@gmod/vcf - npm Package Compare versions

Comparing version 7.0.4 to 7.0.5

dist/parse.d.ts

 import { Variant } from './Variant.ts';
+import type { MetaField, MetaMap } from './parseInfo.ts';
 export { Variant } from './Variant.ts';
-/**
- * Class representing a VCF parser, instantiated with the VCF header.
- *
- * @param {object} args
- *
- * @param {string} args.header - The VCF header. Supports both LF and CRLF
- * newlines.
- *
- * @param {boolean} args.strict - Whether to parse in strict mode or not
- * (default true)
- */
+type Metadata = Record<string, MetaMap | MetaField | string | undefined>;
 export default class VCFParser {
@@ -22,30 +13,7 @@ private metadata;
     });
-    /**
-     * Parse a VCF metadata line (i.e. a line that starts with "##") and add its
-     * properties to the object.
-     *
-     * @param {string} line - A line from the VCF. Supports both LF and CRLF
-     * newlines.
-     */
     private parseMetadata;
-    /**
-     * Get metadata filtered by the elements in args. For example, can pass
-     * ('INFO', 'DP') to only get info on an metadata tag that was like
-     * "##INFO=<ID=DP,...>"
-     *
-     * @param  {...string} args - List of metadata filter strings.
-     *
-     * @returns {any} An object, string, or number, depending on the filtering
-     */
-    getMetadata(...args: string[]): unknown;
-    /**
-     * Parse a VCF line into a Variant object.
-     *
-     * The returned Variant has SAMPLES() and GENOTYPES() methods which are
-     * lazily evaluated to avoid parsing the potentially long list of samples from
-     * e.g. 1000 genotypes data unless requested.
-     *
-     * @param {string} line - A string of a line from a VCF
-     */
+    getMetadata(): Metadata;
+    getMetadata(section: string): MetaMap | MetaField | string | undefined;
+    getMetadata(section: string, ...rest: string[]): unknown;
     parseLine(line: string): Variant;
 }

dist/parse.js

@@ -12,13 +12,2 @@ "use strict";
 Object.defineProperty(exports, "Variant", { enumerable: true, get: function () { return Variant_ts_2.Variant; } });
-/**
- * Class representing a VCF parser, instantiated with the VCF header.
- *
- * @param {object} args
- *
- * @param {string} args.header - The VCF header. Supports both LF and CRLF
- * newlines.
- *
- * @param {boolean} args.strict - Whether to parse in strict mode or not
- * (default true)
- */
 class VCFParser {
@@ -80,9 +69,2 @@ metadata;
     }
-    /**
-     * Parse a VCF metadata line (i.e. a line that starts with "##") and add its
-     * properties to the object.
-     *
-     * @param {string} line - A line from the VCF. Supports both LF and CRLF
-     * newlines.
-     */
     parseMetadata(line) {
@@ -96,15 +78,12 @@ const match = /^##(.+?)=(.*)/.exec(line.trim());
         if (metaVal?.startsWith('<')) {
-            if (!(r in this.metadata)) {
-                this.metadata[r] = {};
-            }
+            const existing = this.metadata[r];
+            const section = existing && typeof existing === 'object' ? existing : {};
             const [id, keyVals] = (0, parseMetaString_ts_1.parseStructuredMetaVal)(metaVal);
             if (typeof id === 'string') {
-                // if there is an ID field in the <> metadata
-                // e.g. ##INFO=<ID=AF_ESP,...>
-                ;
-                this.metadata[r][id] = keyVals;
+                // ##INFO=<ID=AF_ESP,...>
+                section[id] = keyVals;
+                this.metadata[r] = section;
             }
             else {
-                // if there is not an ID field in the <> metadata
-                // e.g. ##ID=<Description="ClinVar Variation ID">
+                // ##ID=<Description="ClinVar Variation ID">
                 this.metadata[r] = keyVals;
@@ -117,11 +96,2 @@ }
     }
-    /**
-     * Get metadata filtered by the elements in args. For example, can pass
-     * ('INFO', 'DP') to only get info on an metadata tag that was like
-     * "##INFO=<ID=DP,...>"
-     *
-     * @param  {...string} args - List of metadata filter strings.
-     *
-     * @returns {any} An object, string, or number, depending on the filtering
-     */
     getMetadata(...args) {
@@ -140,11 +110,3 @@ let filteredMetadata = this.metadata;
     }
-    /**
-     * Parse a VCF line into a Variant object.
-     *
-     * The returned Variant has SAMPLES() and GENOTYPES() methods which are
-     * lazily evaluated to avoid parsing the potentially long list of samples from
-     * e.g. 1000 genotypes data unless requested.
-     *
-     * @param {string} line - A string of a line from a VCF
-     */
+    // SAMPLES() and GENOTYPES() on the returned Variant are lazily evaluated.
     parseLine(line) {
@@ -151,0 +113,0 @@ return new Variant_ts_1.Variant(line, this.metadata.INFO, this.metadata.FORMAT, this.samples, this.strict);

dist/parse.js.map

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dist/parseGenotypesOnly.d.ts

@@ -1,4 +0,1 @@
-/**
- * Extracts genotype (GT) values from VCF sample data.
- */
 export declare function parseGenotypesOnly(format: string, prerest: string, samples: string[]): Record<string, string>;

