\t}\n\t}\n\n\tconst sampleobjlst = []\n\tfor (const samplename of sample) {\n\t\tconst a = { name: samplename }\n\n\t\t// this enables adding key4annotation to match with .ds.cohort.annotation\n\n\t\tsampleobjlst.push(a)\n\t}\n\n\t// reserved INFO fields\n\tif (info.CSQ) {\n\t\tconst lst = info.CSQ.Description.split(' Format: ')\n\t\tif (lst[1]) {\n\t\t\tconst lst2 = lst[1].split('|')\n\t\t\tif (lst2.length > 1) {\n\t\t\t\t// fix csq headers so to allow configuring show/hide of csq fields\n\t\t\t\tinfo.CSQ.csqheader = []\n\t\t\t\tfor (const str of lst2) {\n\t\t\t\t\tconst attr = { name: str }\n\t\t\t\t\tinfo.CSQ.csqheader.push(attr)\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\terrlst.push('unknown format for CSQ header: ' + info.CSQ.Description)\n\t\t\t}\n\t\t} else {\n\t\t\terrlst.push('unknown format for CSQ header: ' + info.CSQ.Description)\n\t\t}\n\t}\n\n\tif (info.ANN) {\n\t\tconst lst = info.ANN.Description.split(\"'\")\n\t\tif (lst[1]) {\n\t\t\tconst lst2 = lst[1].split(' | ')\n\t\t\tif (lst2.length) {\n\t\t\t\tinfo.ANN.annheader = []\n\t\t\t\tfor (const s of lst2) {\n\t\t\t\t\tconst attr = { name: s }\n\t\t\t\t\tinfo.ANN.annheader.push(attr)\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\terrlst.push('no \" | \" joined annotation fields for ANN (snpEff annotation): ' + info.ANN.Description)\n\t\t\t}\n\t\t} else {\n\t\t\terrlst.push('no single-quote enclosed annotation fields for ANN (snpEff annotation): ' + info.ANN.Description)\n\t\t}\n\t}\n\n\treturn [hasinfo ? info : null, hasformat ? format : null, sampleobjlst, errlst.length ? errlst : null]\n}\n\nexport function vcfparseline(line, vcf) {\n\t/*\n\tvcf, samples/info is generated by vcfparsemeta()\n\t\t.nochr BOOL\n\t\t.samples [ {} ]\n\t\t\t.name\n\t\t.info {}\n\t\t.format {}\n\n\treturn:\n\t\terror message STR\n\t\taltinvalid []\n\t\tmlst [ m ]   one m per alt allele\n\t\t\tchr\n\t\t\tpos\n\t\t\tname\n\t\t\ttype\n\t\t\tref\n\t\t\talt\n\t\t\taltstr\n\t\t\tsampledata []\n\t\t\taltinfo\n\t*/\n\n\tconst lst = line.split('\\t')\n\tif (lst.length < 8) {\n\t\t// no good\n\t\treturn ['line has less than 8 fields', null, null]\n\t}\n\n\tconst rawpos = Number.parseInt(lst[2 - 1])\n\tif (!Number.isInteger(rawpos)) {\n\t\treturn ['invalid value for genomic position', null, null]\n\t}\n\n\tconst refallele = lst[4 - 1]\n\n\tconst m = {\n\t\tvcf_ID: lst[3 - 1],\n\t\tchr: (vcf.nochr ? 'chr' : '') + lst[1 - 1],\n\t\tpos: rawpos - 1,\n\t\tref: refallele,\n\t\t//refstr:refallele, // e.g. GA>GCC, ref:A, refstr:GA, \"refstr\" is required for matching in FORMAT\n\t\taltstr: lst[5 - 1],\n\t\talleles: [\n\t\t\t{\n\t\t\t\t/*\n\t\t\t\tref allele only a placeholder, to be removed, this array only contains alt alleles\n\t\t\t\tthis is a must\n\t\t\t\talso allows GT allele index to work\n\t\t\t\t*/\n\t\t\t\tallele: refallele,\n\t\t\t\tsampledata: []\n\t\t\t}\n\t\t],\n\n\t\tinfo: {}, // locus info, do not contain allele info\n\n\t\tname: lst[3 - 1] == '.' ? null : lst[3 - 1]\n\t}\n\n\t// parse alt\n\tconst altinvalid = []\n\tfor (const alt of lst[5 - 1].split(',')) {\n\t\tconst a = {\n\t\t\tref: m.ref, // may be corrected just below!\n\t\t\tallele: alt,\n\t\t\t// 5078356.TATCAGAGAA.GGGAGGA keep original allele for matching with csq which hardcodes original allele\n\t\t\tallele_original: alt,\n\t\t\tsampledata: [],\n\t\t\t_m: m,\n\t\t\tinfo: {} // allele info, do not contain locus info\n\t\t}\n\t\tm.alleles.push(a)\n\t\tif (alt[0] == '<') {\n\t\t\t/*\n\t\t\tsymbolic allele, show text within <> as name\n\t\t\tFIXME match INFO\n\t\t\t*/\n\t\t\tconst tmp = alt.match(getallelename)\n\t\t\tif (!tmp) {\n\t\t\t\taltinvalid.push(alt)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\ta.type = tmp[1]\n\n\t\t\ta.allele = tmp[1]\n\t\t\ta.issymbolicallele = true\n\t\t} else {\n\t\t\t// normal nucleotide\n\n\t\t\tconst [p, ref, alt] = correctRefAlt(m.pos, m.ref, a.allele)\n\t\t\ta.pos = p\n\t\t\ta.ref = ref\n\t\t\ta.allele = alt\n\t\t}\n\t}\n\n\tif (lst[9 - 1] && lst[10 - 1]) {\n\t\tparse_FORMAT2(lst, m, vcf)\n\t}\n\n\t/*\n\tremove ref allele