@gmod/vcf - npm Package Compare versions

Comparing version 7.0.8 to 7.0.9

dist/processGenotypes.d.ts

@@ -7,12 +7,2 @@ /**
 export type GenotypeCallback = (str: string, start: number, end: number, sampleIdx: number) => unknown;
-/**
- * Process genotypes by calling a callback for each one, avoiding intermediate
- * object/string allocation. This is useful for operations like counting alleles
- * where you don't need to build the full genotypes object.
- *
- * @param format - The FORMAT field from the VCF line
- * @param prerest - The sample data portion of the VCF line (after FORMAT)
- * @param samplesLen - Number of samples
- * @param callback - Called for each genotype with (string, startIndex, endIndex)
- */
 export declare function processGenotypes(format: string, prerest: string, samplesLen: number, callback: GenotypeCallback): void;

dist/processGenotypes.js

@@ -14,6 +14,28 @@ "use strict";
  */
+const TAB = 9;
+const COLON = 58;
+const G = 71;
+const T = 84;
+// Column index of the exact "GT" field among the colon-separated FORMAT
+// keys, or -1 if absent. Matches the field exactly so keys that merely
+// contain "GT" (e.g. GATK's PGT) are not mistaken for it.
+function gtColumnIndex(format) {
+    let col = 0;
+    let start = 0;
+    const len = format.length;
+    for (let j = 0; j <= len; j++) {
+        if (j === len || format.charCodeAt(j) === COLON) {
+            if (j - start === 2 &&
+                format.charCodeAt(start) === G &&
+                format.charCodeAt(start + 1) === T) {
+                return col;
+            }
+            col++;
+            start = j + 1;
+        }
+    }
+    return -1;
+}
 function processGenotypes(format, prerest, samplesLen, callback) {
     const prerestLen = prerest.length;
-    const TAB = 9;
-    const COLON = 58;
     let pos = 0;
@@ -32,9 +54,8 @@ // Fast path: format is exactly "GT"
     }
-    // Check if GT field exists
-    const gtIdx = format.indexOf('GT');
-    if (gtIdx === -1) {
+    const colonCount = gtColumnIndex(format);
+    if (colonCount === -1) {
         return;
     }
     // GT is first field but not only field
-    if (gtIdx === 0) {
+    if (colonCount === 0) {
         for (let idx = 0; idx < samplesLen; idx++) {
@@ -55,9 +76,3 @@ const start = pos;
     }
-    // GT is not first field - need to skip to the right column
-    let colonCount = 0;
-    for (let j = 0; j < gtIdx; j++) {
-        if (format.charCodeAt(j) === COLON) {
-            colonCount++;
-        }
-    }
+    // GT is not first field - skip to its column (colonCount fields precede it)
     for (let idx = 0; idx < samplesLen; idx++) {
@@ -64,0 +79,0 @@ const sampleStart = pos;

dist/processGenotypes.js.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"processGenotypes.js","sourceRoot":"","sources":["../src/processGenotypes.ts"],"names":[],"mappings":";;AAkDA,4CAqEC;AA3GD;;;;;;;;;GASG;AACH,MAAM,GAAG,GAAG,CAAC,CAAA;AACb,MAAM,KAAK,GAAG,EAAE,CAAA;AAChB,MAAM,CAAC,GAAG,EAAE,CAAA;AACZ,MAAM,CAAC,GAAG,EAAE,CAAA;AAEZ,wEAAwE;AACxE,uEAAuE;AACvE,0DAA0D;AAC1D,SAAS,aAAa,CAAC,MAAc;IACnC,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAA;IACzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;QAC9B,IAAI,CAAC,KAAK,GAAG,IAAI,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,EAAE,CAAC;YAChD,IACE,CAAC,GAAG,KAAK,KAAK,CAAC;gBACf,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,KAAK,CAAC;gBAC9B,MAAM,CAAC,UAAU,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,EAClC,CAAC;gBACD,OAAO,GAAG,CAAA;YACZ,CAAC;YACD,GAAG,EAAE,CAAA;YACL,KAAK,GAAG,CAAC,GAAG,CAAC,CAAA;QACf,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAC,CAAA;AACX,CAAC;AAED,SAAgB,gBAAgB,CAC9B,MAAc,EACd,OAAe,EACf,UAAkB,EAClB,QAA0B;IAE1B,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAA;IACjC,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,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;YAClC,GAAG,EAAE,CAAA;QACP,CAAC;QACD,OAAM;IACR,CAAC;IAED,MAAM,UAAU,GAAG,aAAa,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;QACtB,OAAM;IACR,CAAC;IAED,uCAAuC;IACvC,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;QACrB,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,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;YAClC,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,OAAM;IACR,CAAC;IAED,4EAA4E;IAC5E,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,QAAQ,CAAC,OAAO,EAAE,UAAU,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBACrC,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;AACH,CAAC"}