dist/parseGenotypesOnly.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseGenotypesOnly = parseGenotypesOnly;
-/**
- * Extracts genotype (GT) values from VCF sample data.
- */
+const processGenotypes_ts_1 = require("./processGenotypes.js");
 function parseGenotypesOnly(format, prerest, samples) {
     const genotypes = Object.create(null);
-    const samplesLen = samples.length;
-    const prerestLen = prerest.length;
-    const TAB = 9;
-    const COLON = 58;
-    let pos = 0;
-    // Fast path: format is exactly "GT"
-    if (format === 'GT') {
-        for (let idx = 0; idx < samplesLen; idx++) {
-            const start = pos;
-            while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
-                pos++;
-            }
-            genotypes[samples[idx] ?? ''] = prerest.slice(start, pos);
-            pos++;
-        }
-        return genotypes;
-    }
-    // Check if GT field exists
-    const gtIdx = format.indexOf('GT');
-    if (gtIdx === -1) {
-        return genotypes;
-    }
-    // GT is first field but not only field
-    if (gtIdx === 0) {
-        for (let idx = 0; idx < samplesLen; idx++) {
-            const start = pos;
-            while (pos < prerestLen &&
-                prerest.charCodeAt(pos) !== COLON &&
-                prerest.charCodeAt(pos) !== TAB) {
-                pos++;
-            }
-            genotypes[samples[idx] ?? ''] = prerest.slice(start, pos);
-            while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
-                pos++;
-            }
-            pos++;
-        }
-        return genotypes;
-    }
-    // GT is not first field
-    let colonCount = 0;
-    for (let j = 0; j < gtIdx; j++) {
-        if (format.charCodeAt(j) === COLON) {
-            colonCount++;
-        }
-    }
-    for (let idx = 0; idx < samplesLen; idx++) {
-        const sampleStart = pos;
-        let tabIdx = pos;
-        while (tabIdx < prerestLen && prerest.charCodeAt(tabIdx) !== TAB) {
-            tabIdx++;
-        }
-        let colons = 0;
-        let fieldStart = sampleStart;
-        for (let j = sampleStart; j <= tabIdx; j++) {
-            if (j === tabIdx || prerest.charCodeAt(j) === COLON) {
-                if (colons === colonCount) {
-                    genotypes[samples[idx] ?? ''] = prerest.slice(fieldStart, j);
-                    break;
-                }
-                colons++;
-                fieldStart = j + 1;
-            }
-        }
-        pos = tabIdx + 1;
-    }
+    (0, processGenotypes_ts_1.processGenotypes)(format, prerest, samples.length, (str, start, end, idx) => {
+        genotypes[samples[idx] ?? ''] = str.slice(start, end);
+    });
     return genotypes;
 }
 //# sourceMappingURL=parseGenotypesOnly.js.map

dist/parseGenotypesOnly.js.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"parseGenotypesOnly.js","sourceRoot":"","sources":["../src/parseGenotypesOnly.ts"],"names":[],"mappings":";;AAEA,gDAUC;AAZD,+DAAwD;AAExD,SAAgB,kBAAkB,CAChC,MAAc,EACd,OAAe,EACf,OAAiB;IAEjB,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAA2B,CAAA;IAC/D,IAAA,sCAAgB,EAAC,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE;QACzE,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IACvD,CAAC,CAAC,CAAA;IACF,OAAO,SAAS,CAAA;AAClB,CAAC"}

dist/parseInfo.d.ts

@@ -1,3 +0,4 @@
-export declare function parseInfo(infoStr: string, infoMeta: Record<string, {
-    Type?: string;
-}>): Record<string, unknown>;
+export type MetaField = Record<string, string | string[] | number | null | undefined>;
+export type MetaMap = Record<string, MetaField>;
+export type InfoValue = true | (string | number | undefined)[];
+export declare function parseInfo(infoStr: string, infoMeta: MetaMap): Record<string, InfoValue>;

dist/parseInfo.js.map

@@ -1,1 +0,1 @@
-{"version":3,"file":"parseInfo.js","sourceRoot":"","sources":["../src/parseInfo.ts"],"names":[],"mappings":";;AAQA,8BAqCC;AA7CD,SAAS,yBAAyB,CAAC,GAAW;IAC5C,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,SAAgB,SAAS,CACvB,OAAe,EACf,QAA2C;IAE3C,MAAM,MAAM,GAA4B,EAAE,CAAA;IAC1C,MAAM,SAAS,GAAG,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;IACvC,MAAM,SAAS,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACpC,MAAM,QAAQ,GAAG,SAAS,CAAC,MAAM,CAAA;IAEjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,SAAS,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QAC/B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QAC/B,MAAM,GAAG,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAA;QACtD,MAAM,GAAG,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAC5D,MAAM,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,EAAE,IAAI,CAAA;QAEpC,IAAI,QAAQ,KAAK,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC;YAChC,MAAM,CAAC,GAAG,CAAC,GAAG,IAAI,CAAA;QACpB,CAAC;aAAM,CAAC;YACN,MAAM,QAAQ,GAAG,QAAQ,KAAK,SAAS,IAAI,QAAQ,KAAK,OAAO,CAAA;YAC/D,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;YAC/B,MAAM,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAA;YAEhC,MAAM,KAAK,GAAoC,EAAE,CAAA;YACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;gBAC3B,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACd,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;gBACvB,CAAC;qBAAM,CAAC;oBACN,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;oBACtD,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACtC,CAAC;YACH,CAAC;YACD,MAAM,CAAC,GAAG,CAAC,GAAG,KAAK,CAAA;QACrB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC"}
+{"version":3,"file":"parseInfo.js","sourceRoot":"","sources":["../src/parseInfo.ts"],"names":[],"mappings":";;AAiBA,8BAqCC;AA/CD,SAAS,yBAAyB,CAAC,GAAW;IAC5C,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAID,SAAgB,SAAS,CACvB,OAAe,EACf,QAAiB;IAEjB,MAAM,MAAM,GAA8B,EAAE,CAAA;IAC5C,MAAM,SAAS,GAAG,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;IACvC,MAAM,SAAS,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACpC,MAAM,QAAQ,GAAG,SAAS,CAAC,MAAM,CAAA;IAEjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,SAAS,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QAC/B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QAC/B,MAAM,GAAG,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAA;QACtD,MAAM,GAAG,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAC5D,MAAM,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,EAAE,IAAI,CAAA;QAEpC,IAAI,QAAQ,KAAK,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC;YAChC,MAAM,CAAC,GAAG,CAAC,GAAG,IAAI,CAAA;QACpB,CAAC;aAAM,CAAC;YACN,MAAM,QAAQ,GAAG,QAAQ,KAAK,SAAS,IAAI,QAAQ,KAAK,OAAO,CAAA;YAC/D,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;YAC/B,MAAM,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAA;YAEhC,MAAM,KAAK,GAAoC,EAAE,CAAA;YACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;gBAC3B,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACd,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;gBACvB,CAAC;qBAAM,CAAC;oBACN,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;oBACtD,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACtC,CAAC;YACH,CAAC;YACD,MAAM,CAAC,GAAG,CAAC,GAAG,KAAK,CAAA;QACrB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC"}

