@gmod/vcf - npm Package Compare versions

Comparing version 7.0.0 to 7.0.1

dist/parse.d.ts

@@ -49,3 +49,3 @@ import { Variant } from './Variant.ts';
      */
-    getMetadata(...args: string[]): any;
+    getMetadata(...args: string[]): unknown;
     /**
@@ -52,0 +52,0 @@ * Parse a VCF line into a Variant object.

dist/parse.js

@@ -41,3 +41,3 @@ "use strict";
         for (let i = 0; i < headerLines.length; i++) {
-            const line = headerLines[i];
+            const line = headerLines[i] ?? '';
             if (!line.startsWith('#')) {
@@ -89,4 +89,4 @@ throw new Error(`Bad line in header:\n${line}`);
         }
-        const [metaKey, metaVal] = match.slice(1, 3);
-        const r = metaKey;
+        const r = match[1] ?? '';
+        const metaVal = match[2];
         if (metaVal?.startsWith('<')) {
@@ -97,3 +97,3 @@ if (!(r in this.metadata)) {
             const [id, keyVals] = this.parseStructuredMetaVal(metaVal);
-            if (id) {
+            if (typeof id === 'string') {
                 // if there is an ID field in the <> metadata
@@ -147,3 +147,6 @@ // e.g. ##INFO=<ID=AF_ESP,...>
         for (let i = 0; i < argsLen; i++) {
-            filteredMetadata = filteredMetadata[args[i]];
+            if (typeof filteredMetadata !== 'object' || filteredMetadata === null) {
+                return undefined;
+            }
+            filteredMetadata = filteredMetadata[args[i] ?? ''];
             if (!filteredMetadata) {
@@ -150,0 +153,0 @@ return filteredMetadata;

dist/parse.js.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"parse.js","sourceRoot":"","sources":["../src/parse.ts"],"names":[],"mappings":";;;;;;AAAA,6CAAsC;AACtC,6DAAsD;AACtD,sEAA0C;AAE1C,2CAAsC;AAA7B,qGAAA,OAAO,OAAA;AAEhB;;;;;;;;;;GAUG;AACH,MAAqB,SAAS;IAK5B,YAAY,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI,EAAwC;QACzE,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC;YACnB,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAA;QAC1C,CAAC;QACD,MAAM,WAAW,GAAG,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;QAC3D,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;QACxD,CAAC;QAED,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;QACpB,IAAI,CAAC,QAAQ,GAAG;YACd,IAAI,EAAE,EAAE,GAAG,wBAAW,CAAC,UAAU,EAAE;YACnC,MAAM,EAAE,EAAE,GAAG,wBAAW,CAAC,cAAc,EAAE;YACzC,GAAG,EAAE,EAAE,GAAG,wBAAW,CAAC,QAAQ,EAAE;YAChC,MAAM,EAAE,EAAE,GAAG,wBAAW,CAAC,WAAW,EAAE;SACvC,CAAA;QAED,IAAI,QAA4B,CAAA;QAChC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5C,MAAM,IAAI,GAAG,WAAW,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;YACjC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC1B,MAAM,IAAI,KAAK,CAAC,wBAAwB,IAAI,EAAE,CAAC,CAAA;YACjD,CAAC;iBAAM,IAAI,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;gBACjC,IAAI,CAAC,aAAa,CAAC,IAAI,CAAC,CAAA;YAC1B,CAAC;iBAAM,CAAC;gBACN,QAAQ,GAAG,IAAI,CAAA;YACjB,CAAC;QACH,CAAC;QAED,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAA;QACnD,CAAC;QACD,MAAM,MAAM,GAAG,QAAQ,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1C,MAAM,UAAU,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACrC,MAAM,aAAa,GAAG;YACpB,QAAQ;YACR,KAAK;YACL,IAAI;YACJ,KAAK;YACL,KAAK;YACL,MAAM;YACN,QAAQ;YACR,MAAM;SACP,CAAA;QACD,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACtB,MAAM,IAAI,KAAK,CAAC,gCAAgC,QAAQ,EAAE,CAAC,CAAA;QAC7D,CAAC;aAAM,IACL,UAAU,CAAC,MAAM,KAAK,aAAa,CAAC,MAAM;YAC1C,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,KAAK,aAAa,CAAC,KAAK,CAAC,CAAC,EACnE,CAAC;YACD,MAAM,IAAI,KAAK,CAAC,oCAAoC,QAAQ,EAAE,CAAC,CAAA;QACjE,CAAC;QACD,IAAI,CAAC,OAAO,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IAChC,CAAC;IAED;;;;;;OAMG;IACK,aAAa,CAAC,IAAY;QAChC,MAAM,KAAK,GAAG,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,CAAA;QAC/C,IAAI,CAAC,KAAK,EAAE,CAAC;YACX,MAAM,IAAI,KAAK,CAAC,sCAAsC,IAAI,EAAE,CAAC,CAAA;QAC/D,CAAC;QACD,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACxB,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;QACxB,IAAI,OAAO,EAAE,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC7B,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC;gBAC1B,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;YACvB,CAAC;YACD,MAAM,CAAC,EAAE,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC,sBAAsB,CAAC,OAAO,CAAC,CAAA;YAC1D,IAAI,OAAO,EAAE,KAAK,QAAQ,EAAE,CAAC;gBAC3B,6CAA6C;gBAC7C,8BAA8B;gBAC9B,CAAC;gBAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAA6B,CAAC,EAAE,CAAC,GAAG,OAAO,CAAA;YAC9D,CAAC;iBAAM,CAAC;gBACN,iDAAiD;gBACjD,iDAAiD;gBACjD,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,OAAO,CAAA;YAC5B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,OAAO,CAAA;QAC5B,CAAC;IACH,CAAC;IAED;;;;;;;;OAQG;IACK,sBAAsB,CAAC,OAAe;QAC5C,MAAM,OAAO,GACX,IAAA,oCAAe,EAAC,OAAO,CAAC,CAAA;QAC1B,MAAM,EAAE,GAAG,OAAO,CAAC,EAAE,CAAA;QACrB,OAAO,OAAO,CAAC,EAAE,CAAA;QACjB,IAAI,QAAQ,IAAI,OAAO,EAAE,CAAC;YACxB,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC;gBAC1C,OAAO,CAAC,MAAM,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YACzC,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,EAAE,OAAO,CAAU,CAAA;IAC/B,CAAC;IAED;;;;;;;;OAQG;IACH,WAAW,CAAC,GAAG,IAAc;QAC3B,IAAI,gBAAgB,GAAY,IAAI,CAAC,QAAQ,CAAA;QAC7C,MAAM,OAAO,GAAG,IAAI,CAAC,MAAM,CAAA;QAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE,CAAC;YACjC,IAAI,OAAO,gBAAgB,KAAK,QAAQ,IAAI,gBAAgB,KAAK,IAAI,EAAE,CAAC;gBACtE,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,gBAAgB,GAAI,gBAA4C,CAC9D,IAAI,CAAC,CAAC,CAAC,IAAI,EAAE,CACd,CAAA;YACD,IAAI,CAAC,gBAAgB,EAAE,CAAC;gBACtB,OAAO,gBAAgB,CAAA;YACzB,CAAC;QACH,CAAC;QACD,OAAO,gBAAgB,CAAA;IACzB,CAAC;IAED;;;;;;;;OAQG;IACH,SAAS,CAAC,IAAY;QACpB,OAAO,IAAI,oBAAO,CAChB,IAAI,EACJ,IAAI,CAAC,QAAQ,CAAC,IAAyC,EACvD,IAAI,CAAC,QAAQ,CAAC,MAA2C,EACzD,IAAI,CAAC,OAAO,EACZ,IAAI,CAAC,MAAM,CACZ,CAAA;IACH,CAAC;CACF;AA/JD,4BA+JC"}

dist/parseBreakend.js

@@ -18,5 +18,3 @@ "use strict";
         let MatePosition;
-        const tokensLen = tokens.length;
-        for (let i = 0; i < tokensLen; i++) {
-            const tok = tokens[i];
+        for (const tok of tokens) {
             if (tok) {
@@ -62,3 +60,3 @@ if (tok.includes(':')) {
                 MateDirection: 'right',
-                MatePosition: `<${res[1]}>:1`,
+                MatePosition: `<${res[1] ?? ''}>:1`,
             }
@@ -78,3 +76,3 @@ : undefined;
                 MateDirection: 'right',
-                MatePosition: `<${res[2]}>:1`,
+                MatePosition: `<${res[2] ?? ''}>:1`,
             }
@@ -81,0 +79,0 @@ : undefined;