so it only contain alternative alleles\n\tso that parse_INFO can safely apply Number=A fields to m.alleles\n\t*/\n\tm.alleles.shift()\n\n\t// info\n\tconst tmp = lst[8 - 1] == '.' ? [] : dissect_INFO(lst[8 - 1])\n\tlet badinfokeys = []\n\n\tif (vcf.info) {\n\t\tbadinfokeys = parse_INFO(tmp, m, vcf)\n\t} else {\n\t\t// vcf meta lines told nothing about INFO, do not parse\n\t\tm.info = tmp\n\t}\n\n\tconst mlst = []\n\tfor (const a of m.alleles) {\n\t\tconst m2 = {}\n\t\tfor (const k in m) {\n\t\t\tif (k != 'alleles') {\n\t\t\t\tm2[k] = m[k]\n\t\t\t}\n\t\t}\n\t\tfor (const k in a) {\n\t\t\tif (k == 'allele') {\n\t\t\t\tm2.alt = a[k]\n\t\t\t} else if (k == 'info') {\n\t\t\t\tm2.altinfo = a[k]\n\t\t\t} else {\n\t\t\t\tm2[k] = a[k]\n\t\t\t}\n\t\t}\n\t\tif (!m2.issymbolicallele && m2.alt != 'NON_REF') {\n\t\t\tm2.type = getVariantType(m2.ref, m2.alt)\n\t\t\t/*\n\t\t\t// valid alt allele, apply Dr. J's cool method\n\t\t\tconst [p,ref,alt]=correctRefAlt(m2.pos, m2.ref, m2.alt)\n\t\t\tm2.pos=p\n\t\t\tm2.ref=ref\n\t\t\tm2.alt=alt\n\t\t\t*/\n\t\t}\n\t\tmlst.push(m2)\n\t}\n\treturn [\n\t\tbadinfokeys.length ? 'unknown info keys: ' + badinfokeys.join(',') : null,\n\t\tmlst,\n\t\taltinvalid.length > 0 ? altinvalid : null\n\t]\n}\n\nfunction correctRefAlt(p, ref, alt) {\n\t// for oligos, always trim the last identical base\n\twhile (ref.length > 1 && alt.length > 1 && ref[ref.length - 1] == alt[alt.length - 1]) {\n\t\tref = ref.substr(0, ref.length - 1)\n\t\talt = alt.substr(0, alt.length - 1)\n\t}\n\t// move position up as long as first positions are equal\n\twhile (ref.length > 1 && alt.length > 1 && ref[0] == alt[0]) {\n\t\tref = ref.substr(1)\n\t\talt = alt.substr(1)\n\t\tp++\n\t}\n\treturn [p, ref, alt]\n}\n\nfunction parse_FORMAT2(lst, m, vcf) {\n\t/*\n\tm.alleles[0] is ref allele\n\n\teach allele:\n\t\t.ref\n\t\t.allele\n\t\t.allele_original\n\t\t.sampledata[]     blank array\n\t*/\n\tconst formatfields = lst[9 - 1].split(':')\n\n\tfor (let _sampleidx = 9; _sampleidx < lst.length; _sampleidx++) {\n\t\t// for each sample\n\n\t\tconst valuelst = lst[_sampleidx].split(':')\n\t\t{\n\t\t\t// tell if this sample have any data in this line (variant), if .:., then skip\n\t\t\tlet none = true\n\t\t\tfor (const v of valuelst) {\n\t\t\t\tif (v != '.') {\n\t\t\t\t\tnone = false\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (none) {\n\t\t\t\t// this sample has no format value\n\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\n\t\t/* should create an object of {format:value} of this sample\n\t\twith this object, for each alt allele this sample has,\n\t\tput a copy in m.allele[x].sampledata[]\n\t\t*/\n\n\t\tconst sampleidx = _sampleidx - 9\n\n\t\t/*\n\t\tfor each alt allele, initialize obj of this sample and store in this allele\n\t\tlater, to iterate over format fields and put in appropriate values\n\t\tnote that this sample may not actually have this allele\n\t\t*/\n\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\tconst sobj = {}\n\t\t\tif (vcf.samples && vcf.samples[sampleidx]) {\n\t\t\t\tfor (const k in vcf.samples[sampleidx]) {\n\t\t\t\t\tsobj[k] = vcf.samples[sampleidx][k]\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tsobj.name = 'missing_samplename_from_vcf_header'\n\t\t\t}\n\t\t\tm.alleles[i].sampledata.push({\n\t\t\t\tsampleobj: sobj\n\t\t\t})\n\t\t}\n\n\t\tfor (let fi = 0; fi < formatfields.length; fi++) {\n\t\t\t// for each field of this sample\n\n\t\t\tconst field = formatfields[fi]\n\t\t\tconst value = valuelst[fi]\n\t\t\tif (value == '.') {\n\t\t\t\t// no value for this field\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tif (field == 'GT') {\n\t\t\t\tconst splitter = value.indexOf('/') != -1 ? '/' : '|'\n\t\t\t\tlet gtsum = 0 // for calculating gtallref=true, old\n\t\t\t\tlet unknowngt = false // if any is '.', then won't calculate gtallref\n\t\t\t\tconst gtalleles = []\n\t\t\t\tfor (const i of value.split(splitter)) {\n\t\t\t\t\tif (i == '.') {\n\t\t\t\t\t\tunknowngt = true\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tconst j = Number.parseInt(i)\n\t\t\t\t\tif (Number.isNaN(j)) {\n\t\t\t\t\t\tunknowngt = true\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tgtsum += j\n\t\t\t\t\tconst ale = m.alleles[j]\n\t\t\t\t\tif (ale) {\n\t\t\t\t\t\tgtalleles.push(ale.allele)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tlet gtallref = false\n\t\t\t\tif (!unknowngt) {\n\t\t\t\t\tgtallref = gtsum == 0\n\t\t\t\t}\n\n\t\t\t\tconst genotype = gtalleles.join(splitter)\n\t\t\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\t\t\tconst ms = m.alleles[i].sampledata[m.alleles[i].sampledata.length - 1]\n\t\t\t\t\tms.GT = value\n\t\t\t\t\tms.genotype = genotype\n\t\t\t\t\tif (gtallref) {\n\t\t\t\t\t\tms.gtallref = true\n\t\t\t\t\t}\n\n\t\t\t\t\t// for mds vcf to drop out samples that do not have this alt allele\n\t\t\t\t\tms.__gtalleles = gtalleles\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\t// other data fields\n\t\t\tconst formatdesc = vcf.format ? vcf.format[field] : null\n\t\t\tif (!formatdesc) {\n\t\t\t\t// unspecified field, put to all alt alleles\n\t\t\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\t\t\tm.alleles[i].sampledata[m.alleles[i].sampledata.length - 1][field] = value\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tconst isinteger = formatdesc.Type == 'Integer'\n\t\t\tconst isfloat = formatdesc.Type == 'Float'\n\n\t\t\tif ((formatdesc.Number && formatdesc.Number == 'R') || field == 'AD') {\n\t\t\t\t/*\n\t\t\t\tper-allele value, including ref\n\t\t\t\tv4.1 has AD not with \"R\", must process as R\n\t\t\t\t*/\n\t\t\t\tconst fvlst = value.split(',').map(i => {\n\t\t\t\t\tif (isinteger) return Number.parseInt(i)\n\t\t\t\t\tif (isfloat) return Number.parseFloat(i)\n\t\t\t\t\treturn i\n\t\t\t\t})\n\t\t\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\t\t\tif (fvlst[i] != undefined) {\n\t\t\t\t\t\t// this allele has value\n\t\t\t\t\t\tconst m2 = m.alleles[i]\n\t\t\t\t\t\tconst m2s = m2.sampledata[m2.sampledata.length - 1]\n\t\t\t\t\t\t// use this allele's ref/alt (after nt trimming)\n\t\t\t\t\t\tm2s[field] = {}\n\t\t\t\t\t\tm2s[field][m2.ref] = fvlst[0]\n\t\t\t\t\t\tm2s[field][m2.allele] = fvlst[i]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (formatdesc.Number && formatdesc.Number == 'A') {\n\t\t\t\t// per alt-allele value\n\t\t\t\tconst fvlst = value.split(',').map(i => {\n\t\t\t\t\tif (isinteger) return Number.parseInt(i)\n\t\t\t\t\tif (isfloat) return Number.parseFloat(i)\n\t\t\t\t\treturn i\n\t\t\t\t})\n\t\t\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\t\t\tif (fvlst[i - 1] != undefined) {\n\t\t\t\t\t\t// this allele has value\n\t\t\t\t\t\tconst m2 = m.alleles[i]\n\t\t\t\t\t\tconst m2s = m2.sampledata[m2.sampledata.length - 1]\n\t\t\t\t\t\t// use this allele's ref/alt (after nt trimming)\n\t\t\t\t\t\tm2s[field] = {}\n\t\t\t\t\t\tm2s[field][m2.allele] = fvlst[i - 1]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\t// otherwise, append this field to all alt\n\t\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\t\tm.alleles[i].sampledata[m.alleles[i].sampledata.length - 1][field] = value\n\t\t\t}\n\t\t}\n\t}\n\n\t// compatible with old ds: make allele2readcount from AD\n\tfor (const a of m.alleles) {\n\t\tfor (const s of a.sampledata) {\n\t\t\tif (s.AD) {\n\t\t\t\ts.allele2readcount = {}\n\t\t\t\tfor (const k in s.AD) {\n\t\t\t\t\ts.allele2readcount[k] = s.AD[k]\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction tohash(s, hash) {\n\t/*\n\tparse INFO\n\t*/\n\tconst h = {},\n\t\terr = []\n\tlet prev = 0,\n\t\tprevdoublequote = false,\n\t\tk = null\n\tfor (let i = 0; i < s.length; i++) {\n\t\tif (s[i] == '\"') {\n\t\t\ti++\n\t\t\tconst thisstart = i\n\t\t\twhile (s[i] != '\"') {\n\t\t\t\ti++\n\t\t\t}\n\t\t\tif (k) {\n\t\t\t\th[k] = s.substring(thisstart, i)\n\t\t\t\tk = null\n\t\t\t} else {\n\t\t\t\terr.push('k undefined before double quotes')\n\t\t\t}\n\t\t\tprevdoublequote = true\n\t\t\tcontinue\n\t\t}\n\t\tif (s[i] == '=') {\n\t\t\tk = s.substring(prev, i)\n\t\t\tprev = i + 1\n\t\t\tcontinue\n\t\t}\n\t\tif (s[i] == ',') {\n\t\t\tif (prevdoublequote) {\n\t\t\t\tprevdoublequote = false\n\t\t\t} else {\n\t\t\t\tif (k) {\n\t\t\t\t\th[k] = s.substring(prev, i)\n\t\t\t\t\tk = null\n\t\t\t\t} else {\n\t\t\t\t\terr.push('k undefined')\n\t\t\t\t}\n\t\t\t}\n\t\t\tprev = i + 1\n\t\t\tcontinue\n\t\t}\n\t}\n\tif (k) {\n\t\th[k] = s.substring(prev, i)\n\t}\n\tif (h.ID) {\n\t\thash[h.ID] = h\n\t} else {\n\t\treturn 'no ID'\n\t}\n\tif (err.length) return err.join('\\n')\n}\n\nfunction parse_INFO(tmp, m, vcf) {\n\t/*\n\tthis function fills in both m.info{} and m.alleles[].info{}\n\n\tthe m.alleles[] will later be converted to [m], each carrying one alt allele\n\teach m will have .info{} for locus info, and .altinfo{} for alt allele info\n\n\t*/\n\n\tconst badinfokeys = []\n\n\tfor (const key in tmp) {\n\t\tif (vcf.info[key] == undefined) {\n\t\t\tbadinfokeys.push(key)\n\t\t\tcontinue\n\t\t}\n\n\t\tconst value = tmp[key]\n\n\t\t////////////////// hard-coded fields\n\n\t\tif (key == 'CSQ') {\n\t\t\tconst okay = parse_CSQ(value, vcf.info.CSQ.csqheader, m)\n\t\t\tif (!okay) {\n\t\t\t\tm.info[key] = value\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\t\tif (key == 'ANN') {\n\t\t\tconst okay = parse_ANN(value, vcf.info.ANN.annheader, m)\n\t\t\tif (!okay) {\n\t\t\t\tm.info[key] = value\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\n\t\t////////////////// end of hardcoded fields\n\n\t\tif (vcf.info[key].Type == 'Flag') {\n\t\t\t// flag has no value\n\t\t\tm.info[key] = key\n\t\t\tcontinue\n\t\t}\n\n\t\tconst __number = vcf.info[key].Number\n\t\tconst isinteger = vcf.info[key].Type == 'Integer'\n\t\tconst isfloat = vcf.info[key].Type == 'Float'\n\n\t\tif (__number == '0') {\n\t\t\t/*\n\t\t\tno value, should be a Flag\n\t\t\t*/\n\t\t\tm.info[key] = key\n\t\t\tcontinue\n\t\t}\n\n\t\tif (__number == 'A') {\n\t\t\t/*\n\t\t\tper alt allele\n\t\t\t*/\n\t\t\tconst tt = value.split(',')\n\t\t\tfor (let j = 0; j < tt.length; j++) {\n\t\t\t\tif (m.alleles[j]) {\n\t\t\t\t\tm.alleles[j].info[key] = isinteger ? 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-  "names": ["tmp", "alt", "i"]
+  "sources": ["../../src/vcf.ts"],
+  "sourcesContent": ["import { mclass } from './common.js'\nimport { dissect_INFO } from './vcf.info.js'\nimport { parse_CSQ } from './vcf.csq.js'\nimport { parse_ANN } from './vcf.ann.js'\nimport { getVariantType } from './vcf.type.js'\n\n/*\nOnly for parsing vcf files\nis not involved in creating vcf tracks\n\nshared between client-server\n*/\n\n// for telling symbolic alleles e.g. <*:DEL>\nconst getallelename = new RegExp(/<(.+)>/)\n\nconst mclasslabel2key = {}\nfor (const k in mclass) {\n\tmclasslabel2key[mclass[k].label.toUpperCase()] = k\n}\n\nexport function vcfparsemeta(lines) {\n\t/*\n\tinput: array of string, as lines separated by linebreak\n\n\t##INFO for meta lines\n\t#CHROM for header, to get samples\n\n\t*/\n\n\tlet sample = []\n\tconst errlst: string[] = []\n\tconst info: Record<string, any> = {}\n\tlet hasinfo = false\n\tconst format: Record<string, any> = {}\n\tlet hasformat = false\n\n\tfor (const line of lines) {\n\t\tif (!line.startsWith('#')) {\n\t\t\tcontinue\n\t\t}\n\n\t\tif (line.startsWith('#C')) {\n\t\t\t// header, get samples\n\t\t\tsample = line.split('\\t').slice(9)\n\t\t\tcontinue\n\t\t}\n\n\t\tif (line.startsWith('##INFO')) {\n\t\t\tconst e = tohash(line.substring(8, line.length - 1), info)\n\t\t\tif (e) {\n\t\t\t\terrlst.push('INFO error: ' + e)\n\t\t\t} else {\n\t\t\t\thasinfo = true\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\n\t\tif (line.startsWith('##FORMAT')) {\n\t\t\tconst e = tohash(line.substring(10, line.length - 1), format)\n\t\t\tif (e) {\n\t\t\t\terrlst.push('FORMAT error: ' + e)\n\t\t\t} else {\n\t\t\t\thasformat = true\n\t\t\t}\n\t\t}\n\t}\n\n\tconst sampleobjlst: any[] = []\n\tfor (const samplename of sample) {\n\t\tconst a = { name: samplename }\n\n\t\t// this enables adding key4annotation to match with .ds.cohort.annotation\n\n\t\tsampleobjlst.push(a)\n\t}\n\n\t// reserved INFO fields\n\tif (info.CSQ) {\n\t\tconst lst = info.CSQ.Description.split(' Format: ')\n\t\tif (lst[1]) {\n\t\t\tconst lst2 = lst[1].split('|')\n\t\t\tif (lst2.length > 1) {\n\t\t\t\t// fix csq headers so to allow configuring show/hide of csq fields\n\t\t\t\tinfo.CSQ.csqheader = []\n\t\t\t\tfor (const str of lst2) {\n\t\t\t\t\tconst attr = { name: str }\n\t\t\t\t\tinfo.CSQ.csqheader.push(attr)\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\terrlst.push('unknown format for CSQ header: ' + info.CSQ.Description)\n\t\t\t}\n\t\t} else {\n\t\t\terrlst.push('unknown format for CSQ header: ' + info.CSQ.Description)\n\t\t}\n\t}\n\n\tif (info.ANN) {\n\t\tconst lst = info.ANN.Description.split(\"'\")\n\t\tif (lst[1]) {\n\t\t\tconst lst2 = lst[1].split(' | ')\n\t\t\tif (lst2.length) {\n\t\t\t\tinfo.ANN.annheader = []\n\t\t\t\tfor (const s of lst2) {\n\t\t\t\t\tconst attr = { name: s }\n\t\t\t\t\tinfo.ANN.annheader.push(attr)\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\terrlst.push('no \" | \" joined annotation fields for ANN (snpEff annotation): ' + info.ANN.Description)\n\t\t\t}\n\t\t} else {\n\t\t\terrlst.push('no single-quote enclosed annotation fields for ANN (snpEff annotation): ' + info.ANN.Description)\n\t\t}\n\t}\n\n\treturn [hasinfo ? info : null, hasformat ? format : null, sampleobjlst, errlst.length ? errlst : null]\n}\n\nexport function vcfparseline(line, vcf) {\n\t/*\n\tvcf, samples/info is generated by vcfparsemeta()\n\t\t.nochr BOOL\n\t\t.samples [ {} ]\n\t\t\t.name\n\t\t.info {}\n\t\t.format {}\n\n\treturn:\n\t\terror message STR\n\t\taltinvalid []\n\t\tmlst [ m ]   one m per alt allele\n\t\t\tchr\n\t\t\tpos\n\t\t\tname\n\t\t\ttype\n\t\t\tref\n\t\t\talt\n\t\t\taltstr\n\t\t\tsampledata []\n\t\t\taltinfo\n\t*/\n\n\tconst lst = line.split('\\t')\n\tif (lst.length < 8) {\n\t\t// no good\n\t\treturn ['line has less than 8 fields', null, null]\n\t}\n\n\tconst rawpos = Number.parseInt(lst[2 - 1])\n\tif (!Number.isInteger(rawpos)) {\n\t\treturn ['invalid value for genomic position', null, null]\n\t}\n\n\tconst refallele = lst[4 - 1]\n\n\tconst m: Record<string, any> = {\n\t\tvcf_ID: lst[3 - 1],\n\t\tchr: (vcf.nochr ? 'chr' : '') + lst[1 - 1],\n\t\tpos: rawpos - 1,\n\t\tref: refallele,\n\t\t//refstr:refallele, // e.g. GA>GCC, ref:A, refstr:GA, \"refstr\" is required for matching in FORMAT\n\t\taltstr: lst[5 - 1],\n\t\talleles: [\n\t\t\t{\n\t\t\t\t/*\n\t\t\t\tref allele only a placeholder, to be removed, this array only contains alt alleles\n\t\t\t\tthis is a must\n\t\t\t\talso allows GT allele index to work\n\t\t\t\t*/\n\t\t\t\tallele: refallele,\n\t\t\t\tsampledata: []\n\t\t\t}\n\t\t],\n\n\t\tinfo: {}, // locus info, do not contain allele info\n\n\t\tname: lst[3 - 1] == '.' ? null : lst[3 - 1]\n\t}\n\n\t// parse alt\n\tconst altinvalid: string[] = []\n\tfor (const alt of lst[5 - 1].split(',')) {\n\t\tconst a: Record<string, any> = {\n\t\t\tref: m.ref, // may be corrected just below!\n\t\t\tallele: alt,\n\t\t\t// 5078356.TATCAGAGAA.GGGAGGA keep original allele for matching with csq which hardcodes original allele\n\t\t\tallele_original: alt,\n\t\t\tsampledata: [],\n\t\t\t_m: m,\n\t\t\tinfo: {} // allele info, do not contain locus info\n\t\t}\n\t\tm.alleles.push(a)\n\t\tif (alt[0] == '<') {\n\t\t\t/*\n\t\t\tsymbolic allele, show text within <> as name\n\t\t\tFIXME match INFO\n\t\t\t*/\n\t\t\tconst tmp = alt.match(getallelename)\n\t\t\tif (!tmp) {\n\t\t\t\taltinvalid.push(alt)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\ta.type = tmp[1]\n\n\t\t\ta.allele = tmp[1]\n\t\t\ta.issymbolicallele = true\n\t\t} else {\n\t\t\t// normal nucleotide\n\n\t\t\tconst [p, ref, alt] = correctRefAlt(m.pos, m.ref, a.allele)\n\t\t\ta.pos = p\n\t\t\ta.ref = ref\n\t\t\ta.allele = alt\n\t\t}\n\t}\n\n\tif (lst[9 - 1] && lst[10 - 1]) {\n\t\tparse_FORMAT2(lst, m, vcf)\n\t}\n\n\t/*\n\tremove ref allele so it only contain alternative alleles\n\tso that parse_INFO can safely apply Number=A fields to m.alleles\n\t*/\n\tm.alleles.shift()\n\n\t// info\n\tconst tmp = lst[8 - 1] == '.' ? [] : dissect_INFO(lst[8 - 1])\n\tlet badinfokeys: string[] = []\n\n\tif (vcf.info) {\n\t\tbadinfokeys = parse_INFO(tmp, m, vcf)\n\t} else {\n\t\t// vcf meta lines told nothing about INFO, do not parse\n\t\tm.info = tmp\n\t}\n\n\tconst mlst: any[] = []\n\tfor (const a of m.alleles) {\n\t\tconst m2: Record<string, any> = {}\n\t\tfor (const k in m) {\n\t\t\tif (k != 'alleles') {\n\t\t\t\tm2[k] = m[k]\n\t\t\t}\n\t\t}\n\t\tfor (const k in a) {\n\t\t\tif (k == 'allele') {\n\t\t\t\tm2.alt = a[k]\n\t\t\t} else if (k == 'info') {\n\t\t\t\tm2.altinfo = a[k]\n\t\t\t} else {\n\t\t\t\tm2[k] = a[k]\n\t\t\t}\n\t\t}\n\t\tif (!m2.issymbolicallele && m2.alt != 'NON_REF') {\n\t\t\tm2.type = getVariantType(m2.ref, m2.alt)\n\t\t\t/*\n\t\t\t// valid alt allele, apply Dr. J's cool method\n\t\t\tconst [p,ref,alt]=correctRefAlt(m2.pos, m2.ref, m2.alt)\n\t\t\tm2.pos=p\n\t\t\tm2.ref=ref\n\t\t\tm2.alt=alt\n\t\t\t*/\n\t\t}\n\t\tmlst.push(m2)\n\t}\n\treturn [\n\t\tbadinfokeys.length ? 'unknown info keys: ' + badinfokeys.join(',') : null,\n\t\tmlst,\n\t\taltinvalid.length > 0 ? altinvalid : null\n\t]\n}\n\nfunction correctRefAlt(p, ref, alt) {\n\t// for oligos, always trim the last identical base\n\twhile (ref.length > 1 && alt.length > 1 && ref[ref.length - 1] == alt[alt.length - 1]) {\n\t\tref = ref.substr(0, ref.length - 1)\n\t\talt = alt.substr(0, alt.length - 1)\n\t}\n\t// move position up as long as first positions are equal\n\twhile (ref.length > 1 && alt.length > 1 && ref[0] == alt[0]) {\n\t\tref = ref.substr(1)\n\t\talt = alt.substr(1)\n\t\tp++\n\t}\n\treturn [p, ref, alt]\n}\n\nfunction parse_FORMAT2(lst, m, vcf) {\n\t/*\n\tm.alleles[0] is ref allele\n\n\teach allele:\n\t\t.ref\n\t\t.allele\n\t\t.allele_original\n\t\t.sampledata[]     blank array\n\t*/\n\tconst formatfields = lst[9 - 1].split(':')\n\n\tfor (let _sampleidx = 9; _sampleidx < lst.length; _sampleidx++) {\n\t\t// for each sample\n\n\t\tconst valuelst = lst[_sampleidx].split(':')\n\t\t{\n\t\t\t// tell if this sample have any data in this line (variant), if .:., then skip\n\t\t\tlet none = true\n\t\t\tfor (const v of valuelst) {\n\t\t\t\tif (v != '.') {\n\t\t\t\t\tnone = false\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (none) {\n\t\t\t\t// this sample has no format value\n\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\n\t\t/* should create an object of {format:value} of this sample\n\t\twith this object, for each alt allele this sample has,\n\t\tput a copy in m.allele[x].sampledata[]\n\t\t*/\n\n\t\tconst sampleidx = _sampleidx - 9\n\n\t\t/*\n\t\tfor each alt allele, initialize obj of this sample and store in this allele\n\t\tlater, to iterate over format fields and put in appropriate values\n\t\tnote that this sample may not actually have this allele\n\t\t*/\n\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\tconst sobj: Record<string, any> = {}\n\t\t\tif (vcf.samples && vcf.samples[sampleidx]) {\n\t\t\t\tfor (const k in vcf.samples[sampleidx]) {\n\t\t\t\t\tsobj[k] = vcf.samples[sampleidx][k]\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tsobj.name = 'missing_samplename_from_vcf_header'\n\t\t\t}\n\t\t\tm.alleles[i].sampledata.push({\n\t\t\t\tsampleobj: sobj\n\t\t\t})\n\t\t}\n\n\t\tfor (let fi = 0; fi < formatfields.length; fi++) {\n\t\t\t// for each field of this sample\n\n\t\t\tconst field = formatfields[fi]\n\t\t\tconst value = valuelst[fi]\n\t\t\tif (value == '.') {\n\t\t\t\t// no value for this field\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tif (field == 'GT') {\n\t\t\t\tconst splitter = value.indexOf('/') != -1 ? '/' : '|'\n\t\t\t\tlet gtsum = 0 // for calculating gtallref=true, old\n\t\t\t\tlet unknowngt = false // if any is '.', then won't calculate gtallref\n\t\t\t\tconst gtalleles: string[] = []\n\t\t\t\tfor (const i of value.split(splitter)) {\n\t\t\t\t\tif (i == '.') {\n\t\t\t\t\t\tunknowngt = true\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tconst j = Number.parseInt(i)\n\t\t\t\t\tif (Number.isNaN(j)) {\n\t\t\t\t\t\tunknowngt = true\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tgtsum += j\n\t\t\t\t\tconst ale = m.alleles[j]\n\t\t\t\t\tif (ale) {\n\t\t\t\t\t\tgtalleles.push(ale.allele)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tlet gtallref = false\n\t\t\t\tif (!unknowngt) {\n\t\t\t\t\tgtallref = gtsum == 0\n\t\t\t\t}\n\n\t\t\t\tconst genotype = gtalleles.join(splitter)\n\t\t\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\t\t\tconst ms = m.alleles[i].sampledata[m.alleles[i].sampledata.length - 1]\n\t\t\t\t\tms.GT = value\n\t\t\t\t\tms.genotype = genotype\n\t\t\t\t\tif (gtallref) {\n\t\t\t\t\t\tms.gtallref = true\n\t\t\t\t\t}\n\n\t\t\t\t\t// for mds vcf to drop out samples that do not have this alt allele\n\t\t\t\t\tms.