dist/parseMetaString.d.ts

 export declare function parseStructuredMetaVal(metaVal: string): readonly [string | number | string[] | undefined, Record<string, string | number | string[]>];
-export declare function parseMetaString(metaString: string): {
-    [k: string]: string | string[];
-};
+export declare function parseMetaString(metaString: string): Record<string, string | string[]>;

dist/parseMetaString.js

@@ -57,23 +57,20 @@ "use strict";
     const parts = customSplit(inside);
-    const entries = [];
+    const result = {};
     for (const f of parts) {
         const [key, val] = splitFirst(f, '=');
         if (val && val.startsWith('[') && val.endsWith(']')) {
-            entries.push([
-                key,
-                val
-                    .slice(1, -1)
-                    .split(',')
-                    .map(s => s.trim()),
-            ]);
+            result[key] = val
+                .slice(1, -1)
+                .split(',')
+                .map(s => s.trim());
         }
         else if (val && val.startsWith('"') && val.endsWith('"')) {
-            entries.push([key, val.slice(1, -1)]);
+            result[key] = val.slice(1, -1);
         }
         else {
-            entries.push([key, val]);
+            result[key] = val;
         }
     }
-    return Object.fromEntries(entries);
+    return result;
 }
 //# sourceMappingURL=parseMetaString.js.map

dist/parseMetaString.js.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"parseMetaString.js","sourceRoot":"","sources":["../src/parseMetaString.ts"],"names":[],"mappings":";;AAsCA,wDAYC;AAED,0CAkBC;AAtED,SAAS,WAAW,CAAC,GAAW;IAC9B,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,IAAI,QAAQ,GAAG,KAAK,CAAA;IACpB,IAAI,UAAU,GAAG,KAAK,CAAA;IACtB,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,CAAA;IAEzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAChC,MAAM,IAAI,GAAG,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACzB,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;YACjB,QAAQ,GAAG,CAAC,QAAQ,CAAA;YACpB,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;YACxB,UAAU,GAAG,IAAI,CAAA;YACjB,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;YACxB,UAAU,GAAG,KAAK,CAAA;YAClB,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,IAAI,IAAI,KAAK,GAAG,IAAI,CAAC,QAAQ,IAAI,CAAC,UAAU,EAAE,CAAC;YACpD,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;YAClC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAA;QAClB,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;IACH,CAAC;IAED,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACrB,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;IACpC,CAAC;IAED,OAAO,MAAM,CAAA;AACf,CAAC;AAED,SAAS,UAAU,CAAC,GAAW,EAAE,KAAa;IAC5C,MAAM,KAAK,GAAG,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAChC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,GAAG,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAU,CAAA;AAC7D,CAAC;AAED,SAAgB,sBAAsB,CAAC,OAAe;IACpD,MAAM,OAAO,GACX,eAAe,CAAC,OAAO,CAAC,CAAA;IAC1B,MAAM,EAAE,GAAG,OAAO,CAAC,EAAE,CAAA;IACrB,OAAO,OAAO,CAAC,EAAE,CAAA;IACjB,IAAI,QAAQ,IAAI,OAAO,EAAE,CAAC;QACxB,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;QAChC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;YACrB,OAAO,CAAC,MAAM,GAAG,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,CAAC,EAAE,EAAE,OAAO,CAAU,CAAA;AAC/B,CAAC;AAED,SAAgB,eAAe,CAAC,UAAkB;IAChD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACtC,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,CAAA;IACjC,MAAM,MAAM,GAAsC,EAAE,CAAA;IACpD,KAAK,MAAM,CAAC,IAAI,KAAK,EAAE,CAAC;QACtB,MAAM,CAAC,GAAG,EAAE,GAAG,CAAC,GAAG,UAAU,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;QACrC,IAAI,GAAG,IAAI,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;YACpD,MAAM,CAAC,GAAG,CAAC,GAAG,GAAG;iBACd,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;iBACZ,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;QACvB,CAAC;aAAM,IAAI,GAAG,IAAI,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;YAC3D,MAAM,CAAC,GAAG,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QAChC,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,GAAG,CAAC,GAAG,GAAG,CAAA;QACnB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC"}

dist/Variant.d.ts

@@ -0,2 +1,6 @@
+import type { InfoValue, MetaMap } from './parseInfo.ts';
 import type { GenotypeCallback } from './processGenotypes.ts';
+export type SampleValue = (string | number | undefined)[] | undefined;
+export type SampleData = Record<string, SampleValue>;
+export type Samples = Record<string, SampleData>;
 export declare class Variant {
@@ -10,3 +14,3 @@ CHROM: string | undefined;
     FILTER: string | string[] | undefined;
-    INFO: Record<string, unknown>;
+    INFO: Record<string, InfoValue>;
     FORMAT: string | undefined;
@@ -16,8 +20,4 @@ private formatMeta;
     private sampleNames;
-    constructor(line: string, infoMeta: Record<string, {
-        Type?: string;
-    }>, formatMeta: Record<string, {
-        Type?: string;
-    }>, sampleNames: string[], strict: boolean);
-    SAMPLES(): Record<string, Record<string, (string | number | undefined)[] | undefined>>;
+    constructor(line: string, infoMeta: MetaMap, formatMeta: MetaMap, sampleNames: string[], strict: boolean);
+    SAMPLES(): Samples;
     GENOTYPES(): Record<string, string>;
@@ -33,5 +33,5 @@ processGenotypes(callback: GenotypeCallback): void;
         FILTER: string | string[] | undefined;
-        INFO: Record<string, unknown>;
+        INFO: Record<string, InfoValue>;
         FORMAT: string | undefined;
     };
 }