dist/parseBreakend.js.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"parseBreakend.js","sourceRoot":"","sources":["../src/parseBreakend.ts"],"names":[],"mappings":";;AAWA,sCAgFC;AAnFD,MAAM,yBAAyB,GAAG,YAAY,CAAA;AAC9C,MAAM,uBAAuB,GAAG,YAAY,CAAA;AAE5C,SAAgB,aAAa,CAAC,cAAsB;IAClD,MAAM,SAAS,GAAG,cAAc,CAAC,CAAC,CAAC,CAAA;IACnC,MAAM,QAAQ,GAAG,cAAc,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IAE1D,IACE,SAAS,KAAK,GAAG;QACjB,SAAS,KAAK,GAAG;QACjB,QAAQ,KAAK,GAAG;QAChB,QAAQ,KAAK,GAAG,EAChB,CAAC;QACD,MAAM,MAAM,GAAG,cAAc,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;QAC5C,MAAM,aAAa,GAAG,cAAc,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;QACrE,IAAI,IAAI,CAAA;QACR,IAAI,WAAW,CAAA;QACf,IAAI,YAAY,CAAA;QAChB,KAAK,MAAM,GAAG,IAAI,MAAM,EAAE,CAAC;YACzB,IAAI,GAAG,EAAE,CAAC;gBACR,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBACtB,YAAY,GAAG,GAAG,CAAA;oBAClB,IAAI,GAAG,WAAW,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;gBACvC,CAAC;qBAAM,CAAC;oBACN,WAAW,GAAG,GAAG,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,CAAC,YAAY,IAAI,IAAI,IAAI,WAAW,CAAC,EAAE,CAAC;YAC3C,MAAM,IAAI,KAAK,CAAC,qBAAqB,cAAc,EAAE,CAAC,CAAA;QACxD,CAAC;QACD,OAAO,EAAE,YAAY,EAAE,IAAI,EAAE,WAAW,EAAE,aAAa,EAAE,CAAA;IAC3D,CAAC;IAED,IAAI,SAAS,KAAK,GAAG,EAAE,CAAC;QACtB,OAAO;YACL,IAAI,EAAE,MAAM;YACZ,cAAc,EAAE,IAAI;YACpB,WAAW,EAAE,cAAc,CAAC,KAAK,CAAC,CAAC,CAAC;SACrC,CAAA;IACH,CAAC;IAED,IAAI,QAAQ,KAAK,GAAG,EAAE,CAAC;QACrB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,cAAc,EAAE,IAAI;YACpB,WAAW,EAAE,cAAc,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;SACzC,CAAA;IACH,CAAC;IAED,IAAI,SAAS,KAAK,GAAG,EAAE,CAAC;QACtB,MAAM,GAAG,GAAG,yBAAyB,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;QAC1D,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,IAAI,KAAK,CAAC,mBAAmB,cAAc,EAAE,CAAC,CAAA;QACtD,CAAC;QACD,MAAM,WAAW,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QAC1B,OAAO,WAAW;YAChB,CAAC,CAAC;gBACE,IAAI,EAAE,MAAM;gBACZ,WAAW;gBACX,aAAa,EAAE,OAAO;gBACtB,YAAY,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK;aACpC;YACH,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,IAAI,cAAc,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;QACjC,MAAM,GAAG,GAAG,uBAAuB,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;QACxD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,IAAI,KAAK,CAAC,mBAAmB,cAAc,EAAE,CAAC,CAAA;QACtD,CAAC;QACD,MAAM,WAAW,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QAC1B,OAAO,WAAW;YAChB,CAAC,CAAC;gBACE,IAAI,EAAE,OAAO;gBACb,WAAW;gBACX,aAAa,EAAE,OAAO;gBACtB,YAAY,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK;aACpC;YACH,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,OAAO,SAAS,CAAA;AAClB,CAAC"}

dist/parseGenotypesOnly.js

@@ -21,3 +21,3 @@ "use strict";
             }
-            genotypes[samples[idx]] = prerest.slice(start, pos);
+            genotypes[samples[idx] ?? ''] = prerest.slice(start, pos);
             pos++;
@@ -41,3 +41,3 @@ }
             }
-            genotypes[samples[idx]] = prerest.slice(start, pos);
+            genotypes[samples[idx] ?? ''] = prerest.slice(start, pos);
             while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
@@ -68,3 +68,3 @@ pos++;
                 if (colons === colonCount) {
-                    genotypes[samples[idx]] = prerest.slice(fieldStart, j);
+                    genotypes[samples[idx] ?? ''] = prerest.slice(fieldStart, j);
                     break;
@@ -71,0 +71,0 @@ }

dist/parseGenotypesOnly.js.map

@@ -1,1 +0,1 @@
-{"version":3,"file":"parseGenotypesOnly.js","sourceRoot":"","sources":["../src/parseGenotypesOnly.ts"],"names":[],"mappings":";;AAGA,gDAkFC;AArFD;;GAEG;AACH,SAAgB,kBAAkB,CAChC,MAAc,EACd,OAAe,EACf,OAAiB;IAEjB,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAA2B,CAAA;IAE/D,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAA;IACjC,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAA;IACjC,MAAM,GAAG,GAAG,CAAC,CAAA;IACb,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,IAAI,GAAG,GAAG,CAAC,CAAA;IAEX,oCAAoC;IACpC,IAAI,MAAM,KAAK,IAAI,EAAE,CAAC;QACpB,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;YAC1C,MAAM,KAAK,GAAG,GAAG,CAAA;YACjB,OAAO,GAAG,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAAE,CAAC;gBAC3D,GAAG,EAAE,CAAA;YACP,CAAC;YACD,SAAS,CAAC,OAAO,CAAC,GAAG,CAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACpD,GAAG,EAAE,CAAA;QACP,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,2BAA2B;IAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;IAClC,IAAI,KAAK,KAAK,CAAC,CAAC,EAAE,CAAC;QACjB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,uCAAuC;IACvC,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;QAChB,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;YAC1C,MAAM,KAAK,GAAG,GAAG,CAAA;YACjB,OACE,GAAG,GAAG,UAAU;gBAChB,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,KAAK;gBACjC,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAC/B,CAAC;gBACD,GAAG,EAAE,CAAA;YACP,CAAC;YACD,SAAS,CAAC,OAAO,CAAC,GAAG,CAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACpD,OAAO,GAAG,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAAE,CAAC;gBAC3D,GAAG,EAAE,CAAA;YACP,CAAC;YACD,GAAG,EAAE,CAAA;QACP,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,wBAAwB;IACxB,IAAI,UAAU,GAAG,CAAC,CAAA;IAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;QAC/B,IAAI,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,EAAE,CAAC;YACnC,UAAU,EAAE,CAAA;QACd,CAAC;IACH,CAAC;IACD,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;QAC1C,MAAM,WAAW,GAAG,GAAG,CAAA;QACvB,IAAI,MAAM,GAAG,GAAG,CAAA;QAChB,OAAO,MAAM,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,MAAM,CAAC,KAAK,GAAG,EAAE,CAAC;YACjE,MAAM,EAAE,CAAA;QACV,CAAC;QAED,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,IAAI,UAAU,GAAG,WAAW,CAAA;QAC5B,KAAK,IAAI,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3C,IAAI,CAAC,KAAK,MAAM,IAAI,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,EAAE,CAAC;gBACpD,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;oBAC1B,SAAS,CAAC,OAAO,CAAC,GAAG,CAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;oBACvD,MAAK;gBACP,CAAC;gBACD,MAAM,EAAE,CAAA;gBACR,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;YACpB,CAAC;QACH,CAAC;QACD,GAAG,GAAG,MAAM,GAAG,CAAC,CAAA;IAClB,CAAC;IAED,OAAO,SAAS,CAAA;AAClB,CAAC"}
+{"version":3,"file":"parseGenotypesOnly.js","sourceRoot":"","sources":["../src/parseGenotypesOnly.ts"],"names":[],"mappings":";;AAGA,gDAkFC;AArFD;;GAEG;AACH,SAAgB,kBAAkB,CAChC,MAAc,EACd,OAAe,EACf,OAAiB;IAEjB,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAA2B,CAAA;IAE/D,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAA;IACjC,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAA;IACjC,MAAM,GAAG,GAAG,CAAC,CAAA;IACb,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,IAAI,GAAG,GAAG,CAAC,CAAA;IAEX,oCAAoC;IACpC,IAAI,MAAM,KAAK,IAAI,EAAE,CAAC;QACpB,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;YAC1C,MAAM,KAAK,GAAG,GAAG,CAAA;YACjB,OAAO,GAAG,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAAE,CAAC;gBAC3D,GAAG,EAAE,CAAA;YACP,CAAC;YACD,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACzD,GAAG,EAAE,CAAA;QACP,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,2BAA2B;IAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;IAClC,IAAI,KAAK,KAAK,CAAC,CAAC,EAAE,CAAC;QACjB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,uCAAuC;IACvC,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;QAChB,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;YAC1C,MAAM,KAAK,GAAG,GAAG,CAAA;YACjB,OACE,GAAG,GAAG,UAAU;gBAChB,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,KAAK;gBACjC,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAC/B,CAAC;gBACD,GAAG,EAAE,CAAA;YACP,CAAC;YACD,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACzD,OAAO,GAAG,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAAE,CAAC;gBAC3D,GAAG,EAAE,CAAA;YACP,CAAC;YACD,GAAG,EAAE,CAAA;QACP,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,wBAAwB;IACxB,IAAI,UAAU,GAAG,CAAC,CAAA;IAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;QAC/B,IAAI,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,EAAE,CAAC;YACnC,UAAU,EAAE,CAAA;QACd,CAAC;IACH,CAAC;IACD,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;QAC1C,MAAM,WAAW,GAAG,GAAG,CAAA;QACvB,IAAI,MAAM,GAAG,GAAG,CAAA;QAChB,OAAO,MAAM,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,MAAM,CAAC,KAAK,GAAG,EAAE,CAAC;YACjE,MAAM,EAAE,CAAA;QACV,CAAC;QAED,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,IAAI,UAAU,GAAG,WAAW,CAAA;QAC5B,KAAK,IAAI,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3C,IAAI,CAAC,KAAK,MAAM,IAAI,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,EAAE,CAAC;gBACpD,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;oBAC1B,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;oBAC5D,MAAK;gBACP,CAAC;gBACD,MAAM,EAAE,CAAA;gBACR,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;YACpB,CAAC;QACH,CAAC;QACD,GAAG,GAAG,MAAM,GAAG,CAAC,CAAA;IAClB,CAAC;IAED,OAAO,SAAS,CAAA;AAClB,CAAC"}

dist/parseMetaString.d.ts

 export declare function parseMetaString(metaString: string): {
-    [k: string]: any;
+    [k: string]: string | string[];
 };

dist/parseMetaString.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseMetaString = parseMetaString;
-// constructed with the assistance of claude AI
-//
-// I first prompted it with a regex that splits a comma separated string with
-// awareness of quotation from this stackoverflow question
-// https://stackoverflow.com/a/18893443/2129219, and asked it to add support
-// for square brackets
-//
-// it undid the regex into serial logic and the result was this function
 function customSplit(str) {
@@ -19,3 +11,3 @@ const result = [];
     for (let i = 0; i < strLen; i++) {
-        const char = str[i];
+        const char = str[i] ?? '';
         if (char === '"') {
@@ -54,11 +46,12 @@ inQuotes = !inQuotes;
     const entries = [];
-    for (let i = 0; i < parts.length; i++) {
-        const f = parts[i];
+    for (const f of parts) {
         const [key, val] = splitFirst(f, '=');
         if (val && val.startsWith('[') && val.endsWith(']')) {
-            const items = val.slice(1, -1).split(',');
-            for (let j = 0; j < items.length; j++) {
-                items[j] = items[j].trim();
-            }
-            entries.push([key, items]);
+            entries.push([
+                key,
+                val
+                    .slice(1, -1)
+                    .split(',')
+                    .map(s => s.trim()),
+            ]);
         }
@@ -65,0 +58,0 @@ else if (val && val.startsWith('"') && val.endsWith('"')) {

dist/parseMetaString.js.map

@@ -1,1 +0,1 @@
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dist/processGenotypes.d.ts

