@gmod/tabix 3.1.0 → 3.1.2

package/CHANGELOG.md

@@ -1,7 +1,13 @@
-# [3.1.0](https://github.com/GMOD/tabix-js/compare/v3.0.5...v3.1.0) (2025-10-01)
+## [3.1.2](https://github.com/GMOD/tabix-js/compare/v3.1.1...v3.1.2) (2025-11-24)
+
+
 
+## [3.1.1](https://github.com/GMOD/tabix-js/compare/v3.1.0...v3.1.1) (2025-11-19)
 
 
+
+# [3.1.0](https://github.com/GMOD/tabix-js/compare/v3.0.5...v3.1.0) (2025-10-01)
+
 ## [3.0.5](https://github.com/GMOD/tabix-js/compare/v3.0.4...v3.0.5) (2025-05-26)
 
 ## [3.0.4](https://github.com/GMOD/tabix-js/compare/v3.0.3...v3.0.4) (2025-05-13)

package/dist/csi.d.ts

@@ -21,10 +21,6 @@ export default class CSI extends IndexFile {
         format: string;
         coordinateType: string;
     };
-    _parseNameBytes(namesBytes: Uint8Array): {
-        refNameToId: Record<string, number>;
-        refIdToName: string[];
-    };
     _parse(opts?: Options): Promise<{
         csi: boolean;
         refCount: number;

package/dist/csi.js

@@ -85,7 +85,7 @@ class CSI extends indexFile_ts_1.default {
         const dataView = new DataView(bytes.buffer);
         const formatFlags = dataView.getInt32(offset, true);
         const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
-        const format = formats[(formatFlags & 0xF)];
+        const format = formats[(formatFlags & 0xf)];
         if (!format) {
             throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
         }
@@ -109,28 +109,6 @@ class CSI extends indexFile_ts_1.default {
             coordinateType,
         };
     }
-    _parseNameBytes(namesBytes) {
-        let currRefId = 0;
-        let currNameStart = 0;
-        const refIdToName = [];
-        const refNameToId = {};
-        const decoder = new TextDecoder('utf8');
-        for (let i = 0; i < namesBytes.length; i += 1) {
-            if (!namesBytes[i]) {
-                if (currNameStart < i) {
-                    const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
-                    refIdToName[currRefId] = refName;
-                    refNameToId[refName] = currRefId;
-                }
-                currNameStart = i + 1;
-                currRefId += 1;
-            }
-        }
-        return {
-            refNameToId,
-            refIdToName,
-        };
-    }
     async _parse(opts = {}) {
         const bytes = await (0, bgzf_filehandle_1.unzip)(await this.filehandle.readFile(opts));
         const dataView = new DataView(bytes.buffer);

package/dist/csi.js.map

@@ -1 +1 @@
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+{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAmD;AACnD,uCAAmD;AACnD,uCAA0C;AAC1C,uEAA6D;AAE7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,OAAO,GAAG;IACd,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,KAAK;IACR,CAAC,EAAE,KAAK;CACT,CAAA;AAED,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAIxC,YAAY,IAAS;QACnB,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACD,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE,CAAC;YACV,OAAO,KAAK,CAAC,SAAS,CAAA;QACxB,CAAC;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;IACxD,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACnD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,WAAW,GAAG,GAAG,CAAc,CAAC,CAAA;QACxD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACvE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CAAA;QAED,OAAO;YACL,WAAW;YACX,WAAW;YACX,SAAS;YACT,QAAQ;YACR,aAAa;YACb,MAAM;YACN,cAAc;SACf,CAAA;IACH,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAA;QAC/D,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,0BAA0B;QAC1B,IAAI,UAAU,CAAA;QACd,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,UAAU,EAAE,CAAC;YAC/C,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,UAAU,EAAE,CAAC;YACtD,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1D,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GACP,SAAS,IAAI,SAAS,IAAI,EAAE;YAC1B,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC;YAC9B,CAAC,CAAC;gBACE,WAAW,EAAE,EAAE;gBACf,WAAW,EAAE,EAAE;gBACf,QAAQ,EAAE,SAAS;gBACnB,aAAa,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE;gBAC3C,cAAc,EAAE,sBAAsB;gBACtC,MAAM,EAAE,SAAS;aAClB,CAAA;QACP,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,+CAA+C;QAC/C,IAAI,aAAwC,CAAA;QAC5C,IAAI,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QACnC,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;YACnD,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACpD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;gBAChD,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,mEAAmE;oBACnE,2BAA2B;oBAC3B,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oBAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;gBACnC,CAAC;qBAAM,CAAC;oBACN,MAAM,OAAO,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oBAChD,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,OAAO,CAAC,CAAA;oBAC3D,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;oBAC3D,UAAU,IAAI,EAAE,CAAA;oBAChB,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;oBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAA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package/dist/indexFile.d.ts