dist/Variant.js

@@ -75,5 +75,6 @@ "use strict";
                     if (j === sampleStrLen || sampleStr[j] === ':') {
+                        const key = formatKeys[colIdx] ?? '';
                         const val = sampleStr.slice(colStart, j);
                         if (val === '' || val === '.') {
-                            sampleData[formatKeys[colIdx] ?? ''] = undefined;
+                            sampleData[key] = undefined;
                         }
@@ -89,3 +90,3 @@ else {
                             }
-                            sampleData[formatKeys[colIdx] ?? ''] = result;
+                            sampleData[key] = result;
                         }
@@ -92,0 +93,0 @@ colStart = j + 1;

dist/Variant.js.map

@@ -1,1 +0,1 @@
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esm/parse.d.ts

 import { Variant } from './Variant.ts';
+import type { MetaField, MetaMap } from './parseInfo.ts';
 export { Variant } from './Variant.ts';
-/**
- * Class representing a VCF parser, instantiated with the VCF header.
- *
- * @param {object} args
- *
- * @param {string} args.header - The VCF header. Supports both LF and CRLF
- * newlines.
- *
- * @param {boolean} args.strict - Whether to parse in strict mode or not
- * (default true)
- */
+type Metadata = Record<string, MetaMap | MetaField | string | undefined>;
 export default class VCFParser {
@@ -22,30 +13,7 @@ private metadata;
     });
-    /**
-     * Parse a VCF metadata line (i.e. a line that starts with "##") and add its
-     * properties to the object.
-     *
-     * @param {string} line - A line from the VCF. Supports both LF and CRLF
-     * newlines.
-     */
     private parseMetadata;
-    /**
-     * Get metadata filtered by the elements in args. For example, can pass
-     * ('INFO', 'DP') to only get info on an metadata tag that was like
-     * "##INFO=<ID=DP,...>"
-     *
-     * @param  {...string} args - List of metadata filter strings.
-     *
-     * @returns {any} An object, string, or number, depending on the filtering
-     */
-    getMetadata(...args: string[]): unknown;
-    /**
-     * Parse a VCF line into a Variant object.
-     *
-     * The returned Variant has SAMPLES() and GENOTYPES() methods which are
-     * lazily evaluated to avoid parsing the potentially long list of samples from
-     * e.g. 1000 genotypes data unless requested.
-     *
-     * @param {string} line - A string of a line from a VCF
-     */
+    getMetadata(): Metadata;
+    getMetadata(section: string): MetaMap | MetaField | string | undefined;
+    getMetadata(section: string, ...rest: string[]): unknown;
     parseLine(line: string): Variant;
 }

esm/parse.js

@@ -5,13 +5,2 @@ import { Variant } from "./Variant.js";
 export { Variant } from "./Variant.js";
-/**
- * Class representing a VCF parser, instantiated with the VCF header.
- *
- * @param {object} args
- *
- * @param {string} args.header - The VCF header. Supports both LF and CRLF
- * newlines.
- *
- * @param {boolean} args.strict - Whether to parse in strict mode or not
- * (default true)
- */
 export default class VCFParser {
@@ -73,9 +62,2 @@ metadata;
     }
-    /**
-     * Parse a VCF metadata line (i.e. a line that starts with "##") and add its
-     * properties to the object.
-     *
-     * @param {string} line - A line from the VCF. Supports both LF and CRLF
-     * newlines.
-     */
     parseMetadata(line) {
@@ -89,15 +71,12 @@ const match = /^##(.+?)=(.*)/.exec(line.trim());
         if (metaVal?.startsWith('<')) {
-            if (!(r in this.metadata)) {
-                this.metadata[r] = {};
-            }
+            const existing = this.metadata[r];
+            const section = existing && typeof existing === 'object' ? existing : {};
             const [id, keyVals] = parseStructuredMetaVal(metaVal);
             if (typeof id === 'string') {
-                // if there is an ID field in the <> metadata
-                // e.g. ##INFO=<ID=AF_ESP,...>
-                ;
-                this.metadata[r][id] = keyVals;
+                // ##INFO=<ID=AF_ESP,...>
+                section[id] = keyVals;
+                this.metadata[r] = section;
             }
             else {
-                // if there is not an ID field in the <> metadata
-                // e.g. ##ID=<Description="ClinVar Variation ID">
+                // ##ID=<Description="ClinVar Variation ID">
                 this.metadata[r] = keyVals;
@@ -110,11 +89,2 @@ }
     }
-    /**
-     * Get metadata filtered by the elements in args. For example, can pass
-     * ('INFO', 'DP') to only get info on an metadata tag that was like
-     * "##INFO=<ID=DP,...>"
-     *
-     * @param  {...string} args - List of metadata filter strings.
-     *
-     * @returns {any} An object, string, or number, depending on the filtering
-     */
     getMetadata(...args) {
@@ -133,11 +103,3 @@ let filteredMetadata = this.metadata;
     }
-    /**
-     * Parse a VCF line into a Variant object.
-     *
-     * The returned Variant has SAMPLES() and GENOTYPES() methods which are
-     * lazily evaluated to avoid parsing the potentially long list of samples from
-     * e.g. 1000 genotypes data unless requested.
-     *
-     * @param {string} line - A string of a line from a VCF
-     */
+    // SAMPLES() and GENOTYPES() on the returned Variant are lazily evaluated.
     parseLine(line) {
@@ -144,0 +106,0 @@ return new Variant(line, this.metadata.INFO, this.metadata.FORMAT, this.samples, this.strict);

esm/parse.js.map

@@ -1,1 +0,1 @@
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esm/parseGenotypesOnly.d.ts