esm/processGenotypes.d.ts

@@ -7,12 +7,2 @@ /**
 export type GenotypeCallback = (str: string, start: number, end: number, sampleIdx: number) => unknown;
-/**
- * Process genotypes by calling a callback for each one, avoiding intermediate
- * object/string allocation. This is useful for operations like counting alleles
- * where you don't need to build the full genotypes object.
- *
- * @param format - The FORMAT field from the VCF line
- * @param prerest - The sample data portion of the VCF line (after FORMAT)
- * @param samplesLen - Number of samples
- * @param callback - Called for each genotype with (string, startIndex, endIndex)
- */
 export declare function processGenotypes(format: string, prerest: string, samplesLen: number, callback: GenotypeCallback): void;

esm/processGenotypes.js

@@ -11,6 +11,28 @@ /**
  */
+const TAB = 9;
+const COLON = 58;
+const G = 71;
+const T = 84;
+// Column index of the exact "GT" field among the colon-separated FORMAT
+// keys, or -1 if absent. Matches the field exactly so keys that merely
+// contain "GT" (e.g. GATK's PGT) are not mistaken for it.
+function gtColumnIndex(format) {
+    let col = 0;
+    let start = 0;
+    const len = format.length;
+    for (let j = 0; j <= len; j++) {
+        if (j === len || format.charCodeAt(j) === COLON) {
+            if (j - start === 2 &&
+                format.charCodeAt(start) === G &&
+                format.charCodeAt(start + 1) === T) {
+                return col;
+            }
+            col++;
+            start = j + 1;
+        }
+    }
+    return -1;
+}
 export function processGenotypes(format, prerest, samplesLen, callback) {
     const prerestLen = prerest.length;
-    const TAB = 9;
-    const COLON = 58;
     let pos = 0;
@@ -29,9 +51,8 @@ // Fast path: format is exactly "GT"
     }
-    // Check if GT field exists
-    const gtIdx = format.indexOf('GT');
-    if (gtIdx === -1) {
+    const colonCount = gtColumnIndex(format);
+    if (colonCount === -1) {
         return;
     }
     // GT is first field but not only field
-    if (gtIdx === 0) {
+    if (colonCount === 0) {
         for (let idx = 0; idx < samplesLen; idx++) {
@@ -52,9 +73,3 @@ const start = pos;
     }
-    // GT is not first field - need to skip to the right column
-    let colonCount = 0;
-    for (let j = 0; j < gtIdx; j++) {
-        if (format.charCodeAt(j) === COLON) {
-            colonCount++;
-        }
-    }
+    // GT is not first field - skip to its column (colonCount fields precede it)
     for (let idx = 0; idx < samplesLen; idx++) {
@@ -61,0 +76,0 @@ const sampleStart = pos;