__gtalleles = gtalleles\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\t// other data fields\n\t\t\tconst formatdesc = vcf.format ? vcf.format[field] : null\n\t\t\tif (!formatdesc) {\n\t\t\t\t// unspecified field, put to all alt alleles\n\t\t\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\t\t\tm.alleles[i].sampledata[m.alleles[i].sampledata.length - 1][field] = value\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tconst isinteger = formatdesc.Type == 'Integer'\n\t\t\tconst isfloat = formatdesc.Type == 'Float'\n\n\t\t\tif ((formatdesc.Number && formatdesc.Number == 'R') || field == 'AD') {\n\t\t\t\t/*\n\t\t\t\tper-allele value, including ref\n\t\t\t\tv4.1 has AD not with \"R\", must process as R\n\t\t\t\t*/\n\t\t\t\tconst fvlst = value.split(',').map(i => {\n\t\t\t\t\tif (isinteger) return Number.parseInt(i)\n\t\t\t\t\tif (isfloat) return Number.parseFloat(i)\n\t\t\t\t\treturn i\n\t\t\t\t})\n\t\t\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\t\t\tif (fvlst[i] != undefined) {\n\t\t\t\t\t\t// this allele has value\n\t\t\t\t\t\tconst m2 = m.alleles[i]\n\t\t\t\t\t\tconst m2s = m2.sampledata[m2.sampledata.length - 1]\n\t\t\t\t\t\t// use this allele's ref/alt (after nt trimming)\n\t\t\t\t\t\tm2s[field] = {}\n\t\t\t\t\t\tm2s[field][m2.ref] = fvlst[0]\n\t\t\t\t\t\tm2s[field][m2.allele] = fvlst[i]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (formatdesc.Number && formatdesc.Number == 'A') {\n\t\t\t\t// per alt-allele value\n\t\t\t\tconst fvlst = value.split(',').map(i => {\n\t\t\t\t\tif (isinteger) return Number.parseInt(i)\n\t\t\t\t\tif (isfloat) return Number.parseFloat(i)\n\t\t\t\t\treturn i\n\t\t\t\t})\n\t\t\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\t\t\tif (fvlst[i - 1] != undefined) {\n\t\t\t\t\t\t// this allele has value\n\t\t\t\t\t\tconst m2 = m.alleles[i]\n\t\t\t\t\t\tconst m2s = m2.sampledata[m2.sampledata.length - 1]\n\t\t\t\t\t\t// use this allele's ref/alt (after nt trimming)\n\t\t\t\t\t\tm2s[field] = {}\n\t\t\t\t\t\tm2s[field][m2.allele] = fvlst[i - 1]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\t// otherwise, append this field to all alt\n\t\t\tfor (let i = 1; i < m.alleles.length; i++) {\n\t\t\t\tm.alleles[i].sampledata[m.alleles[i].sampledata.length - 1][field] = value\n\t\t\t}\n\t\t}\n\t}\n\n\t// compatible with old ds: make allele2readcount from AD\n\tfor (const a of m.alleles) {\n\t\tfor (const s of a.sampledata) {\n\t\t\tif (s.AD) {\n\t\t\t\ts.allele2readcount = {}\n\t\t\t\tfor (const k in s.AD) {\n\t\t\t\t\ts.allele2readcount[k] = s.AD[k]\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\nfunction tohash(s, hash) {\n\t/*\n\tparse INFO\n\t*/\n\tconst h: Record<string, any> = {},\n\t\terr: string[] = []\n\tlet prev = 0,\n\t\tprevdoublequote = false,\n\t\tk = null\n\tfor (let i = 0; i < s.length; i++) {\n\t\tif (s[i] == '\"') {\n\t\t\ti++\n\t\t\tconst thisstart = i\n\t\t\twhile (s[i] != '\"') {\n\t\t\t\ti++\n\t\t\t}\n\t\t\tif (k) {\n\t\t\t\th[k] = s.substring(thisstart, i)\n\t\t\t\tk = null\n\t\t\t} else {\n\t\t\t\terr.push('k undefined before double quotes')\n\t\t\t}\n\t\t\tprevdoublequote = true\n\t\t\tcontinue\n\t\t}\n\t\tif (s[i] == '=') {\n\t\t\tk = s.substring(prev, i)\n\t\t\tprev = i + 1\n\t\t\tcontinue\n\t\t}\n\t\tif (s[i] == ',') {\n\t\t\tif (prevdoublequote) {\n\t\t\t\tprevdoublequote = false\n\t\t\t} else {\n\t\t\t\tif (k) {\n\t\t\t\t\th[k] = s.substring(prev, i)\n\t\t\t\t\tk = null\n\t\t\t\t} else {\n\t\t\t\t\terr.push('k