@@ -5,3 +5,3 @@ /**
  */
-export type GenotypeCallback = (str: string, start: number, end: number) => any;
+export type GenotypeCallback = (str: string, start: number, end: number) => unknown;
 /**
@@ -8,0 +8,0 @@ * Process genotypes by calling a callback for each one, avoiding intermediate

dist/processGenotypes.js.map

@@ -1,1 +0,1 @@
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dist/Variant.js

@@ -29,3 +29,3 @@ "use strict";
         const [CHROM, POS, ID, REF, ALT, QUAL, FILTER] = fields;
-        const filter = FILTER === '.' ? undefined : FILTER.split(';');
+        const filter = FILTER === '.' ? undefined : FILTER?.split(';');
         if (strict && !fields[7]) {
@@ -35,7 +35,8 @@ throw new Error("no INFO field specified, must contain at least a '.' (turn off strict mode to allow)");
         this.CHROM = CHROM;
-        this.POS = +POS;
-        this.ID = ID === '.' ? undefined : ID.split(';');
+        this.POS = POS !== undefined ? +POS : 0;
+        this.ID = ID === '.' ? undefined : ID?.split(';');
         this.REF = REF;
-        this.ALT = ALT === '.' ? undefined : ALT.split(',');
-        this.QUAL = QUAL === '.' ? undefined : +QUAL;
+        this.ALT = ALT === '.' ? undefined : ALT?.split(',');
+        this.QUAL =
+            QUAL === '.' ? undefined : QUAL !== undefined ? +QUAL : undefined;
         this.FILTER = filter?.length === 1 && filter[0] === 'PASS' ? 'PASS' : filter;
@@ -57,3 +58,3 @@ this.INFO =
         for (let i = 0; i < pairsLen; i++) {
-            const pair = infoPairs[i];
+            const pair = infoPairs[i] ?? '';
             const eqIdx = pair.indexOf('=');
@@ -73,29 +74,14 @@ const key = eqIdx === -1 ? pair : pair.slice(0, eqIdx);
                 const itemsLen = rawItems.length;
-                if (hasDecode) {
-                    const items = [];
-                    for (let j = 0; j < itemsLen; j++) {
-                        const v = rawItems[j];
-                        if (v === '.') {
-                            items.push(undefined);
-                        }
-                        else {
-                            const decoded = decodeURIComponentNoThrow(v);
-                            items.push(isNumber ? Number(decoded) : decoded);
-                        }
+                const items = [];
+                for (let j = 0; j < itemsLen; j++) {
+                    const v = rawItems[j] ?? '';
+                    if (v === '.') {
+                        items.push(undefined);
                     }
-                    result[key] = items;
-                }
-                else {
-                    const items = [];
-                    for (let j = 0; j < itemsLen; j++) {
-                        const v = rawItems[j];
-                        if (v === '.') {
-                            items.push(undefined);
-                        }
-                        else {
-                            items.push(isNumber ? Number(v) : v);
-                        }
+                    else {
+                        const w = hasDecode ? decodeURIComponentNoThrow(v) : v;
+                        items.push(isNumber ? Number(w) : w);
                     }
-                    result[key] = items;
                 }
+                result[key] = items;
             }
@@ -113,3 +99,3 @@ }
             for (let i = 0; i < formatKeys.length; i++) {
-                const r = this.formatMeta[formatKeys[i]]?.Type;
+                const r = this.formatMeta[formatKeys[i] ?? '']?.Type;
                 isNumberType.push(r === 'Integer' || r === 'Float');
@@ -120,5 +106,5 @@ }
             for (let i = 0; i < samplesLen; i++) {
-                const sample = this.sampleNames[i];
+                const sample = this.sampleNames[i] ?? '';
                 const sampleData = {};
-                const sampleStr = rest[i];
+                const sampleStr = rest[i] ?? '';
                 const sampleStrLen = sampleStr.length;
@@ -131,3 +117,3 @@ let colStart = 0;
                         if (val === '' || val === '.') {
-                            sampleData[formatKeys[colIdx]] = undefined;
+                            sampleData[formatKeys[colIdx] ?? ''] = undefined;
                         }
@@ -139,3 +125,3 @@ else {
                                 for (let k = 0; k < items.length; k++) {
-                                    const ent = items[k];
+                                    const ent = items[k] ?? '';
                                     result.push(ent === '.' ? undefined : +ent);
@@ -146,7 +132,7 @@ }
                                 for (let k = 0; k < items.length; k++) {
-                                    const ent = items[k];
+                                    const ent = items[k] ?? '';
                                     result.push(ent === '.' ? undefined : ent);
                                 }
                             }
-                            sampleData[formatKeys[colIdx]] = result;
+                            sampleData[formatKeys[colIdx] ?? ''] = result;
                         }
@@ -153,0 +139,0 @@ colStart = j + 1;

dist/Variant.js.map

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

@@ -49,3 +49,3 @@ import { Variant } from './Variant.ts';
      */
-    getMetadata(...args: string[]): any;
+    getMetadata(...args: string[]): unknown;
     /**
@@ -52,0 +52,0 @@ * Parse a VCF line into a Variant object.

esm/parse.js

@@ -34,3 +34,3 @@ import { Variant } from "./Variant.js";
         for (let i = 0; i < headerLines.length; i++) {
-            const line = headerLines[i];
+            const line = headerLines[i] ?? '';
             if (!line.startsWith('#')) {
@@ -82,4 +82,4 @@ throw new Error(`Bad line in header:\n${line}`);
         }
-        const [metaKey, metaVal] = match.slice(1, 3);
-        const r = metaKey;
+        const r = match[1] ?? '';
+        const metaVal = match[2];
         if (metaVal?.startsWith('<')) {
@@ -90,3 +90,3 @@ if (!(r in this.metadata)) {
             const [id, keyVals] = this.parseStructuredMetaVal(metaVal);
-            if (id) {
+            if (typeof id === 'string') {
                 // if there is an ID field in the <> metadata
@@ -140,3 +140,6 @@ // e.g. ##INFO=<ID=AF_ESP,...>
         for (let i = 0; i < argsLen; i++) {
-            filteredMetadata = filteredMetadata[args[i]];
+            if (typeof filteredMetadata !== 'object' || filteredMetadata === null) {
+                return undefined;
+            }
+            filteredMetadata = filteredMetadata[args[i] ?? ''];
             if (!filteredMetadata) {
@@ -143,0 +146,0 @@ return filteredMetadata;

esm/parse.js.map

@@ -1,1 +0,1 @@
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esm/parseBreakend.js

@@ -15,5 +15,3 @@ const ANGLE_BRACKET_START_REGEX = /<(.*)>(.*)/;
         let MatePosition;
-        const tokensLen = tokens.length;
-        for (let i = 0; i < tokensLen; i++) {
-            const tok = tokens[i];
+        for (const tok of tokens) {
             if (tok) {
@@ -59,3 +57,3 @@ if (tok.includes(':')) {
                 MateDirection: 'right',
-                MatePosition: `<${res[1]}>:1`,
+                MatePosition: `<${res[1] ?? ''}>:1`,
             }
@@ -75,3 +73,3 @@ : undefined;
                 MateDirection: 'right',
-                MatePosition: `<${res[2]}>:1`,
+                MatePosition: `<${res[2] ?? ''}>:1`,
             }
@@ -78,0 +76,0 @@ : undefined;