@@ -1,4 +0,1 @@
-/**
- * Extracts genotype (GT) values from VCF sample data.
- */
 export declare function parseGenotypesOnly(format: string, prerest: string, samples: string[]): Record<string, string>;

esm/parseGenotypesOnly.js

@@ -1,74 +0,9 @@
-/**
- * Extracts genotype (GT) values from VCF sample data.
- */
+import { processGenotypes } from "./processGenotypes.js";
 export function parseGenotypesOnly(format, prerest, samples) {
     const genotypes = Object.create(null);
-    const samplesLen = samples.length;
-    const prerestLen = prerest.length;
-    const TAB = 9;
-    const COLON = 58;
-    let pos = 0;
-    // Fast path: format is exactly "GT"
-    if (format === 'GT') {
-        for (let idx = 0; idx < samplesLen; idx++) {
-            const start = pos;
-            while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
-                pos++;
-            }
-            genotypes[samples[idx] ?? ''] = prerest.slice(start, pos);
-            pos++;
-        }
-        return genotypes;
-    }
-    // Check if GT field exists
-    const gtIdx = format.indexOf('GT');
-    if (gtIdx === -1) {
-        return genotypes;
-    }
-    // GT is first field but not only field
-    if (gtIdx === 0) {
-        for (let idx = 0; idx < samplesLen; idx++) {
-            const start = pos;
-            while (pos < prerestLen &&
-                prerest.charCodeAt(pos) !== COLON &&
-                prerest.charCodeAt(pos) !== TAB) {
-                pos++;
-            }
-            genotypes[samples[idx] ?? ''] = prerest.slice(start, pos);
-            while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
-                pos++;
-            }
-            pos++;
-        }
-        return genotypes;
-    }
-    // GT is not first field
-    let colonCount = 0;
-    for (let j = 0; j < gtIdx; j++) {
-        if (format.charCodeAt(j) === COLON) {
-            colonCount++;
-        }
-    }
-    for (let idx = 0; idx < samplesLen; idx++) {
-        const sampleStart = pos;
-        let tabIdx = pos;
-        while (tabIdx < prerestLen && prerest.charCodeAt(tabIdx) !== TAB) {
-            tabIdx++;
-        }
-        let colons = 0;
-        let fieldStart = sampleStart;
-        for (let j = sampleStart; j <= tabIdx; j++) {
-            if (j === tabIdx || prerest.charCodeAt(j) === COLON) {
-                if (colons === colonCount) {
-                    genotypes[samples[idx] ?? ''] = prerest.slice(fieldStart, j);
-                    break;
-                }
-                colons++;
-                fieldStart = j + 1;
-            }
-        }
-        pos = tabIdx + 1;
-    }
+    processGenotypes(format, prerest, samples.length, (str, start, end, idx) => {
+        genotypes[samples[idx] ?? ''] = str.slice(start, end);
+    });
     return genotypes;
 }
 //# sourceMappingURL=parseGenotypesOnly.js.map

esm/parseGenotypesOnly.js.map

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esm/parseInfo.d.ts

@@ -1,3 +0,4 @@
-export declare function parseInfo(infoStr: string, infoMeta: Record<string, {
-    Type?: string;
-}>): Record<string, unknown>;
+export type MetaField = Record<string, string | string[] | number | null | undefined>;
+export type MetaMap = Record<string, MetaField>;
+export type InfoValue = true | (string | number | undefined)[];
+export declare function parseInfo(infoStr: string, infoMeta: MetaMap): Record<string, InfoValue>;

esm/parseInfo.js.map

@@ -1,1 +0,1 @@
-{"version":3,"file":"parseInfo.js","sourceRoot":"","sources":["../src/parseInfo.ts"],"names":[],"mappings":"AAAA,SAAS,yBAAyB,CAAC,GAAW;IAC5C,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,MAAM,UAAU,SAAS,CACvB,OAAe,EACf,QAA2C;IAE3C,MAAM,MAAM,GAA4B,EAAE,CAAA;IAC1C,MAAM,SAAS,GAAG,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;IACvC,MAAM,SAAS,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACpC,MAAM,QAAQ,GAAG,SAAS,CAAC,MAAM,CAAA;IAEjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,SAAS,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QAC/B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QAC/B,MAAM,GAAG,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAA;QACtD,MAAM,GAAG,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAC5D,MAAM,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,EAAE,IAAI,CAAA;QAEpC,IAAI,QAAQ,KAAK,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC;YAChC,MAAM,CAAC,GAAG,CAAC,GAAG,IAAI,CAAA;QACpB,CAAC;aAAM,CAAC;YACN,MAAM,QAAQ,GAAG,QAAQ,KAAK,SAAS,IAAI,QAAQ,KAAK,OAAO,CAAA;YAC/D,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;YAC/B,MAAM,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAA;YAEhC,MAAM,KAAK,GAAoC,EAAE,CAAA;YACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;gBAC3B,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACd,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;gBACvB,CAAC;qBAAM,CAAC;oBACN,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;oBACtD,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACtC,CAAC;YACH,CAAC;YACD,MAAM,CAAC,GAAG,CAAC,GAAG,KAAK,CAAA;QACrB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC"}
+{"version":3,"file":"parseInfo.js","sourceRoot":"","sources":["../src/parseInfo.ts"],"names":[],"mappings":"AAOA,SAAS,yBAAyB,CAAC,GAAW;IAC5C,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAID,MAAM,UAAU,SAAS,CACvB,OAAe,EACf,QAAiB;IAEjB,MAAM,MAAM,GAA8B,EAAE,CAAA;IAC5C,MAAM,SAAS,GAAG,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;IACvC,MAAM,SAAS,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACpC,MAAM,QAAQ,GAAG,SAAS,CAAC,MAAM,CAAA;IAEjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,SAAS,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QAC/B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QAC/B,MAAM,GAAG,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAA;QACtD,MAAM,GAAG,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAC5D,MAAM,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,EAAE,IAAI,CAAA;QAEpC,IAAI,QAAQ,KAAK,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC;YAChC,MAAM,CAAC,GAAG,CAAC,GAAG,IAAI,CAAA;QACpB,CAAC;aAAM,CAAC;YACN,MAAM,QAAQ,GAAG,QAAQ,KAAK,SAAS,IAAI,QAAQ,KAAK,OAAO,CAAA;YAC/D,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;YAC/B,MAAM,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAA;YAEhC,MAAM,KAAK,GAAoC,EAAE,CAAA;YACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;gBAC3B,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACd,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;gBACvB,CAAC;qBAAM,CAAC;oBACN,MAAM,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;oBACtD,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACtC,CAAC;YACH,CAAC;YACD,MAAM,CAAC,GAAG,CAAC,GAAG,KAAK,CAAA;QACrB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC"}