@@ -44,4 +44,8 @@ export default abstract class IndexFile {
     _findFirstData(currentFdl: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
     parse(opts?: Options): Promise<IndexData>;
     hasRefSeq(seqId: number, opts?: Options): Promise<boolean>;
+    _parseNameBytes(namesBytes: Uint8Array): {
+        refNameToId: Record<string, number>;
+        refIdToName: string[];
+    };
 }

package/dist/indexFile.js

@@ -32,6 +32,28 @@ class IndexFile {
         const idx = await this.parse(opts);
         return !!idx.indices[seqId]?.binIndex;
     }
+    _parseNameBytes(namesBytes) {
+        let currRefId = 0;
+        let currNameStart = 0;
+        const refIdToName = [];
+        const refNameToId = {};
+        const decoder = new TextDecoder('utf8');
+        for (let i = 0; i < namesBytes.length; i += 1) {
+            if (!namesBytes[i]) {
+                if (currNameStart < i) {
+                    const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
+                    refIdToName[currRefId] = refName;
+                    refNameToId[refName] = currRefId;
+                }
+                currNameStart = i + 1;
+                currRefId += 1;
+            }
+        }
+        return {
+            refNameToId,
+            refIdToName,
+        };
+    }
 }
 exports.default = IndexFile;
 //# sourceMappingURL=indexFile.js.map

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package/dist/package.json

@@ -0,0 +1 @@
+{"type": "commonjs"}

package/dist/tabix-bundle.js

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e)(!t||r.maxv.compareTo(t)>0)&&(void 0===a?(n.push(r),a=r):i(a,r)?r.maxv.compareTo(a.maxv)>0&&(a.maxv=r.maxv):(n.push(r),a=r));return n};class n extends Error{}function a(e){if(e&&e.aborted){if("undefined"==typeof DOMException){const e=new n("aborted");throw e.code="ERR_ABORTED",e}throw new DOMException("aborted","AbortError")}}function i(e,t){return t.minv.blockPosition-e.maxv.blockPosition<65e3&&t.maxv.blockPosition-e.minv.blockPosition<5e6}},990:(e,t,n)=>{Object.defineProperty(t,"__esModule",{value:!0}),t._tr_init=function(e){ee||(function(){var e,t,n,a,i,b=new Array(O+1);for(r(s=new Array(2*(k+2))),r(o=new Array(2*x)),r(l=new Array(C)),r(h=new Array(w-p+1)),r(d=new Array(v)),r(f=new 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t,n=4093624447;for(t=0;t<=31;t++,n>>>=1)if(1&n&&0!==e.dyn_ltree[2*t])return a.Z_BINARY;if(0!==e.dyn_ltree[18]||0!==e.dyn_ltree[20]||0!==e.dyn_ltree[26])return a.Z_TEXT;for(t=32;t<y;t++)if(0!==e.dyn_ltree[2*t])return a.Z_TEXT;return a.Z_BINARY}(e)),X(e,e.l_desc),X(e,e.d_desc),h=function(e){var t;for(J(e,e.dyn_ltree,e.l_desc.max_code),J(e,e.dyn_dtree,e.d_desc.max_code),X(e,e.bl_desc),t=S-1;t>=3&&0===e.bl_tree[2*N[t]+1];t--);return e.opt_len+=3*(t+1)+5+5+4,t}(e),r=e.opt_len+3+7>>>3,(l=e.static_len+3+7>>>3)<=r&&(r=l)):r=l=n+5,n+4<=r&&-1!==t?te(e,t,n,i):e.strategy===a.Z_FIXED||l===r?(j(e,(g<<1)+(i?1:0),3),G(e,s,o)):(j(e,(m<<1)+(i?1:0),3),function(e,t,n,a){var i;for(j(e,t-257,5),j(e,n-1,5),j(e,a-4,4),i=0;i<a;i++)j(e,e.bl_tree[2*N[i]+1],3);Q(e,e.dyn_ltree,t-1),Q(e,e.dyn_dtree,n-1)}(e,e.l_desc.max_code+1,e.d_desc.max_code+1,h+1),G(e,e.dyn_ltree,e.dyn_dtree)),W(e),i&&Y(e)},t._tr_tally=function(e,t,n){return e.pending_buf[e.d_buf+2*e.last_lit]=t>>>8&255,e.pending_buf[e.d_buf+2*e.last_lit+1]=255&t,e.pending_buf[e.l_buf+e.last_lit]=255&n,e.last_lit++,0===t?e.dyn_ltree[2*n]++:(e.matches++,t--,e.dyn_ltree[2*(h[n]+y+1)]++,e.dyn_dtree[2*L(t)]++),e.last_lit===e.lit_bufsize-1};const a=n(842),i=n(702);function r(e){for(var t=e.length;--t>=0;)e[t]=0}var s,o,l,h,d,f,u,c,_,b=0,g=1,m=2,p=3,w=258,v=29,y=256,k=y+1+v,x=30,S=19,E=2*k+1,O=15,z=16,R=7,B=256,Z=16,T=17,I=18,A=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0],P=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13],F=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7],N=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15],C=512;function M(e,t,n,a,i){this.static_tree=e,this.extra_bits=t,this.extra_base=n,this.elems=a,this.max_length=i,this.has_stree=e&&e.length}function D(e,t){this.dyn_tree=e,this.max_code=0,this.stat_desc=t}function L(e){return e<256?l[e]:l[256+(e>>>7)]}function 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Q(e,t,n){var a,i,r=-1,s=t[1],o=0,l=7,h=4;for(0===s&&(l=138,h=3),a=0;a<=n;a++)if(i=s,s=t[2*(a+1)+1],!(++o<l&&i===s)){if(o<h)do{H(e,i,e.bl_tree)}while(0!==--o);else 0!==i?(i!==r&&(H(e,i,e.bl_tree),o--),H(e,Z,e.bl_tree),j(e,o-3,2)):o<=10?(H(e,T,e.bl_tree),j(e,o-3,3)):(H(e,I,e.bl_tree),j(e,o-11,7));o=0,r=i,0===s?(l=138,h=3):i===s?(l=6,h=3):(l=7,h=4)}}var ee=!1;function te(e,t,n,a){j(e,(b<<1)+(a?1:0),3),function(e,t,n){Y(e),U(e,n),U(e,~n),(0,i.arraySet)(e.pending_buf,e.window,t,n,e.pending),e.pending+=n}(e,t,n)}}},t={},n=function n(a){var i=t[a];if(void 0!==i)return i.exports;var r=t[a]={exports:{}};return e[a].call(r.exports,r,r.exports,n),r.exports}(159);window.gmodTABIX=n})();