esm/parseBreakend.js.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"parseBreakend.js","sourceRoot":"","sources":["../src/parseBreakend.ts"],"names":[],"mappings":"AAQA,MAAM,yBAAyB,GAAG,YAAY,CAAA;AAC9C,MAAM,uBAAuB,GAAG,YAAY,CAAA;AAE5C,MAAM,UAAU,aAAa,CAAC,cAAsB;IAClD,MAAM,SAAS,GAAG,cAAc,CAAC,CAAC,CAAC,CAAA;IACnC,MAAM,QAAQ,GAAG,cAAc,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IAE1D,IACE,SAAS,KAAK,GAAG;QACjB,SAAS,KAAK,GAAG;QACjB,QAAQ,KAAK,GAAG;QAChB,QAAQ,KAAK,GAAG,EAChB,CAAC;QACD,MAAM,MAAM,GAAG,cAAc,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;QAC5C,MAAM,aAAa,GAAG,cAAc,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;QACrE,IAAI,IAAI,CAAA;QACR,IAAI,WAAW,CAAA;QACf,IAAI,YAAY,CAAA;QAChB,KAAK,MAAM,GAAG,IAAI,MAAM,EAAE,CAAC;YACzB,IAAI,GAAG,EAAE,CAAC;gBACR,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBACtB,YAAY,GAAG,GAAG,CAAA;oBAClB,IAAI,GAAG,WAAW,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAA;gBACvC,CAAC;qBAAM,CAAC;oBACN,WAAW,GAAG,GAAG,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,CAAC,YAAY,IAAI,IAAI,IAAI,WAAW,CAAC,EAAE,CAAC;YAC3C,MAAM,IAAI,KAAK,CAAC,qBAAqB,cAAc,EAAE,CAAC,CAAA;QACxD,CAAC;QACD,OAAO,EAAE,YAAY,EAAE,IAAI,EAAE,WAAW,EAAE,aAAa,EAAE,CAAA;IAC3D,CAAC;IAED,IAAI,SAAS,KAAK,GAAG,EAAE,CAAC;QACtB,OAAO;YACL,IAAI,EAAE,MAAM;YACZ,cAAc,EAAE,IAAI;YACpB,WAAW,EAAE,cAAc,CAAC,KAAK,CAAC,CAAC,CAAC;SACrC,CAAA;IACH,CAAC;IAED,IAAI,QAAQ,KAAK,GAAG,EAAE,CAAC;QACrB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,cAAc,EAAE,IAAI;YACpB,WAAW,EAAE,cAAc,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;SACzC,CAAA;IACH,CAAC;IAED,IAAI,SAAS,KAAK,GAAG,EAAE,CAAC;QACtB,MAAM,GAAG,GAAG,yBAAyB,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;QAC1D,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,IAAI,KAAK,CAAC,mBAAmB,cAAc,EAAE,CAAC,CAAA;QACtD,CAAC;QACD,MAAM,WAAW,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QAC1B,OAAO,WAAW;YAChB,CAAC,CAAC;gBACE,IAAI,EAAE,MAAM;gBACZ,WAAW;gBACX,aAAa,EAAE,OAAO;gBACtB,YAAY,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK;aACpC;YACH,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,IAAI,cAAc,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;QACjC,MAAM,GAAG,GAAG,uBAAuB,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;QACxD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,IAAI,KAAK,CAAC,mBAAmB,cAAc,EAAE,CAAC,CAAA;QACtD,CAAC;QACD,MAAM,WAAW,GAAG,GAAG,CAAC,CAAC,CAAC,CAAA;QAC1B,OAAO,WAAW;YAChB,CAAC,CAAC;gBACE,IAAI,EAAE,OAAO;gBACb,WAAW;gBACX,aAAa,EAAE,OAAO;gBACtB,YAAY,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK;aACpC;YACH,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,OAAO,SAAS,CAAA;AAClB,CAAC"}

esm/parseGenotypesOnly.js

@@ -18,3 +18,3 @@ /**
             }
-            genotypes[samples[idx]] = prerest.slice(start, pos);
+            genotypes[samples[idx] ?? ''] = prerest.slice(start, pos);
             pos++;
@@ -38,3 +38,3 @@ }
             }
-            genotypes[samples[idx]] = prerest.slice(start, pos);
+            genotypes[samples[idx] ?? ''] = prerest.slice(start, pos);
             while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
@@ -65,3 +65,3 @@ pos++;
                 if (colons === colonCount) {
-                    genotypes[samples[idx]] = prerest.slice(fieldStart, j);
+                    genotypes[samples[idx] ?? ''] = prerest.slice(fieldStart, j);
                     break;
@@ -68,0 +68,0 @@ }

esm/parseGenotypesOnly.js.map

@@ -1,1 +0,1 @@
-{"version":3,"file":"parseGenotypesOnly.js","sourceRoot":"","sources":["../src/parseGenotypesOnly.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,MAAM,UAAU,kBAAkB,CAChC,MAAc,EACd,OAAe,EACf,OAAiB;IAEjB,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAA2B,CAAA;IAE/D,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAA;IACjC,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAA;IACjC,MAAM,GAAG,GAAG,CAAC,CAAA;IACb,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,IAAI,GAAG,GAAG,CAAC,CAAA;IAEX,oCAAoC;IACpC,IAAI,MAAM,KAAK,IAAI,EAAE,CAAC;QACpB,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;YAC1C,MAAM,KAAK,GAAG,GAAG,CAAA;YACjB,OAAO,GAAG,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAAE,CAAC;gBAC3D,GAAG,EAAE,CAAA;YACP,CAAC;YACD,SAAS,CAAC,OAAO,CAAC,GAAG,CAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACpD,GAAG,EAAE,CAAA;QACP,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,2BAA2B;IAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;IAClC,IAAI,KAAK,KAAK,CAAC,CAAC,EAAE,CAAC;QACjB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,uCAAuC;IACvC,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;QAChB,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;YAC1C,MAAM,KAAK,GAAG,GAAG,CAAA;YACjB,OACE,GAAG,GAAG,UAAU;gBAChB,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,KAAK;gBACjC,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAC/B,CAAC;gBACD,GAAG,EAAE,CAAA;YACP,CAAC;YACD,SAAS,CAAC,OAAO,CAAC,GAAG,CAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACpD,OAAO,GAAG,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAAE,CAAC;gBAC3D,GAAG,EAAE,CAAA;YACP,CAAC;YACD,GAAG,EAAE,CAAA;QACP,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,wBAAwB;IACxB,IAAI,UAAU,GAAG,CAAC,CAAA;IAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;QAC/B,IAAI,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,EAAE,CAAC;YACnC,UAAU,EAAE,CAAA;QACd,CAAC;IACH,CAAC;IACD,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;QAC1C,MAAM,WAAW,GAAG,GAAG,CAAA;QACvB,IAAI,MAAM,GAAG,GAAG,CAAA;QAChB,OAAO,MAAM,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,MAAM,CAAC,KAAK,GAAG,EAAE,CAAC;YACjE,MAAM,EAAE,CAAA;QACV,CAAC;QAED,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,IAAI,UAAU,GAAG,WAAW,CAAA;QAC5B,KAAK,IAAI,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3C,IAAI,CAAC,KAAK,MAAM,IAAI,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,EAAE,CAAC;gBACpD,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;oBAC1B,SAAS,CAAC,OAAO,CAAC,GAAG,CAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;oBACvD,MAAK;gBACP,CAAC;gBACD,MAAM,EAAE,CAAA;gBACR,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;YACpB,CAAC;QACH,CAAC;QACD,GAAG,GAAG,MAAM,GAAG,CAAC,CAAA;IAClB,CAAC;IAED,OAAO,SAAS,CAAA;AAClB,CAAC"}
+{"version":3,"file":"parseGenotypesOnly.js","sourceRoot":"","sources":["../src/parseGenotypesOnly.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,MAAM,UAAU,kBAAkB,CAChC,MAAc,EACd,OAAe,EACf,OAAiB;IAEjB,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAA2B,CAAA;IAE/D,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAA;IACjC,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAA;IACjC,MAAM,GAAG,GAAG,CAAC,CAAA;IACb,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,IAAI,GAAG,GAAG,CAAC,CAAA;IAEX,oCAAoC;IACpC,IAAI,MAAM,KAAK,IAAI,EAAE,CAAC;QACpB,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;YAC1C,MAAM,KAAK,GAAG,GAAG,CAAA;YACjB,OAAO,GAAG,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAAE,CAAC;gBAC3D,GAAG,EAAE,CAAA;YACP,CAAC;YACD,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACzD,GAAG,EAAE,CAAA;QACP,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,2BAA2B;IAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;IAClC,IAAI,KAAK,KAAK,CAAC,CAAC,EAAE,CAAC;QACjB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,uCAAuC;IACvC,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;QAChB,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;YAC1C,MAAM,KAAK,GAAG,GAAG,CAAA;YACjB,OACE,GAAG,GAAG,UAAU;gBAChB,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,KAAK;gBACjC,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAC/B,CAAC;gBACD,GAAG,EAAE,CAAA;YACP,CAAC;YACD,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACzD,OAAO,GAAG,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,GAAG,EAAE,CAAC;gBAC3D,GAAG,EAAE,CAAA;YACP,CAAC;YACD,GAAG,EAAE,CAAA;QACP,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,wBAAwB;IACxB,IAAI,UAAU,GAAG,CAAC,CAAA;IAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;QAC/B,IAAI,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,EAAE,CAAC;YACnC,UAAU,EAAE,CAAA;QACd,CAAC;IACH,CAAC;IACD,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;QAC1C,MAAM,WAAW,GAAG,GAAG,CAAA;QACvB,IAAI,MAAM,GAAG,GAAG,CAAA;QAChB,OAAO,MAAM,GAAG,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,MAAM,CAAC,KAAK,GAAG,EAAE,CAAC;YACjE,MAAM,EAAE,CAAA;QACV,CAAC;QAED,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,IAAI,UAAU,GAAG,WAAW,CAAA;QAC5B,KAAK,IAAI,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3C,IAAI,CAAC,KAAK,MAAM,IAAI,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,EAAE,CAAC;gBACpD,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;oBAC1B,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;oBAC5D,MAAK;gBACP,CAAC;gBACD,MAAM,EAAE,CAAA;gBACR,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;YACpB,CAAC;QACH,CAAC;QACD,GAAG,GAAG,MAAM,GAAG,CAAC,CAAA;IAClB,CAAC;IAED,OAAO,SAAS,CAAA;AAClB,CAAC"}

esm/parseMetaString.d.ts

 export declare function parseMetaString(metaString: string): {
-    [k: string]: any;
+    [k: string]: string | string[];
 };

esm/parseMetaString.js

@@ -1,9 +0,1 @@
-// constructed with the assistance of claude AI
-//
-// I first prompted it with a regex that splits a comma separated string with
-// awareness of quotation from this stackoverflow question
-// https://stackoverflow.com/a/18893443/2129219, and asked it to add support
-// for square brackets
-//
-// it undid the regex into serial logic and the result was this function
 function customSplit(str) {
@@ -16,3 +8,3 @@ const result = [];
     for (let i = 0; i < strLen; i++) {
-        const char = str[i];
+        const char = str[i] ?? '';
         if (char === '"') {
@@ -51,11 +43,12 @@ inQuotes = !inQuotes;
     const entries = [];
-    for (let i = 0; i < parts.length; i++) {
-        const f = parts[i];
+    for (const f of parts) {
         const [key, val] = splitFirst(f, '=');
         if (val && val.startsWith('[') && val.endsWith(']')) {
-            const items = val.slice(1, -1).split(',');
-            for (let j = 0; j < items.length; j++) {
-                items[j] = items[j].trim();
-            }
-            entries.push([key, items]);
+            entries.push([
+                key,
+                val
+                    .slice(1, -1)
+                    .split(',')
+                    .map(s => s.trim()),
+            ]);
         }
@@ -62,0 +55,0 @@ else if (val && val.startsWith('"') && val.endsWith('"')) {

esm/parseMetaString.js.map

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

@@ -5,3 +5,3 @@ /**
  */
-export type GenotypeCallback = (str: string, start: number, end: number) => any;
+export type GenotypeCallback = (str: string, start: number, end: number) => unknown;
 /**
@@ -8,0 +8,0 @@ * Process genotypes by calling a callback for each one, avoiding intermediate

esm/processGenotypes.js.map

@@ -1,1 +0,1 @@
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esm/Variant.js