esm/parseMetaString.d.ts

 export declare function parseStructuredMetaVal(metaVal: string): readonly [string | number | string[] | undefined, Record<string, string | number | string[]>];
-export declare function parseMetaString(metaString: string): {
-    [k: string]: string | string[];
-};
+export declare function parseMetaString(metaString: string): Record<string, string | string[]>;

esm/parseMetaString.js

@@ -53,23 +53,20 @@ function customSplit(str) {
     const parts = customSplit(inside);
-    const entries = [];
+    const result = {};
     for (const f of parts) {
         const [key, val] = splitFirst(f, '=');
         if (val && val.startsWith('[') && val.endsWith(']')) {
-            entries.push([
-                key,
-                val
-                    .slice(1, -1)
-                    .split(',')
-                    .map(s => s.trim()),
-            ]);
+            result[key] = val
+                .slice(1, -1)
+                .split(',')
+                .map(s => s.trim());
         }
         else if (val && val.startsWith('"') && val.endsWith('"')) {
-            entries.push([key, val.slice(1, -1)]);
+            result[key] = val.slice(1, -1);
         }
         else {
-            entries.push([key, val]);
+            result[key] = val;
         }
     }
-    return Object.fromEntries(entries);
+    return result;
 }
 //# sourceMappingURL=parseMetaString.js.map

esm/parseMetaString.js.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"parseMetaString.js","sourceRoot":"","sources":["../src/parseMetaString.ts"],"names":[],"mappings":"AAAA,SAAS,WAAW,CAAC,GAAW;IAC9B,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,IAAI,QAAQ,GAAG,KAAK,CAAA;IACpB,IAAI,UAAU,GAAG,KAAK,CAAA;IACtB,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,CAAA;IAEzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAChC,MAAM,IAAI,GAAG,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACzB,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;YACjB,QAAQ,GAAG,CAAC,QAAQ,CAAA;YACpB,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;YACxB,UAAU,GAAG,IAAI,CAAA;YACjB,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;YACxB,UAAU,GAAG,KAAK,CAAA;YAClB,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,IAAI,IAAI,KAAK,GAAG,IAAI,CAAC,QAAQ,IAAI,CAAC,UAAU,EAAE,CAAC;YACpD,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;YAClC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAA;QAClB,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;IACH,CAAC;IAED,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACrB,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;IACpC,CAAC;IAED,OAAO,MAAM,CAAA;AACf,CAAC;AAED,SAAS,UAAU,CAAC,GAAW,EAAE,KAAa;IAC5C,MAAM,KAAK,GAAG,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAChC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,GAAG,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAU,CAAA;AAC7D,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,OAAe;IACpD,MAAM,OAAO,GACX,eAAe,CAAC,OAAO,CAAC,CAAA;IAC1B,MAAM,EAAE,GAAG,OAAO,CAAC,EAAE,CAAA;IACrB,OAAO,OAAO,CAAC,EAAE,CAAA;IACjB,IAAI,QAAQ,IAAI,OAAO,EAAE,CAAC;QACxB,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;QAChC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;YACrB,OAAO,CAAC,MAAM,GAAG,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,CAAC,EAAE,EAAE,OAAO,CAAU,CAAA;AAC/B,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,UAAkB;IAChD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACtC,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,CAAA;IACjC,MAAM,MAAM,GAAsC,EAAE,CAAA;IACpD,KAAK,MAAM,CAAC,IAAI,KAAK,EAAE,CAAC;QACtB,MAAM,CAAC,GAAG,EAAE,GAAG,CAAC,GAAG,UAAU,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;QACrC,IAAI,GAAG,IAAI,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;YACpD,MAAM,CAAC,GAAG,CAAC,GAAG,GAAG;iBACd,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;iBACZ,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;QACvB,CAAC;aAAM,IAAI,GAAG,IAAI,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;YAC3D,MAAM,CAAC,GAAG,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QAChC,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,GAAG,CAAC,GAAG,GAAG,CAAA;QACnB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC"}

esm/Variant.d.ts

@@ -0,2 +1,6 @@
+import type { InfoValue, MetaMap } from './parseInfo.ts';
 import type { GenotypeCallback } from './processGenotypes.ts';
+export type SampleValue = (string | number | undefined)[] | undefined;
+export type SampleData = Record<string, SampleValue>;
+export type Samples = Record<string, SampleData>;
 export declare class Variant {
@@ -10,3 +14,3 @@ CHROM: string | undefined;
     FILTER: string | string[] | undefined;
-    INFO: Record<string, unknown>;
+    INFO: Record<string, InfoValue>;
     FORMAT: string | undefined;
@@ -16,8 +20,4 @@ private formatMeta;
     private sampleNames;
-    constructor(line: string, infoMeta: Record<string, {
-        Type?: string;
-    }>, formatMeta: Record<string, {
-        Type?: string;
-    }>, sampleNames: string[], strict: boolean);
-    SAMPLES(): Record<string, Record<string, (string | number | undefined)[] | undefined>>;
+    constructor(line: string, infoMeta: MetaMap, formatMeta: MetaMap, sampleNames: string[], strict: boolean);
+    SAMPLES(): Samples;
     GENOTYPES(): Record<string, string>;
@@ -33,5 +33,5 @@ processGenotypes(callback: GenotypeCallback): void;
         FILTER: string | string[] | undefined;
-        INFO: Record<string, unknown>;
+        INFO: Record<string, InfoValue>;
         FORMAT: string | undefined;
     };
 }

esm/Variant.js

@@ -72,5 +72,6 @@ import { parseGenotypesOnly } from "./parseGenotypesOnly.js";
                     if (j === sampleStrLen || sampleStr[j] === ':') {
+                        const key = formatKeys[colIdx] ?? '';
                         const val = sampleStr.slice(colStart, j);
                         if (val === '' || val === '.') {
-                            sampleData[formatKeys[colIdx] ?? ''] = undefined;
+                            sampleData[key] = undefined;
                         }
@@ -86,3 +87,3 @@ else {
                             }
-                            sampleData[formatKeys[colIdx] ?? ''] = result;
+                            sampleData[key] = result;
                         }
@@ -89,0 +90,0 @@ colStart = j + 1;

esm/Variant.js.map

@@ -1,1 +0,1 @@
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package.json