package/dist/tabixIndexedFile.d.ts

@@ -69,6 +69,7 @@ export default class TabixIndexedFile {
      * @returns promise that is resolved when the whole read is finished,
      * rejected on error
      */
+    private calculateFileOffset;
     getLines(refName: string, s: number | undefined, e: number | undefined, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
     getMetadata(opts?: Options): Promise<{
         [key: string]: any;

package/dist/tabixIndexedFile.js

@@ -10,10 +10,6 @@ const quick_lru_1 = __importDefault(require("quick-lru"));
 const csi_ts_1 = __importDefault(require("./csi.js"));
 const tbi_ts_1 = __importDefault(require("./tbi.js"));
 const util_ts_1 = require("./util.js");
-function isASCII(str) {
-    // eslint-disable-next-line no-control-regex
-    return /^[\u0000-\u007F]*$/.test(str);
-}
 class TabixIndexedFile {
     /**
      * @param {object} args
@@ -124,6 +120,12 @@ class TabixIndexedFile {
      * @returns promise that is resolved when the whole read is finished,
      * rejected on error
      */
+    calculateFileOffset(cpositions, dpositions, pos, blockStart, minvDataPosition) {
+        return (cpositions[pos] * (1 << 8) +
+            (blockStart - dpositions[pos]) +
+            minvDataPosition +
+            1);
+    }
     async getLines(refName, s, e, opts) {
         let signal;
         let options = {};
@@ -156,60 +158,71 @@ class TabixIndexedFile {
             let blockStart = 0;
             let pos = 0;
             // fast path, Buffer is just ASCII chars and not gigantor, can be
-            // converted to string and processed directly. if it is not ASCII or
-            // gigantic (chrome max str len is 512Mb), we have to decode line by line
+            // converted to string and processed directly.
+            //
+            // if it is not ASCII or, we have to decode line by line, as it is
+            // otherwise hard to get the right 'fileOffset' based feature IDs
+            //
+            // we use a basic check for isASCII: string length equals buffer length
+            // if it is ASCII...no multi-byte decodings
             const str = decoder.decode(buffer);
-            const strIsASCII = isASCII(str);
-            while (blockStart < str.length) {
-                let line;
-                let n;
-                if (strIsASCII) {
-                    n = str.indexOf('\n', blockStart);
+            const strIsASCII = buffer.length == str.length;
+            if (strIsASCII) {
+                while (blockStart < str.length) {
+                    const n = str.indexOf('\n', blockStart);
                     if (n === -1) {
                         break;
                     }
-                    line = str.slice(blockStart, n);
+                    const line = str.slice(blockStart, n);
+                    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                    if (dpositions) {
+                        const target = blockStart + c.minv.dataPosition;
+                        while (pos < dpositions.length && target >= dpositions[pos]) {
+                            pos++;
+                        }
+                    }
+                    // filter the line for whether it is within the requested range
+                    const { startCoordinate, overlaps } = this.checkLine(metadata, refName, start, end, line);
+                    if (overlaps) {
+                        callback(line, this.calculateFileOffset(cpositions, dpositions, pos, blockStart, c.minv.dataPosition));
+                    }
+                    else if (startCoordinate !== undefined && startCoordinate >= end) {
+                        // the lines were overlapping the region, but now have stopped, so we
+                        // must be at the end of the relevant data and we can stop processing
+                        // data now
+                        return;
+                    }
+                    blockStart = n + 1;
                 }
-                else {
-                    n = buffer.indexOf('\n'.charCodeAt(0), blockStart);
+            }
+            else {
+                while (blockStart < buffer.length) {
+                    const n = buffer.indexOf('\n'.charCodeAt(0), blockStart);
                     if (n === -1) {
                         break;
                     }
                     const b = buffer.slice(blockStart, n);
-                    line = decoder.decode(b);
-                }
-                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-                if (dpositions) {
-                    while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
-                    pos--;
-                }