@@ -26,3 +26,3 @@ import { parseGenotypesOnly } from "./parseGenotypesOnly.js";
         const [CHROM, POS, ID, REF, ALT, QUAL, FILTER] = fields;
-        const filter = FILTER === '.' ? undefined : FILTER.split(';');
+        const filter = FILTER === '.' ? undefined : FILTER?.split(';');
         if (strict && !fields[7]) {
@@ -32,7 +32,8 @@ throw new Error("no INFO field specified, must contain at least a '.' (turn off strict mode to allow)");
         this.CHROM = CHROM;
-        this.POS = +POS;
-        this.ID = ID === '.' ? undefined : ID.split(';');
+        this.POS = POS !== undefined ? +POS : 0;
+        this.ID = ID === '.' ? undefined : ID?.split(';');
         this.REF = REF;
-        this.ALT = ALT === '.' ? undefined : ALT.split(',');
-        this.QUAL = QUAL === '.' ? undefined : +QUAL;
+        this.ALT = ALT === '.' ? undefined : ALT?.split(',');
+        this.QUAL =
+            QUAL === '.' ? undefined : QUAL !== undefined ? +QUAL : undefined;
         this.FILTER = filter?.length === 1 && filter[0] === 'PASS' ? 'PASS' : filter;
@@ -54,3 +55,3 @@ this.INFO =
         for (let i = 0; i < pairsLen; i++) {
-            const pair = infoPairs[i];
+            const pair = infoPairs[i] ?? '';
             const eqIdx = pair.indexOf('=');
@@ -70,29 +71,14 @@ const key = eqIdx === -1 ? pair : pair.slice(0, eqIdx);
                 const itemsLen = rawItems.length;
-                if (hasDecode) {
-                    const items = [];
-                    for (let j = 0; j < itemsLen; j++) {
-                        const v = rawItems[j];
-                        if (v === '.') {
-                            items.push(undefined);
-                        }
-                        else {
-                            const decoded = decodeURIComponentNoThrow(v);
-                            items.push(isNumber ? Number(decoded) : decoded);
-                        }
+                const items = [];
+                for (let j = 0; j < itemsLen; j++) {
+                    const v = rawItems[j] ?? '';
+                    if (v === '.') {
+                        items.push(undefined);
                     }
-                    result[key] = items;
-                }
-                else {
-                    const items = [];
-                    for (let j = 0; j < itemsLen; j++) {
-                        const v = rawItems[j];
-                        if (v === '.') {
-                            items.push(undefined);
-                        }
-                        else {
-                            items.push(isNumber ? Number(v) : v);
-                        }
+                    else {
+                        const w = hasDecode ? decodeURIComponentNoThrow(v) : v;
+                        items.push(isNumber ? Number(w) : w);
                     }
-                    result[key] = items;
                 }
+                result[key] = items;
             }
@@ -110,3 +96,3 @@ }
             for (let i = 0; i < formatKeys.length; i++) {
-                const r = this.formatMeta[formatKeys[i]]?.Type;
+                const r = this.formatMeta[formatKeys[i] ?? '']?.Type;
                 isNumberType.push(r === 'Integer' || r === 'Float');
@@ -117,5 +103,5 @@ }
             for (let i = 0; i < samplesLen; i++) {
-                const sample = this.sampleNames[i];
+                const sample = this.sampleNames[i] ?? '';
                 const sampleData = {};
-                const sampleStr = rest[i];
+                const sampleStr = rest[i] ?? '';
                 const sampleStrLen = sampleStr.length;
@@ -128,3 +114,3 @@ let colStart = 0;
                         if (val === '' || val === '.') {
-                            sampleData[formatKeys[colIdx]] = undefined;
+                            sampleData[formatKeys[colIdx] ?? ''] = undefined;
                         }
@@ -136,3 +122,3 @@ else {
                                 for (let k = 0; k < items.length; k++) {
-                                    const ent = items[k];
+                                    const ent = items[k] ?? '';
                                     result.push(ent === '.' ? undefined : +ent);
@@ -143,7 +129,7 @@ }
                                 for (let k = 0; k < items.length; k++) {
-                                    const ent = items[k];
+                                    const ent = items[k] ?? '';
                                     result.push(ent === '.' ? undefined : ent);
                                 }
                             }
-                            sampleData[formatKeys[colIdx]] = result;
+                            sampleData[formatKeys[colIdx] ?? ''] = result;
                         }
@@ -150,0 +136,0 @@ colStart = j + 1;

esm/Variant.js.map

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

 {
   "name": "@gmod/vcf",
-  "version": "7.0.0",
+  "version": "7.0.1",
   "description": "High performance streaming Variant Call Format (VCF) parser in pure JavaScript",
@@ -8,10 +8,9 @@ "type": "module",
   "exports": {
-    "import": {
-      "import": "./esm/index.js"
-    },
-    "require": {
-      "require": "./dist/index.js"
-    }
+    "import": "./esm/index.js",
+    "require": "./dist/index.js"
   },
-  "repository": "github:GMOD/vcf-js",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/vcf-js.git"
+  },
   "author": {
@@ -32,5 +31,2 @@ "name": "Garrett Stevens",
   ],
-  "engines": {
-    "node": ">=6"
-  },
   "scripts": {
@@ -41,12 +37,10 @@ "test": "vitest",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
-    "docs": "documentation readme src/parse.ts --section=API  --shallow",
     "format": "prettier --write .",
-    "postdocs": "prettier --write README.md",
     "clean": "rimraf dist esm",
     "build:esm": "tsc --target es2020 --outDir esm",
-    "build:es5": "tsc --target es2020 --module commonjs --outDir dist",
-    "build": "yarn build:esm && yarn build:es5",
-    "prebuild": "yarn clean",
+    "build:es5": "tsc --target es2020 --module commonjs --moduleResolution bundler --outDir dist",
+    "build": "pnpm build:esm && pnpm build:es5",
+    "prebuild": "pnpm clean",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
-    "preversion": "yarn lint && yarn test --run && yarn build",
+    "preversion": "pnpm lint && pnpm test --run && pnpm build",
     "version": "standard-changelog && git add CHANGELOG.md",
@@ -56,18 +50,17 @@ "postversion": "git push --follow-tags"
   "devDependencies": {
-    "@babel/core": "^7.20.5",
-    "@eslint/js": "^9.7.0",
-    "@types/node": "^24.10.1",
-    "@typescript-eslint/eslint-plugin": "^8.48.0",
-    "@typescript-eslint/parser": "^8.48.0",
-    "@vitest/coverage-v8": "^4.0.14",
-    "documentation": "^14.0.1",
-    "eslint": "^9.7.0",
+    "@babel/core": "^7.29.0",
+    "@eslint/js": "^10.0.1",
+    "@types/node": "^25.6.0",
+    "@typescript-eslint/eslint-plugin": "^8.59.0",
+    "@typescript-eslint/parser": "^8.59.0",
+    "@vitest/coverage-v8": "^4.1.5",
+    "eslint": "^10.2.1",
     "eslint-plugin-import": "^2.32.0",
-    "eslint-plugin-unicorn": "^62.0.0",
-    "prettier": "^3.2.4",
-    "rimraf": "^6.0.1",
+    "eslint-plugin-unicorn": "^64.0.0",
+    "prettier": "^3.8.3",
+    "rimraf": "^6.1.3",
     "standard-changelog": "^7.0.1",
-    "typescript": "^5.3.3",
-    "typescript-eslint": "^8.48.0",
-    "vitest": "^4.0.14"
+    "typescript": "^6.0.3",
+    "typescript-eslint": "^8.59.0",
+    "vitest": "^4.1.5"
   },
@@ -74,0 +67,0 @@ "keywords": [

README.md

 # vcf-js
 
-High performance Variant Call Format (VCF) parser in pure JavaScript.
+VCF (variant call format) parser
 
-## Status
-
 [![NPM version](https://img.shields.io/npm/v/@gmod/vcf.svg?logo=npm&style=flat-square)](https://npmjs.org/package/@gmod/vcf)
-[![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/vcf-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/vcf-js/branch/master)
-[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/vcf-js/push.yml?branch=master)](https://github.com/GMOD/vcf-js/actions)
+[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/vcf-js/push.yml?branch=main)](https://github.com/GMOD/vcf-js/actions)
 