 {
   "name": "@gmod/vcf",
-  "version": "7.0.4",
+  "version": "7.0.5",
   "description": "High performance streaming Variant Call Format (VCF) parser in pure JavaScript",
@@ -5,0 +5,0 @@ "type": "module",

README.md

@@ -62,3 +62,3 @@ # vcf-js
 let homRef = 0
-variant.processGenotypes((str, start, end) => {
+variant.processGenotypes((str, start, end, sampleIdx) => {
   if (
@@ -65,0 +65,0 @@ end - start === 3 && // e.g. "0|0"

src/parse.ts

@@ -5,17 +5,10 @@ import { Variant } from './Variant.ts'
 
+import type { MetaField, MetaMap } from './parseInfo.ts'
+
 export { Variant } from './Variant.ts'
 
-/**
- * Class representing a VCF parser, instantiated with the VCF header.
- *
- * @param {object} args
- *
- * @param {string} args.header - The VCF header. Supports both LF and CRLF
- * newlines.
- *
- * @param {boolean} args.strict - Whether to parse in strict mode or not
- * (default true)
- */
+type Metadata = Record<string, MetaMap | MetaField | string | undefined>
+
 export default class VCFParser {
-  private metadata: Record<string, unknown>
+  private metadata: Metadata
   public strict: boolean
@@ -79,9 +72,2 @@ public samples: string[]
 
-  /**
-   * Parse a VCF metadata line (i.e. a line that starts with "##") and add its
-   * properties to the object.
-   *
-   * @param {string} line - A line from the VCF. Supports both LF and CRLF
-   * newlines.
-   */
   private parseMetadata(line: string) {
@@ -95,13 +81,12 @@ const match = /^##(.+?)=(.*)/.exec(line.trim())
     if (metaVal?.startsWith('<')) {
-      if (!(r in this.metadata)) {
-        this.metadata[r] = {}
-      }
+      const existing = this.metadata[r]
+      const section: MetaMap =
+        existing && typeof existing === 'object' ? (existing as MetaMap) : {}
       const [id, keyVals] = parseStructuredMetaVal(metaVal)
       if (typeof id === 'string') {
-        // if there is an ID field in the <> metadata
-        // e.g. ##INFO=<ID=AF_ESP,...>
-        ;(this.metadata[r] as Record<string, unknown>)[id] = keyVals
+        // ##INFO=<ID=AF_ESP,...>
+        section[id] = keyVals
+        this.metadata[r] = section
       } else {
-        // if there is not an ID field in the <> metadata
-        // e.g. ##ID=<Description="ClinVar Variation ID">
+        // ##ID=<Description="ClinVar Variation ID">
         this.metadata[r] = keyVals
@@ -114,12 +99,6 @@ }
 
-  /**
-   * Get metadata filtered by the elements in args. For example, can pass
-   * ('INFO', 'DP') to only get info on an metadata tag that was like
-   * "##INFO=<ID=DP,...>"
-   *
-   * @param  {...string} args - List of metadata filter strings.
-   *
-   * @returns {any} An object, string, or number, depending on the filtering
-   */
-  getMetadata(...args: string[]) {
+  getMetadata(): Metadata
+  getMetadata(section: string): MetaMap | MetaField | string | undefined
+  getMetadata(section: string, ...rest: string[]): unknown
+  getMetadata(...args: string[]): unknown {
     let filteredMetadata: unknown = this.metadata
@@ -138,16 +117,8 @@ for (const arg of args) {
 
-  /**
-   * Parse a VCF line into a Variant object.
-   *
-   * The returned Variant has SAMPLES() and GENOTYPES() methods which are
-   * lazily evaluated to avoid parsing the potentially long list of samples from
-   * e.g. 1000 genotypes data unless requested.
-   *
-   * @param {string} line - A string of a line from a VCF
-   */
+  // SAMPLES() and GENOTYPES() on the returned Variant are lazily evaluated.
   parseLine(line: string) {
     return new Variant(
       line,
-      this.metadata.INFO as Record<string, { Type?: string }>,
-      this.metadata.FORMAT as Record<string, { Type?: string }>,
+      this.metadata.INFO as MetaMap,
+      this.metadata.FORMAT as MetaMap,
       this.samples,
@@ -154,0 +125,0 @@ this.strict,