-                // filter the line for whether it is within the requested range
-                const { startCoordinate, overlaps } = this.checkLine(metadata, refName, start, end, line);
-                if (overlaps) {
-                    callback(line, 
-                    // cpositions[pos] refers to actual file offset of a bgzip block
-                    // boundaries
-                    //
-                    // we multiply by (1 <<8) in order to make sure each block has a
-                    // "unique" address space so that data in that block could never
-                    // overlap
-                    //
-                    // then the blockStart-dpositions is an uncompressed file offset
-                    // from that bgzip block boundary, and since the cpositions are
-                    // multiplied by (1 << 8) these uncompressed offsets get a unique
-                    // space
-                    cpositions[pos] * (1 << 8) +
-                        (blockStart - dpositions[pos]) +
-                        c.minv.dataPosition +
-                        1);
-                }
-                else if (startCoordinate !== undefined && startCoordinate >= end) {
-                    // the lines were overlapping the region, but now have stopped, so we
-                    // must be at the end of the relevant data and we can stop processing
-                    // data now
-                    return;
+                    const line = decoder.decode(b);
+                    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                    if (dpositions) {
+                        const target = blockStart + c.minv.dataPosition;
+                        while (pos < dpositions.length && target >= dpositions[pos]) {
+                            pos++;
+                        }
+                    }
+                    // filter the line for whether it is within the requested range
+                    const { startCoordinate, overlaps } = this.checkLine(metadata, refName, start, end, line);
+                    if (overlaps) {
+                        callback(line, this.calculateFileOffset(cpositions, dpositions, pos, blockStart, c.minv.dataPosition));
+                    }
+                    else if (startCoordinate !== undefined && startCoordinate >= end) {
+                        // the lines were overlapping the region, but now have stopped, so we
+                        // must be at the end of the relevant data and we can stop processing
+                        // data now
+                        return;
+                    }
+                    blockStart = n + 1;
                 }
-                blockStart = n + 1;
             }
         }
     }
@@ -354,11 +367,11 @@ class TabixIndexedFile {
                         };
                     }
                 }
-                currentColumnStart = i + 1;
-                currentColumnNumber += 1;
-                if (currentColumnNumber > maxColumn) {
+                if (currentColumnNumber === maxColumn) {
                     break;
                 }
+                currentColumnStart = i + 1;
+                currentColumnNumber += 1;
             }
         }
         return {
@@ -375,17 +388,10 @@ class TabixIndexedFile {
         // be another pairwise feature at the end of this one
         const isTRA = info.includes('SVTYPE=TRA');
         if (info[0] !== '.' && !isTRA) {
-            let prevChar = ';';
-            for (let j = 0; j < info.length; j += 1) {
-                if (prevChar === ';' && info.slice(j, j + 4) === 'END=') {
-                    let valueEnd = info.indexOf(';', j);
-                    if (valueEnd === -1) {
-                        valueEnd = info.length;
-                    }
-                    endCoordinate = Number.parseInt(info.slice(j + 4, valueEnd), 10);
-                    break;
-                }
-                prevChar = info[j];
+            const endRegex = /(?:^|;)END=([^;]+)/;
+            const match = endRegex.exec(info);
+            if (match) {
+                endCoordinate = Number.parseInt(match[1], 10);
             }
         }
         else if (isTRA) {

package/dist/tabixIndexedFile.js.map

@@ -1 +1 @@
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package/dist/tbi.d.ts

@@ -30,9 +30,5 @@ export default class TabixIndex extends IndexFile {
     parsePseudoBin(bytes: Uint8Array, offset: number): {
         lineCount: number;
     };
-    _parseNameBytes(namesBytes: Uint8Array): {
-        refNameToId: Record<string, number>;
-        refIdToName: string[];
-    };
     blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
 }