 ## Usage
 
-This module is best used when combined with some easy way of retrieving the
-header and individual lines from a VCF, like the `@gmod/tabix` module.
-
 ```typescript
 import { TabixIndexedFile } from '@gmod/tabix'
+import VCF from '@gmod/vcf'
 
-// with import
-import VCF, { parseBreakend, Variant } from '@gmod/vcf'
-
-// with require
-const { default: VCF, parseBreakend } = require('@gmod/vcf')
-
 const tbiIndexed = new TabixIndexedFile({ path: '/path/to/my.vcf.gz' })
 
-async function doStuff() {
-  const headerText = await tbiIndexed.getHeader()
-  const tbiVCFParser = new VCF({ header: headerText })
-  const variants = []
-  await tbiIndexed.getLines('ctgA', 200, 300, line =>
-    variants.push(tbiVCFParser.parseLine(line)),
-  )
-  console.log(variants)
-}
-```
+const headerText = await tbiIndexed.getHeader()
+const parser = new VCF({ header: headerText }) // strict?: boolean (default true)
 
-If you want to stream a VCF file, you can alternatively use something like this
-
-```typescript
-const fs = require('fs')
-const VCF = require('@gmod/vcf').default
-const { createGunzip } = require('zlib')
-const readline = require('readline')
-
-const rl = readline.createInterface({
-  input: fs.createReadStream(process.argv[2]).pipe(createGunzip()),
-})
-
-let header = []
-let elts = []
-let parser = undefined
-
-rl.on('line', function (line) {
-  if (line.startsWith('#')) {
-    header.push(line)
-    return
-  } else if (!parser) {
-    parser = new VCF({ header: header.join('\n') })
-  }
-  const elt = parser.parseLine(line)
-  elts.push(elt.INFO.AN[0])
-})
-
-rl.on('close', function () {
-  console.log(elts.reduce((a, b) => a + b, 0) / elts.length)
-})
+const variants = []
+await tbiIndexed.getLines('ctgA', 200, 300, line =>
+  variants.push(parser.parseLine(line)),
+)
 ```
 
-This method is used to test @gmod/vcf in https://github.com/brentp/vcf-bench
+## Variant
 
-## Methods
+`parseLine(line)` returns a `Variant` with these fields:
 
-Given a VCF with a single variant line
-
-```text
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00096
-contigA	3000	rs17883296	G	T,A	100	PASS	NS=3;DP=14;AF=0.5;DB;XYZ=5	GT:AP	0|0:0.000,0.000
-```
-
-The `Variant` object returned by `parseLine()` has these properties:
-
 ```typescript
@@ -91,3 +37,3 @@ {
   QUAL: 100,
-  FILTER: 'PASS',
+  FILTER: 'PASS', // 'PASS' | string[] of filter names | undefined if '.'
   INFO: {
@@ -97,4 +43,4 @@ NS: [3],
     AF: [0.5],
-    DB: true,
-    XYZ: ['5'],
+    DB: true,   // Flag type
+    XYZ: ['5'], // unknown fields default to Number=1, Type=String
   },
@@ -104,234 +50,120 @@ }
 
-The `Variant` class also has methods for accessing sample data:
+INFO and FORMAT values are typed using header metadata. Values are arrays unless
+`Type=Flag`, in which case they are `true`. Fields defined in the
+[VCF spec](https://samtools.github.io/hts-specs/VCFv4.3.pdf) are typed even
+without a header entry.
 
-- `variant.SAMPLES()` - returns full sample data with all FORMAT fields parsed
-- `variant.GENOTYPES()` - returns just the GT strings (faster if that's all you
-  need)
-- `variant.processGenotypes(callback)` - calls a callback for each genotype
-  without allocating strings (fastest for counting/iteration)
+### Sample methods
 
-These methods lazily parse the genotype data, so they only do work when called.
-This saves time especially if your VCF has many samples (e.g. 1000 Genomes).
+- `variant.SAMPLES()` — full sample data with all FORMAT fields parsed
+- `variant.GENOTYPES()` — GT strings only (faster)
+- `variant.processGenotypes(callback)` — iterate genotypes without allocating
+  strings (fastest)
 
-The parser will try to convert the values in INFO and FORMAT to the proper types
-using the header metadata. For example, if there is a header line like
-
-```text
-##INFO=<ID=ABC,Number=2,Type=Integer,Description="A description">
+```typescript
+let homRef = 0
+variant.processGenotypes((str, start, end) => {
+  if (
+    end - start === 3 && // e.g. "0|0"
+    str.charCodeAt(start) === 48 && // 48 = '0'
+    str.charCodeAt(start + 2) === 48
+  ) {
+    homRef++
+  }
+})
 ```
 
-The parser will expect any INFO entry ABC to be an array of two integers, so it
-would convert `ABC=12,20` to `{ ABC: [12, 20] }`.
+Sample data is lazily parsed — nothing is computed until these methods are
+called.
 
-Each INFO entry value will be an array unless `Type=Flag` is specified, in which
-case it will be `true`. If no metadata can be found for the entry, it will
-assume `Number=1` and `Type=String`.
+## Metadata
 
-Some fields are pre-defined by the
-[VCF spec](https://samtools.github.io/hts-specs/VCFv4.3.pdf), which is why in
-the variant object above "DP" was parsed as an integer (it is defined in the VCF
-spec), but "XYZ" was left as a string (it is not defined in either the VCF spec
-or the header).
+`parser.getMetadata(...keys)` returns header metadata, filtered by the keys
+provided:
 
-Metadata can be accessed with the `getMetadata()` method, including all the
-built-in metadata from the VCF spec. With no parameters it will return all the
-data. Any parameters passed will further filter the metadata. For example, for a
-VCF with this header:
+```typescript
+parser.getMetadata('INFO', 'DP')
+// { Number: 1, Type: 'Integer', Description: 'Total Depth' }
 
-```text
-##INFO=<ID=ABC,Number=2,Type=Integer,Description="A description">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+parser.getMetadata('INFO', 'DP', 'Number')
+// 1
 ```
 
-you can access the VCF's header metadata like (some output omitted for clarity):
+Call with no arguments to get all metadata. `parser.samples` lists sample names.
 
-```typescript
-> console.log(vcfParser.getMetadata())
-{ INFO:
-   { AA:
-      { Number: 1, Type: 'String', Description: 'Ancestral Allele' },
+## Streaming
 
-...
+To parse a plain VCF without tabix, collect header lines until the first
+non-header line, then construct the parser:
 
-     ABC: { Number: 2, Type: 'Integer', Description: 'A description' } },
-  FORMAT:
-   { AD:
-      { Number: 'R',
-        Type: 'Integer',
-        Description: 'Read depth for each allele' },
+```typescript
+import fs from 'fs'
+import VCF from '@gmod/vcf'
+import { createGunzip } from 'zlib'
+import readline from 'readline'
 
-...
+const rl = readline.createInterface({
+  input: fs.createReadStream('file.vcf.gz').pipe(createGunzip()),
+})
 
-  ALT:
-   { DEL: { Description: 'Deletion relative to the reference' },
+const header = []
+let parser
 
-...
-
-  FILTER: { PASS: { Description: 'Passed all filters' } } }
-
-> console.log(vcfParser.getMetadata('INFO'))
-{ AA:
-   { Number: 1, Type: 'String', Description: 'Ancestral Allele' },
-  AC:
-   { Number: 'A',
-     Type: 'Integer',
-     Description:
-      'Allele count in genotypes, for each ALT allele, in the same order as listed' },
-  AD:
-   { Number: 'R',
-     Type: 'Integer',
-     Description: 'Total read depth for each allele' },
-
-...
-
-  ABC: { Number: 2, Type: 'Integer', Description: 'A description' } }
-
-> console.log(vcfParser.getMetadata('INFO', 'DP'))
-{ Number: 1, Type: 'Integer', Description: 'Total Depth' }
-
-> console.log(vcfParser.getMetadata('INFO', 'DP', 'Number'))
-1
+rl.on('line', line => {
+  if (line.startsWith('#')) {
+    header.push(line)
+  } else {
+    if (!parser) {
+      parser = new VCF({ header: header.join('\n') })
+    }
+    const variant = parser.parseLine(line)
+    console.log(variant.CHROM, variant.POS)
+  }
+})
 ```
 
-A list of sample names is also available in the `samples` attribute of the
-parser object:
-
-```typescript
-> console.log(vcfParser.samples)
-[ 'HG00096' ]
-```
-
 ## Breakends
 
-We offer a helper function to parse breakend strings. We used to parse these
-automatically but it is now a helper function
+`parseBreakend(alt)` parses a breakend ALT string:
 
