@gmod/tabix 2.0.4 → 2.0.5

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Files changed (9) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/README.md +3 -3
  3. package/dist/indexFile.d.ts +0 -1
  4. package/dist/indexFile.js.map +1 -1
  5. package/dist/tabix-bundle.js +1 -1
  6. package/esm/indexFile.d.ts +0 -1
  7. package/esm/indexFile.js.map +1 -1
  8. package/package.json +5 -5
  9. package/src/indexFile.ts +0 -2
package/CHANGELOG.md CHANGED
@@ -1,3 +1,7 @@
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+ ## [2.0.5](https://github.com/GMOD/tabix-js/compare/v2.0.4...v2.0.5) (2025-03-18)
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+
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  ## [2.0.4](https://github.com/GMOD/tabix-js/compare/v2.0.3...v2.0.4) (2024-12-18)
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package/README.md CHANGED
@@ -72,11 +72,11 @@ const remoteTbiIndexed = new TabixIndexedFile({
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  ```
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  You can also alternatively supply a filehandle-like object with the
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- [generic-filehandle](https://github.com/GMOD/generic-filehandle): example
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+ [generic-filehandle2](https://github.com/GMOD/generic-filehandle2): example
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  ```typescript
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- // use a remote file or other filehandle, note RemoteFile comes from https://github.com/GMOD/generic-filehandle
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- const { RemoteFile } = require('generic-filehandle')
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+ // use a remote file or other filehandle, note RemoteFile comes from https://github.com/GMOD/generic-filehandle2
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+ const { RemoteFile } = require('generic-filehandle2')
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  const remoteTbiIndexed = new TabixIndexedFile({
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  filehandle: new RemoteFile('http://yourhost/file.vcf.gz'),
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  tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi'), // can also be csiFilehandle
package/dist/indexFile.d.ts CHANGED
@@ -2,7 +2,6 @@ import { GenericFilehandle } from 'generic-filehandle2';
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  import VirtualOffset from './virtualOffset';
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  import Chunk from './chunk';
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  export interface Options {
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- [key: string]: unknown;
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  signal?: AbortSignal;
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  }
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  export interface IndexData {
package/dist/indexFile.js.map CHANGED
@@ -1 +1 @@
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package/dist/tabix-bundle.js CHANGED
@@ -1 +1 @@