src/parseGenotypesOnly.ts

@@ -1,4 +0,3 @@
-/**
- * Extracts genotype (GT) values from VCF sample data.
- */
+import { processGenotypes } from './processGenotypes.ts'
+
 export function parseGenotypesOnly(
@@ -10,78 +9,6 @@ format: string,
   const genotypes = Object.create(null) as Record<string, string>
-
-  const samplesLen = samples.length
-  const prerestLen = prerest.length
-  const TAB = 9
-  const COLON = 58
-  let pos = 0
-
-  // Fast path: format is exactly "GT"
-  if (format === 'GT') {
-    for (let idx = 0; idx < samplesLen; idx++) {
-      const start = pos
-      while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
-        pos++
-      }
-      genotypes[samples[idx] ?? ''] = prerest.slice(start, pos)
-      pos++
-    }
-    return genotypes
-  }
-
-  // Check if GT field exists
-  const gtIdx = format.indexOf('GT')
-  if (gtIdx === -1) {
-    return genotypes
-  }
-
-  // GT is first field but not only field
-  if (gtIdx === 0) {
-    for (let idx = 0; idx < samplesLen; idx++) {
-      const start = pos
-      while (
-        pos < prerestLen &&
-        prerest.charCodeAt(pos) !== COLON &&
-        prerest.charCodeAt(pos) !== TAB
-      ) {
-        pos++
-      }
-      genotypes[samples[idx] ?? ''] = prerest.slice(start, pos)
-      while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
-        pos++
-      }
-      pos++
-    }
-    return genotypes
-  }
-
-  // GT is not first field
-  let colonCount = 0
-  for (let j = 0; j < gtIdx; j++) {
-    if (format.charCodeAt(j) === COLON) {
-      colonCount++
-    }
-  }
-  for (let idx = 0; idx < samplesLen; idx++) {
-    const sampleStart = pos
-    let tabIdx = pos
-    while (tabIdx < prerestLen && prerest.charCodeAt(tabIdx) !== TAB) {
-      tabIdx++
-    }
-
-    let colons = 0
-    let fieldStart = sampleStart
-    for (let j = sampleStart; j <= tabIdx; j++) {
-      if (j === tabIdx || prerest.charCodeAt(j) === COLON) {
-        if (colons === colonCount) {
-          genotypes[samples[idx] ?? ''] = prerest.slice(fieldStart, j)
-          break
-        }
-        colons++
-        fieldStart = j + 1
-      }
-    }
-    pos = tabIdx + 1
-  }
-
+  processGenotypes(format, prerest, samples.length, (str, start, end, idx) => {
+    genotypes[samples[idx] ?? ''] = str.slice(start, end)
+  })
   return genotypes
 }

src/parseInfo.ts

@@ -0,1 +1,8 @@
+export type MetaField = Record<
+  string,
+  string | string[] | number | null | undefined
+>
+
+export type MetaMap = Record<string, MetaField>
+
 function decodeURIComponentNoThrow(uri: string) {
@@ -9,7 +16,9 @@ try {
 
+export type InfoValue = true | (string | number | undefined)[]
+
 export function parseInfo(
   infoStr: string,
-  infoMeta: Record<string, { Type?: string }>,
-) {
-  const result: Record<string, unknown> = {}
+  infoMeta: MetaMap,
+): Record<string, InfoValue> {
+  const result: Record<string, InfoValue> = {}
   const hasDecode = infoStr.includes('%')
@@ -16,0 +25,0 @@ const infoPairs = infoStr.split(';')

src/parseMetaString.ts

@@ -56,20 +56,17 @@ function customSplit(str: string) {
   const parts = customSplit(inside)
-  const entries: [string, string | string[]][] = []
+  const result: Record<string, string | string[]> = {}
   for (const f of parts) {
     const [key, val] = splitFirst(f, '=')
     if (val && val.startsWith('[') && val.endsWith(']')) {
-      entries.push([
-        key,
-        val
-          .slice(1, -1)
-          .split(',')
-          .map(s => s.trim()),
-      ])
+      result[key] = val
+        .slice(1, -1)
+        .split(',')
+        .map(s => s.trim())
     } else if (val && val.startsWith('"') && val.endsWith('"')) {
-      entries.push([key, val.slice(1, -1)])
+      result[key] = val.slice(1, -1)
     } else {
-      entries.push([key, val])
+      result[key] = val
     }
   }
-  return Object.fromEntries(entries)
+  return result
 }

src/Variant.ts

@@ -5,4 +5,9 @@ import { parseGenotypesOnly } from './parseGenotypesOnly.ts'
 
+import type { InfoValue, MetaMap } from './parseInfo.ts'
 import type { GenotypeCallback } from './processGenotypes.ts'
 
+export type SampleValue = (string | number | undefined)[] | undefined
+export type SampleData = Record<string, SampleValue>
+export type Samples = Record<string, SampleData>
+
 export class Variant {
@@ -16,6 +21,6 @@ CHROM: string | undefined
   FILTER: string | string[] | undefined
-  INFO: Record<string, unknown>
+  INFO: Record<string, InfoValue>
   FORMAT: string | undefined
 
-  private formatMeta: Record<string, { Type?: string }>
+  private formatMeta: MetaMap
   private rest: string
@@ -26,4 +31,4 @@ private sampleNames: string[]
     line: string,
-    infoMeta: Record<string, { Type?: string }>,
-    formatMeta: Record<string, { Type?: string }>,
+    infoMeta: MetaMap,
+    formatMeta: MetaMap,
     sampleNames: string[],
@@ -71,7 +76,4 @@ strict: boolean,
 
-  SAMPLES() {
-    const genotypes = {} as Record<
-      string,
-      Record<string, (string | number | undefined)[] | undefined>
-    >
+  SAMPLES(): Samples {
+    const genotypes: Samples = {}
     const format = this.FORMAT
@@ -89,6 +91,3 @@ if (format) {
         const sample = this.sampleNames[i] ?? ''
-        const sampleData: Record<
-          string,
-          (string | number | undefined)[] | undefined
-        > = {}
+        const sampleData: SampleData = {}
         const sampleStr = rest[i] ?? ''
@@ -101,5 +100,6 @@ const sampleStrLen = sampleStr.length
           if (j === sampleStrLen || sampleStr[j] === ':') {
+            const key = formatKeys[colIdx] ?? ''
             const val = sampleStr.slice(colStart, j)
             if (val === '' || val === '.') {
-              sampleData[formatKeys[colIdx] ?? ''] = undefined
+              sampleData[key] = undefined
             } else {
@@ -114,3 +114,3 @@ const items = val.split(',')
               }
-              sampleData[formatKeys[colIdx] ?? ''] = result
+              sampleData[key] = result
             }
@@ -117,0 +117,0 @@ colStart = j + 1

No alert changes

Worsened metrics

Total package byte prevSize

162304

-8.35%

Lines of code

3496

-9.76%

No dependency changes