-```js
+```typescript
 import { parseBreakend } from '@gmod/vcf'
+
 parseBreakend('C[2:321682[')
-
-// output
-//
-//     {
-//       "MateDirection": "right",
-//       "Replacement": "C",
-//       "MatePosition": "2:321682",
-//       "Join": "right"
-//     }
+// { MateDirection: 'right', Replacement: 'C', MatePosition: '2:321682', Join: 'right' }
 ```
 
-- The C\[2:321682\[ parses as "Join": "right" because the BND is after the C
-  base
-- The C\[2:321682\[ also is given "MateDirection": "right" because the square
-  brackets point to the right.
-- The spec never has the square brackets pointing in different directions.
-  Instead, the different types of joins can be imagined as follows
+All four bracket forms from the VCF spec:
 
-For the above vcf line where chr13:123456->C\[2:321682\[ then we have this
+| ALT form | Join  | MateDirection |
+| -------- | ----- | ------------- |
+| `t[p[`   | right | right         |
+| `t]p]`   | right | left          |
+| `[p[t`   | left  | right         |
+| `]p]t`   | left  | left          |
 
-        chr13:123456
-      -------------C\
-                     \
-                      \
-                       \
-                        \
-                         \
-                          \
-                           \
-                            \--------------
-                             chr2:321682
+- `Join` — whether the replacement base appears before (`right`) or after
+  (`left`) the mate position
+- `MateDirection` — `[` means the mate sequence extends rightward; `]` means
+  leftward
 
-If the alt was instead chr13:123456->\[2:321682\[C then the the "Join" would be
-"left" since the "BND" is before "C" and then the breakend structure looks like
-this
+### Single breakends
 
-          chr13:123456
+When the ALT starts or ends with `.`, `parseBreakend` returns
+`SingleBreakend: true` with no `MatePosition`:
 
-          |C--------------------
-          |
-          |
-          |
-          |
-          |
-          |
-          |
-          |
-          |
-          |
-          ----------------------
-           chr2:321682
+```typescript
+parseBreakend('C.')
+// { Join: 'right', Replacement: 'C', SingleBreakend: true }
 
-## API
+parseBreakend('.ACGT')
+// { Join: 'left', Replacement: 'ACGT', SingleBreakend: true }
+```
 
-#### Table of Contents
+## Publishing
 
-- [VCFParser](#vcfparser)
-  - [Parameters](#parameters)
-  - [getMetadata](#getmetadata)
-  - [parseLine](#parseline)
-- [Variant](#variant)
-  - [SAMPLES](#samples)
-  - [GENOTYPES](#genotypes)
-  - [processGenotypes](#processgenotypes)
+[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub Actions.
 
-### VCFParser
-
-Class representing a VCF parser, instantiated with the VCF header.
-
-#### Parameters
-
-- `args.header` **string** - The VCF header. Supports both LF and CRLF newlines.
-- `args.strict` **boolean** - Whether to parse in strict mode or not (default
-  true)
-
-#### getMetadata
-
-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,...>"
-
-##### Parameters
-
-- `...args` **string[]** - List of metadata filter strings.
-
-Returns **any** An object, string, or number, depending on the filtering
-
-#### parseLine
-
-Parse a VCF line into a `Variant` object.
-
-##### Parameters
-
-- `line` **string** - A string of a line from a VCF
-
-Returns **Variant** A Variant instance with the parsed data
-
-### Variant
-
-Class representing a parsed VCF variant line. Has data properties (CHROM, POS,
-ID, REF, ALT, QUAL, FILTER, INFO, FORMAT) and methods for accessing sample data.
-
-#### SAMPLES
-
-Returns full sample data with all FORMAT fields parsed.
-
-Returns **Record\<string, Record\<string, (string | number | undefined)[] |
-undefined>>**
-
-#### GENOTYPES
-
-Returns just the GT strings for each sample (faster than SAMPLES if you only
-need genotypes).
-
-Returns **Record\<string, string>**
-
-#### processGenotypes
-
-Calls a callback for each genotype without allocating strings. Useful for
-counting or iterating over genotypes with minimal memory allocation.
-
-##### Parameters
-
-- `callback` **(str: string, start: number, end: number) => any** - Called for
-  each genotype with the raw string and indices. Use `str.slice(start, end)` to
-  extract the genotype string, or `str.charCodeAt(start)` to read characters
-  without allocation.
+```bash
+npm version patch  # or minor/major
+```

src/parse.ts

@@ -42,3 +42,3 @@ import { Variant } from './Variant.ts'
     for (let i = 0; i < headerLines.length; i++) {
-      const line = headerLines[i]!
+      const line = headerLines[i] ?? ''
       if (!line.startsWith('#')) {
@@ -91,5 +91,4 @@ throw new Error(`Bad line in header:\n${line}`)
     }
-    const [metaKey, metaVal] = match.slice(1, 3)
-
-    const r = metaKey!
+    const r = match[1] ?? ''
+    const metaVal = match[2]
     if (metaVal?.startsWith('<')) {
@@ -100,3 +99,3 @@ if (!(r in this.metadata)) {
       const [id, keyVals] = this.parseStructuredMetaVal(metaVal)
-      if (id) {
+      if (typeof id === 'string') {
         // if there is an ID field in the <> metadata
@@ -125,4 +124,5 @@ // e.g. ##INFO=<ID=AF_ESP,...>
   private parseStructuredMetaVal(metaVal: string) {
-    const keyVals = parseMetaString(metaVal)
-    const id = keyVals.ID!
+    const keyVals: Record<string, string | string[] | number> =
+      parseMetaString(metaVal)
+    const id = keyVals.ID
     delete keyVals.ID
@@ -147,6 +147,11 @@ if ('Number' in keyVals) {
   getMetadata(...args: string[]) {
-    let filteredMetadata: any = this.metadata
+    let filteredMetadata: unknown = this.metadata
     const argsLen = args.length
     for (let i = 0; i < argsLen; i++) {
-      filteredMetadata = filteredMetadata[args[i]!]
+      if (typeof filteredMetadata !== 'object' || filteredMetadata === null) {
+        return undefined
+      }
+      filteredMetadata = (filteredMetadata as Record<string, unknown>)[
+        args[i] ?? ''
+      ]
       if (!filteredMetadata) {
@@ -153,0 +158,0 @@ return filteredMetadata

src/parseBreakend.ts

@@ -27,5 +27,3 @@ export interface Breakend {
     let MatePosition
-    const tokensLen = tokens.length
-    for (let i = 0; i < tokensLen; i++) {
-      const tok = tokens[i]!
+    for (const tok of tokens) {
       if (tok) {
@@ -73,3 +71,3 @@ if (tok.includes(':')) {
           MateDirection: 'right',
-          MatePosition: `<${res[1]!}>:1`,
+          MatePosition: `<${res[1] ?? ''}>:1`,
         }
@@ -90,3 +88,3 @@ : undefined
           MateDirection: 'right',
-          MatePosition: `<${res[2]!}>:1`,
+          MatePosition: `<${res[2] ?? ''}>:1`,
         }
@@ -93,0 +91,0 @@ : undefined

src/parseGenotypesOnly.ts

@@ -24,3 +24,3 @@ /**
       }
-      genotypes[samples[idx]!] = prerest.slice(start, pos)
+      genotypes[samples[idx] ?? ''] = prerest.slice(start, pos)
       pos++
@@ -48,3 +48,3 @@ }
       }
-      genotypes[samples[idx]!] = prerest.slice(start, pos)
+      genotypes[samples[idx] ?? ''] = prerest.slice(start, pos)
       while (pos < prerestLen && prerest.charCodeAt(pos) !== TAB) {
@@ -77,3 +77,3 @@ pos++
         if (colons === colonCount) {
-          genotypes[samples[idx]!] = prerest.slice(fieldStart, j)
+          genotypes[samples[idx] ?? ''] = prerest.slice(fieldStart, j)
           break
@@ -80,0 +80,0 @@ }

src/parseMetaString.ts

@@ -1,9 +0,1 @@
-// constructed with the assistance of claude AI
-//
-// I first prompted it with a regex that splits a comma separated string with
-// awareness of quotation from this stackoverflow question
-// https://stackoverflow.com/a/18893443/2129219, and asked it to add support
-// for square brackets
-//
-// it undid the regex into serial logic and the result was this function
 function customSplit(str: string) {
@@ -17,3 +9,3 @@ const result = []
   for (let i = 0; i < strLen; i++) {
-    const char = str[i]!
+    const char = str[i] ?? ''
     if (char === '"') {
@@ -45,3 +37,3 @@ inQuotes = !inQuotes
   const index = str.indexOf(split)
-  return [str.slice(0, index), str.slice(index + 1)]
+  return [str.slice(0, index), str.slice(index + 1)] as const
 }
@@ -52,16 +44,17 @@
   const parts = customSplit(inside)
-  const entries: [string, any][] = []
-  for (let i = 0; i < parts.length; i++) {
-    const f = parts[i]!
+  const entries: [string, string | string[]][] = []
+  for (const f of parts) {
     const [key, val] = splitFirst(f, '=')
     if (val && val.startsWith('[') && val.endsWith(']')) {
-      const items = val.slice(1, -1).split(',')
-      for (let j = 0; j < items.length; j++) {
-        items[j] = items[j]!.trim()
-      }
-      entries.push([key!, items])
+      entries.push([
+        key,
+        val
+          .slice(1, -1)
+          .split(',')
+          .map(s => s.trim()),
+      ])
     } else if (val && val.startsWith('"') && val.endsWith('"')) {
-      entries.push([key!, val.slice(1, -1)])
+      entries.push([key, val.slice(1, -1)])
     } else {
-      entries.push([key!, val])
+      entries.push([key, val])
     }
@@ -68,0 +61,0 @@ }

src/processGenotypes.ts

@@ -5,3 +5,7 @@ /**
  */
-export type GenotypeCallback = (str: string, start: number, end: number) => any
+export type GenotypeCallback = (
+  str: string,
+  start: number,
+  end: number,
+) => unknown
 
@@ -8,0 +12,0 @@ /**

src/Variant.ts

@@ -49,3 +49,3 @@ import { parseGenotypesOnly } from './parseGenotypesOnly.ts'
     const [CHROM, POS, ID, REF, ALT, QUAL, FILTER] = fields
-    const filter = FILTER === '.' ? undefined : FILTER!.split(';')