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e.insert=0,4===t?(p(e,!0),0===e.strm.avail_out?3:4):(e.strstart>e.block_start&&(p(e,!1),e.strm.avail_out),1)})),new B(4,4,8,4,z),new B(4,5,16,8,z),new B(4,6,32,32,z),new B(4,4,16,16,S),new B(8,16,32,32,S),new B(8,16,128,128,S),new B(8,32,128,256,S),new B(32,128,258,1024,S),new B(32,258,258,4096,S)],t.deflateInit=function(e,t){return C(e,t,8,15,8,0)},t.deflateInit2=C,t.deflateReset=T,t.deflateResetKeep=I,t.deflateSetHeader=function(e,t){return e&&e.state?2!==e.state.wrap?h:(e.state.gzhead=t,0):h},t.deflate=function(e,t){var i,a,s,l;if(!e||!e.state||t>5||t<0)return e?g(e,h):h;if(a=e.state,!e.output||!e.input&&0!==e.avail_in||a.status===_&&4!==t)return g(e,0===e.avail_out?-5:h);if(a.strm=e,i=a.last_flush,a.last_flush=t,42===a.status)if(2===a.wrap)e.adler=0,v(a,31),v(a,139),v(a,8),a.gzhead?(v(a,(a.gzhead.text?1:0)+(a.gzhead.hcrc?2:0)+(a.gzhead.extra?4:0)+(a.gzhead.name?8:0)+(a.gzhead.comment?16:0)),v(a,255&a.gzhead.time),v(a,a.gzhead.time>>8&255),v(a,a.gzhead.time>>16&255),v(a,a.gzhead.time>>24&255),v(a,9===a.level?2:a.strategy>=2||a.level<2?4:0),v(a,255&a.gzhead.os),a.gzhead.extra&&a.gzhead.extra.length&&(v(a,255&a.gzhead.extra.length),v(a,a.gzhead.extra.length>>8&255)),a.gzhead.hcrc&&(e.adler=o(e.adler,a.pending_buf,a.pending,0)),a.gzindex=0,a.status=69):(v(a,0),v(a,0),v(a,0),v(a,0),v(a,0),v(a,9===a.level?2:a.strategy>=2||a.level<2?4:0),v(a,3),a.status=u);else{var c=8+(a.w_bits-8<<4)<<8;c|=(a.strategy>=2||a.level<2?0:a.level<6?1:6===a.level?2:3)<<6,0!==a.strstart&&(c|=32),c+=31-c%31,a.status=u,k(a,c),0!==a.strstart&&(k(a,e.adler>>>16),k(a,65535&e.adler)),e.adler=1}if(69===a.status)if(a.gzhead.extra){for(s=a.pending;a.gzindex<(65535&a.gzhead.extra.length)&&(a.pending!==a.pending_buf_size||(a.gzhead.hcrc&&a.pending>s&&(e.adler=o(e.adler,a.pending_buf,a.pending-s,s)),m(e),s=a.pending,a.pending!==a.pending_buf_size));)v(a,255&a.gzhead.extra[a.gzindex]),a.gzindex++;a.gzhead.hcrc&&a.pending>s&&(e.adler=o(e.adler,a.pending_buf,a.pending-s,s)),a.gzindex===a.gzhead.extra.length&&(a.gzindex=0,a.status=73)}else a.status=73;if(73===a.status)if(a.gzhead.name){s=a.pending;do{if(a.pending===a.pending_buf_size&&(a.gzhead.hcrc&&a.pending>s&&(e.adler=o(e.adler,a.pending_buf,a.pending-s,s)),m(e),s=a.pending,a.pending===a.pending_buf_size)){l=1;break}l=a.gzindex<a.gzhead.name.length?255&a.gzhead.name.charCodeAt(a.gzindex++):0,v(a,l)}while(0!==l);a.gzhead.hcrc&&a.pending>s&&(e.adler=o(e.adler,a.pending_buf,a.pending-s,s)),0===l&&(a.gzindex=0,a.status=91)}else a.status=91;if(91===a.status)if(a.gzhead.comment){s=a.pending;do{if(a.pending===a.pending_buf_size&&(a.gzhead.hcrc&&a.pending>s&&(e.adler=o(e.adler,a.pending_buf,a.pending-s,s)),m(e),s=a.pending,a.pending===a.pending_buf_size)){l=1;break}l=a.gzindex<a.gzhead.comment.length?255&a.gzhead.comment.charCodeAt(a.gzindex++):0,v(a,l)}while(0!==l);a.gzhead.hcrc&&a.pending>s&&(e.adler=o(e.adler,a.pending_buf,a.pending-s,s)),0===l&&(a.status=f)}else a.status=f;if(a.status===f&&(a.gzhead.hcrc?(a.pending+2>a.pending_buf_size&&m(e),a.pending+2<=a.pending_buf_size&&(v(a,255&e.adler),v(a,e.adler>>8&255),e.adler=0,a.status=u)):a.status=u),0!==a.pending){if(m(e),0===e.avail_out)return a.last_flush=-1,0}else if(0===e.avail_in&&b(t)<=b(i)&&4!==t)return g(e,-5);if(a.status===_&&0!==e.avail_in)return g(e,-5);if(0!==e.avail_in||0!==a.lookahead||0!==t&&a.status!