esm/processGenotypes.js.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"processGenotypes.js","sourceRoot":"","sources":["../src/processGenotypes.ts"],"names":[],"mappings":"AAYA;;;;;;;;;GASG;AACH,MAAM,GAAG,GAAG,CAAC,CAAA;AACb,MAAM,KAAK,GAAG,EAAE,CAAA;AAChB,MAAM,CAAC,GAAG,EAAE,CAAA;AACZ,MAAM,CAAC,GAAG,EAAE,CAAA;AAEZ,wEAAwE;AACxE,uEAAuE;AACvE,0DAA0D;AAC1D,SAAS,aAAa,CAAC,MAAc;IACnC,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAA;IACzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;QAC9B,IAAI,CAAC,KAAK,GAAG,IAAI,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,KAAK,EAAE,CAAC;YAChD,IACE,CAAC,GAAG,KAAK,KAAK,CAAC;gBACf,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,KAAK,CAAC;gBAC9B,MAAM,CAAC,UAAU,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,EAClC,CAAC;gBACD,OAAO,GAAG,CAAA;YACZ,CAAC;YACD,GAAG,EAAE,CAAA;YACL,KAAK,GAAG,CAAC,GAAG,CAAC,CAAA;QACf,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAC,CAAA;AACX,CAAC;AAED,MAAM,UAAU,gBAAgB,CAC9B,MAAc,EACd,OAAe,EACf,UAAkB,EAClB,QAA0B;IAE1B,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAA;IACjC,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,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;YAClC,GAAG,EAAE,CAAA;QACP,CAAC;QACD,OAAM;IACR,CAAC;IAED,MAAM,UAAU,GAAG,aAAa,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;QACtB,OAAM;IACR,CAAC;IAED,uCAAuC;IACvC,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;QACrB,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,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;YAClC,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,OAAM;IACR,CAAC;IAED,4EAA4E;IAC5E,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,QAAQ,CAAC,OAAO,EAAE,UAAU,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBACrC,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;AACH,CAAC"}

package.json

 {
   "name": "@gmod/vcf",
-  "version": "7.0.8",
+  "version": "7.0.9",
   "description": "High performance streaming Variant Call Format (VCF) parser in pure JavaScript",
@@ -5,0 +5,0 @@ "type": "module",

README.md

@@ -6,3 +6,3 @@ # vcf-js
 [![NPM version](https://img.shields.io/npm/v/@gmod/vcf.svg?logo=npm&style=flat-square)](https://npmjs.org/package/@gmod/vcf)
-[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/vcf-js/publish.yml?branch=main)](https://github.com/GMOD/vcf-js/actions)
+![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/vcf-js/publish.yml?branch=main)
 
@@ -9,0 +9,0 @@ ## Usage

src/processGenotypes.ts

@@ -23,2 +23,30 @@ /**
  */
+const TAB = 9
+const COLON = 58
+const G = 71
+const T = 84
+
+// Column index of the exact "GT" field among the colon-separated FORMAT
+// keys, or -1 if absent. Matches the field exactly so keys that merely
+// contain "GT" (e.g. GATK's PGT) are not mistaken for it.
+function gtColumnIndex(format: string) {
+  let col = 0
+  let start = 0
+  const len = format.length
+  for (let j = 0; j <= len; j++) {
+    if (j === len || format.charCodeAt(j) === COLON) {
+      if (
+        j - start === 2 &&
+        format.charCodeAt(start) === G &&
+        format.charCodeAt(start + 1) === T
+      ) {
+        return col
+      }
+      col++
+      start = j + 1
+    }
+  }
+  return -1
+}
+
 export function processGenotypes(
@@ -31,4 +59,2 @@ format: string,
   const prerestLen = prerest.length
-  const TAB = 9
-  const COLON = 58
   let pos = 0
@@ -49,5 +75,4 @@
 
-  // Check if GT field exists
-  const gtIdx = format.indexOf('GT')
-  if (gtIdx === -1) {
+  const colonCount = gtColumnIndex(format)
+  if (colonCount === -1) {
     return
@@ -57,3 +82,3 @@ }
   // GT is first field but not only field
-  if (gtIdx === 0) {
+  if (colonCount === 0) {
     for (let idx = 0; idx < samplesLen; idx++) {
@@ -77,10 +102,3 @@ const start = pos
 
-  // GT is not first field - need to skip to the right column
-  let colonCount = 0
-  for (let j = 0; j < gtIdx; j++) {
-    if (format.charCodeAt(j) === COLON) {
-      colonCount++
-    }
-  }
-
+  // GT is not first field - skip to its column (colonCount fields precede it)
   for (let idx = 0; idx < samplesLen; idx++) {
@@ -87,0 +105,0 @@ const sampleStart = pos

No alert changes

Improved metrics

Total package byte prevSize

164167

0.89%

Lines of code

3529

0.77%

No dependency changes