undefined')\n\t\t\t\t}\n\t\t\t}\n\t\t\tprev = i + 1\n\t\t\tcontinue\n\t\t}\n\t}\n\tif (k) {\n\t\th[k] = s.substring(prev)\n\t}\n\tif (h.ID) {\n\t\thash[h.ID] = h\n\t} else {\n\t\treturn 'no ID'\n\t}\n\tif (err.length) return err.join('\\n')\n}\n\nfunction parse_INFO(tmp, m, vcf) {\n\t/*\n\tthis function fills in both m.info{} and m.alleles[].info{}\n\n\tthe m.alleles[] will later be converted to [m], each carrying one alt allele\n\teach m will have .info{} for locus info, and .altinfo{} for alt allele info\n\n\t*/\n\n\tconst badinfokeys: string[] = []\n\n\tfor (const key in tmp) {\n\t\tif (vcf.info[key] == undefined) {\n\t\t\tbadinfokeys.push(key)\n\t\t\tcontinue\n\t\t}\n\n\t\tconst value = tmp[key]\n\n\t\t////////////////// hard-coded fields\n\n\t\tif (key == 'CSQ') {\n\t\t\tconst okay = parse_CSQ(value, vcf.info.CSQ.csqheader, m)\n\t\t\tif (!okay) {\n\t\t\t\tm.info[key] = value\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\t\tif (key == 'ANN') {\n\t\t\tconst okay = parse_ANN(value, vcf.info.ANN.annheader, m)\n\t\t\tif (!okay) {\n\t\t\t\tm.info[key] = value\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\n\t\t////////////////// end of hardcoded fields\n\n\t\tif (vcf.info[key].Type == 'Flag') {\n\t\t\t// flag has no value\n\t\t\tm.info[key] = key\n\t\t\tcontinue\n\t\t}\n\n\t\tconst __number = vcf.info[key].Number\n\t\tconst isinteger = vcf.info[key].Type == 'Integer'\n\t\tconst isfloat = vcf.info[key].Type == 'Float'\n\n\t\tif (__number == '0') {\n\t\t\t/*\n\t\t\tno value, should be a Flag\n\t\t\t*/\n\t\t\tm.info[key] = key\n\t\t\tcontinue\n\t\t}\n\n\t\tif (__number == 'A') {\n\t\t\t/*\n\t\t\tper alt allele\n\t\t\t*/\n\t\t\tconst tt = value.split(',')\n\t\t\tfor (let j = 0; j < tt.length; j++) {\n\t\t\t\tif (m.alleles[j]) {\n\t\t\t\t\tm.alleles[j].info[key] = isinteger ? Number.parseInt(tt[j]) : isfloat ? Number.parseFloat(tt[j]) : tt[j]\n\t\t\t\t}\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\n\t\tif (__number == 'R') {\n\t\t\t/*\n\t\t\tFIXME \"R\" is not considered, m.alleles only contain alt, which .info{} for each\n\t\t\tthe current datastructure does not support info for ref allele!\n\t\t\t*/\n\t\t}\n\n\t\tif (__number == '1') {\n\t\t\t/*\n\t\t\tsingle value\n\t\t\t*/\n\t\t\tm.info[key] = isinteger ? Number.parseInt(value) : isfloat ? Number.parseFloat(value) : value\n\t\t\tcontinue\n\t\t}\n\n\t\tif (!value.split) {\n\t\t\t// unknown error\n\t\t\tcontinue\n\t\t}\n\n\t\t// number of values unknown, \"commas are permitted only as delimiters for lists of values\"\n\n\t\tconst lst = value.split(',') // value is always array!!\n\t\tif (isinteger) {\n\t\t\tm.info[key] = lst.map(Number.parseInt)\n\t\t} else if (isfloat) {\n\t\t\tm.info[key] = lst.map(Number.parseFloat)\n\t\t} else {\n\t\t\tm.info[key] = lst\n\t\t}\n\t}\n\treturn badinfokeys\n}\n"],
+  "mappings": 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+  "names": ["tmp", "alt"]
 }

package/dist/src/vcf.type.d.ts

@@ -0,0 +1 @@
+export declare function getVariantType(ref: any, alt: any): "X" | "snv" | "mnv" | "insertion" | "deletion";

package/dist/src/vcf.type.js.map

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../src/vcf.type.js"],
+  "sources": ["../../src/vcf.type.ts"],
   "sourcesContent": ["import { mclassdeletion, mclasssnv, mclassmnv, mclassinsertion, mclassnonstandard } from './common.js'\n\nexport function getVariantType(ref, alt) {\n\tif (ref.length == 1 && alt.length == 1) {\n\t\t// both alleles length of 1\n\t\tif (alt == '.') {\n\t\t\t// alt is missing\n\t\t\treturn mclassdeletion\n\t\t}\n\t\t// snv\n\t\treturn mclasssnv\n\t}\n\tif (ref.length == alt.length) return mclassmnv\n\t// FIXME only when empty length of one allele\n\tif (ref.length < alt.length) return mclassinsertion\n\tif (ref.length > alt.length) return mclassdeletion\n\treturn mclassnonstandard\n}\n"],
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   "names": []

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.188.1",
+  "version": "2.189.0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "dist/src/index.js",