+    const filter = FILTER === '.' ? undefined : FILTER?.split(';')
 
@@ -59,7 +59,8 @@ if (strict && !fields[7]) {
     this.CHROM = CHROM
-    this.POS = +POS!
-    this.ID = ID === '.' ? undefined : ID!.split(';')
+    this.POS = POS !== undefined ? +POS : 0
+    this.ID = ID === '.' ? undefined : ID?.split(';')
     this.REF = REF
-    this.ALT = ALT === '.' ? undefined : ALT!.split(',')
-    this.QUAL = QUAL === '.' ? undefined : +QUAL!
+    this.ALT = ALT === '.' ? undefined : ALT?.split(',')
+    this.QUAL =
+      QUAL === '.' ? undefined : QUAL !== undefined ? +QUAL : undefined
     this.FILTER = filter?.length === 1 && filter[0] === 'PASS' ? 'PASS' : filter
@@ -87,3 +88,3 @@ this.INFO =
     for (let i = 0; i < pairsLen; i++) {
-      const pair = infoPairs[i]!
+      const pair = infoPairs[i] ?? ''
       const eqIdx = pair.indexOf('=')
@@ -103,26 +104,13 @@ const key = eqIdx === -1 ? pair : pair.slice(0, eqIdx)
 
-        if (hasDecode) {
-          const items: (string | number | undefined)[] = []
-          for (let j = 0; j < itemsLen; j++) {
-            const v = rawItems[j]!
-            if (v === '.') {
-              items.push(undefined)
-            } else {
-              const decoded = decodeURIComponentNoThrow(v)
-              items.push(isNumber ? Number(decoded) : decoded)
-            }
+        const items: (string | number | undefined)[] = []
+        for (let j = 0; j < itemsLen; j++) {
+          const v = rawItems[j] ?? ''
+          if (v === '.') {
+            items.push(undefined)
+          } else {
+            const w = hasDecode ? decodeURIComponentNoThrow(v) : v
+            items.push(isNumber ? Number(w) : w)
           }
-          result[key] = items
-        } else {
-          const items: (string | number | undefined)[] = []
-          for (let j = 0; j < itemsLen; j++) {
-            const v = rawItems[j]!
-            if (v === '.') {
-              items.push(undefined)
-            } else {
-              items.push(isNumber ? Number(v) : v)
-            }
-          }
-          result[key] = items
         }
+        result[key] = items
       }
@@ -144,3 +132,3 @@ }
       for (let i = 0; i < formatKeys.length; i++) {
-        const r = this.formatMeta[formatKeys[i]!]?.Type
+        const r = this.formatMeta[formatKeys[i] ?? '']?.Type
         isNumberType.push(r === 'Integer' || r === 'Float')
@@ -151,3 +139,3 @@ }
       for (let i = 0; i < samplesLen; i++) {
-        const sample = this.sampleNames[i]!
+        const sample = this.sampleNames[i] ?? ''
         const sampleData: Record<
@@ -157,3 +145,3 @@ string,
         > = {}
-        const sampleStr = rest[i]!
+        const sampleStr = rest[i] ?? ''
         const sampleStrLen = sampleStr.length
@@ -167,3 +155,3 @@ let colStart = 0
             if (val === '' || val === '.') {
-              sampleData[formatKeys[colIdx]!] = undefined
+              sampleData[formatKeys[colIdx] ?? ''] = undefined
             } else {
@@ -174,3 +162,3 @@ const items = val.split(',')
                 for (let k = 0; k < items.length; k++) {
-                  const ent = items[k]!
+                  const ent = items[k] ?? ''
                   result.push(ent === '.' ? undefined : +ent)
@@ -180,7 +168,7 @@ }
                 for (let k = 0; k < items.length; k++) {
-                  const ent = items[k]!
+                  const ent = items[k] ?? ''
                   result.push(ent === '.' ? undefined : ent)
                 }
               }
-              sampleData[formatKeys[colIdx]!] = result
+              sampleData[formatKeys[colIdx] ?? ''] = result
             }
@@ -187,0 +175,0 @@ colStart = j + 1

CHANGELOG.md

-# [7.0.0](https://github.com/GMOD/vcf-js/compare/v6.1.2...v7.0.0) (2026-01-18)
-
-
-
-## [6.1.2](https://github.com/GMOD/vcf-js/compare/v6.1.1...v6.1.2) (2026-01-18)
-
-# [6.1.0](https://github.com/GMOD/vcf-js/compare/v6.0.9...v6.1.0) (2025-11-26)
-
-## [6.0.9](https://github.com/GMOD/vcf-js/compare/v6.0.8...v6.0.9) (2025-04-01)
-
-## [6.0.8](https://github.com/GMOD/vcf-js/compare/v6.0.7...v6.0.8) (2025-02-13)
-
-## [6.0.7](https://github.com/GMOD/vcf-js/compare/v6.0.6...v6.0.7) (2025-01-29)
-
-## [6.0.6](https://github.com/GMOD/vcf-js/compare/v6.0.5...v6.0.6) (2025-01-16)
-
-## [6.0.5](https://github.com/GMOD/vcf-js/compare/v6.0.4...v6.0.5) (2025-01-16)
-
-## [6.0.4](https://github.com/GMOD/vcf-js/compare/v6.0.3...v6.0.4) (2025-01-16)
-
-## [6.0.3](https://github.com/GMOD/vcf-js/compare/v6.0.2...v6.0.3) (2025-01-16)
-
-## [6.0.2](https://github.com/GMOD/vcf-js/compare/v6.0.1...v6.0.2) (2025-01-07)
-
-## [6.0.1](https://github.com/GMOD/vcf-js/compare/v6.0.0...v6.0.1) (2024-12-17)
-
-# [6.0.0](https://github.com/GMOD/vcf-js/compare/v5.0.10...v6.0.0) (2024-11-30)
-
-- Changes the default Variant object to have a SAMPLES() function call instead
-  of a SAMPLES getter, to make it more abundantly clear that it is a lazy
-  operation. Also adds a GENOTYPES() function that returns the raw string of
-  genotype fields
-
-## [5.0.10](https://github.com/GMOD/vcf-js/compare/v5.0.9...v5.0.10) (2022-12-17)
-
-- Use es2015 for nodejs build
-
-## [5.0.9](https://github.com/GMOD/vcf-js/compare/v5.0.8...v5.0.9) (2022-11-23)
-
-- Fix erroneous parsing of symbolic alleles as breakends
-
-## [5.0.8](https://github.com/GMOD/vcf-js/compare/v5.0.7...v5.0.8) (2022-11-20)
-
-- Parse single breakends and large insertion shorthand notation (#95)
-
-<a name="5.0.7"></a>
-
-## [5.0.7](https://github.com/GMOD/vcf-js/compare/v5.0.6...v5.0.7) (2022-08-24)
-
-- Don't throw error when there is a FORMAT column but no genotypes
-
-<a name="5.0.6"></a>
-
-## [5.0.6](https://github.com/GMOD/vcf-js/compare/v5.0.5...v5.0.6) (2022-03-30)
-
-- Include src directory for better source maps
-
-<a name="5.0.5"></a>
-
-## [5.0.5](https://github.com/GMOD/vcf-js/compare/v5.0.4...v5.0.5) (2022-01-12)
-
-- Add optimization related to better allocation of variant records, thanks to
-  @bpow for contributing
-
-<a name="5.0.4"></a>
-
-## [5.0.4](https://github.com/GMOD/vcf-js/compare/v5.0.3...v5.0.4) (2021-12-23)
-
-- Make the strict field in the constructor optional
-- Export `Breakend` type for typescript users
-
-<a name="5.0.3"></a>
-
-## [5.0.3](https://github.com/GMOD/vcf-js/compare/v5.0.2...v5.0.3) (2021-12-14)
-
-- Add typescripting and esm module build
-
-<a name="5.0.2"></a>
-
-## [5.0.2](https://github.com/GMOD/vcf-js/compare/v5.0.1...v5.0.2) (2021-11-13)
-
-- Update package description to refer to variant call format
-
-<a name="5.0.1"></a>
-
-## [5.0.1](https://github.com/GMOD/vcf-js/compare/v5.0.0...v5.0.1) (2021-11-04)
-
-- Add URI decoding to INFO field
-
-<a name="5.0.0"></a>
-
-# [5.0.0](https://github.com/GMOD/vcf-js/compare/v4.0.4...v5.0.0) (2021-09-06)
-
-- Make parseBreakends an optional helper function, all ALTs are plain strings
-  now instead of string|Breakend. This is a breaking change so a major version
-  bump is applied
-
-<a name="4.0.4"></a>
-
-## [4.0.4](https://github.com/GMOD/vcf-js/compare/v4.0.1...v4.0.4) (2021-08-04)
-
-- Fix issue when there is extra whitespace on the header line
-
-<a name="4.0.3"></a>
-
-## [4.0.3](https://github.com/GMOD/vcf-js/compare/v4.0.1...v4.0.3) (2021-03-31)
-
-- Include github automated fixes in release from before 4.0.2
-
-<a name="4.0.2"></a>
-
-## [4.0.2](https://github.com/GMOD/vcf-js/compare/v4.0.1...v4.0.2) (2021-03-31)
-
-- Avoid modifying built-in exports with parseMetadata, fixes issue with using
-  parseMetadata from jest tests (#63)
-
-<a name="4.0.1"></a>
-
-## [4.0.1](https://github.com/GMOD/vcf-js/compare/v4.0.0...v4.0.1) (2019-10-30)
-
-- Add toString for Breakend ALTs so they are easily interpretable
-
-## [4.0.0](https://github.com/GMOD/vcf-js/compare/v3.0.0...v4.0.0) (2019-06-14)
-
-- Breaking change: INFO entries that are type Flag now evaluate to `true`
-  instead of `null`
-
-## [3.0.0](https://github.com/GMOD/vcf-js/compare/v2.0.3...v3.0.0) (2019-05-31)
-
-- Breaking change: ALT entries in breakend format now parse into a breakend
-  object instead of a string
-- Performance improvements
-
-## [2.0.3](https://github.com/GMOD/vcf-js/compare/v2.0.2...v2.0.3) (2019-02-23)
-
-- Upgrade to Babel 7
-
-## [2.0.2](https://github.com/GMOD/vcf-js/compare/v2.0.1...v2.0.2) (2018-11-26)
-
-- Remove errant unused dependency
-
-## [2.0.1](https://github.com/GMOD/vcf-js/compare/v2.0.0...v2.0.1) (2018-11-08)
-
-- Bugfix for getMetadata()
-
-## [2.0.0](https://github.com/GMOD/vcf-js/compare/v1.0.4...v2.0.0) (2018-11-07)
-
-- Breaking change: SAMPLES attribute of the variant is now evaluated lazily
-
-## [1.0.4](https://github.com/GMOD/vcf-js/compare/v1.0.3...v1.0.4) (2018-11-06)
-
-- Decode %-encoded entries in INFO and FORMAT
-
-## [1.0.3](https://github.com/GMOD/vcf-js/compare/v1.0.2...v1.0.3) (2018-11-05)
-
-- Fix for parsing missing genotypes
-
-## [1.0.2](https://github.com/GMOD/vcf-js/compare/v1.0.1...v1.0.2) (2018-10-11)
-
-- Better handle filter metadata
-
-## [1.0.1](https://github.com/GMOD/vcf-js/compare/v1.0.0...v1.0.1) (2018-10-05)
-
-- Fix bug in interpreting "Number" in header metadata
-
-## 1.0.0 (2018-10-05)
-
-- Initial release

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Found 1 instance in 1 package

Improved metrics

Dev dependency count

15

-6.25%

Number of low supply chain risk alerts

0

-100%

Worsened metrics

Total package byte prevSize

179399

-7.02%

Number of package files

60

-1.64%

Lines of code

3907

-1.29%

Number of lines in readme file

167

-50.15%

No dependency changes