==_){var y=2===a.strategy?function(e,t){for(var i;;){if(0===e.lookahead&&(x(e),0===e.lookahead)){if(0===t)return 1;break}if(e.match_length=0,i=r._tr_tally(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++,i&&(p(e,!1),0===e.strm.avail_out))return 1}return e.insert=0,4===t?(p(e,!0),0===e.strm.avail_out?3:4):e.last_lit&&(p(e,!1),0===e.strm.avail_out)?1:2}(a,t):3===a.strategy?function(e,t){for(var i,n,a,s,o=e.window;;){if(e.lookahead<=d){if(x(e),e.lookahead<=d&&0===t)return 1;if(0===e.lookahead)break}if(e.match_length=0,e.lookahead>=3&&e.strstart>0&&(n=o[a=e.strstart-1])===o[++a]&&n===o[++a]&&n===o[++a]){s=e.strstart+d;do{}while(n===o[++a]&&n===o[++a]&&n===o[++a]&&n===o[++a]&&n===o[++a]&&n===o[++a]&&n===o[++a]&&n===o[++a]&&a<s);e.match_length=d-(s-a),e.match_length>e.lookahead&&(e.match_length=e.lookahead)}if(e.match_length>=3?(i=r._tr_tally(e,1,e.match_length-3),e.lookahead-=e.match_length,e.strstart+=e.match_length,e.match_length=0):(i=r._tr_tally(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++),i&&(p(e,!1),0===e.strm.avail_out))return 1}return e.insert=0,4===t?(p(e,!0),0===e.strm.avail_out?3:4):e.last_lit&&(p(e,!1),0===e.strm.avail_out)?1:2}(a,t):n[a.level].func(a,t);if(3!==y&&4!==y||(a.status=_),1===y||3===y)return 0===e.avail_out&&(a.last_flush=-1),0;if(2===y&&(1===t?r._tr_align(a):5!==t&&(r._tr_stored_block(a,0,0,!1),3===t&&(w(a.head),0===a.lookahead&&(a.strstart=0,a.block_start=0,a.insert=0))),m(e),0===e.avail_out))return a.last_flush=-1,0}return 4!==t?0:a.wrap<=0?1:(2===a.wrap?(v(a,255&e.adler),v(a,e.adler>>8&255),v(a,e.adler>>16&255),v(a,e.adler>>24&255),v(a,255&e.total_in),v(a,e.total_in>>8&255),v(a,e.total_in>>16&255),v(a,e.total_in>>24&255)):(k(a,e.adler>>>16),k(a,65535&e.adler)),m(e),a.wrap>0&&(a.wrap=-a.wrap),0!==a.pending?0:1)},t.deflateEnd=function(e){var t;return e&&e.state?42!==(t=e.state.status)&&69!==t&&73!==t&&91!==t&&t!==f&&t!==u&&t!==_?g(e,h):(e.state=null,t===u?g(e,-3):0):h},t.deflateSetDictionary=function(e,t){var i,n,r,o,l,d,c,f,u=t.length;if(!e||!e.state)return h;if(2===(o=(i=e.state).wrap)||1===o&&42!==i.status||i.lookahead)return h;for(1===o&&(e.adler=s(e.adler,t,u,0)),i.wrap=0,u>=i.w_size&&(0===o&&(w(i.head),i.strstart=0,i.block_start=0,i.insert=0),f=new a.Buf8(i.w_size),a.arraySet(f,t,u-i.w_size,i.w_size,0),t=f,u=i.w_size),l=e.avail_in,d=e.next_in,c=e.input,e.avail_in=u,e.next_in=0,e.input=t,x(i);i.lookahead>=3;){n=i.strstart,r=i.lookahead-2;do{i.ins_h=(i.ins_h<<i.hash_shift^i.window[n+3-1])&i.hash_mask,i.prev[n&i.w_mask]=i.head[i.ins_h],i.head[i.ins_h]=n,n++}while(--r);i.strstart=n,i.lookahead=2,x(i)}return i.strstart+=i.lookahead,i.block_start=i.strstart,i.insert=i.lookahead,i.lookahead=0,i.match_length=i.prev_length=2,i.match_available=0,e.next_in=d,e.input=c,e.avail_in=l,i.wrap=o,0},t.deflateInfo="pako deflate (from Nodeca project)"},414:e=>{"use strict";e.exports=function(){this.text=0,this.time=0,this.xflags=0,this.os=0,this.extra=null,this.extra_len=0,this.name="",this.comment="",this.hcrc=0,this.done=!1}},293:e=>{"use strict";e.exports=function(e,t){var i,n,a,r,s,o,l,h,d,c,f,u,_,g,b,w,m,p,v,k,y,x,z,S,B;i=e.state,n=e.next_in,S=e.input,a=n+(e.avail_in-5),r=e.next_out,B=e.output,s=r-(t-e.avail_out),o=r+(e.avail_out-257),l=i.dmax,h=i.wsize,d=i.whave,c=i.wnext,f=i.window,u=i.hold,_=i.bits,g=i.lencode,b=i.distcode,w=(1<<i.lenbits)-1,m=(1<<i.distbits)-1;e:do{_<15&&(u+=S[n++]<<_,_+=8,u+=S[n++]<<_,_+=8),p=g[u&w];t:for(;;){if(u>>>=v=p>>>24,_-=v,0==(v=p>>>16&255))B[r++]=65535&p;else{if(!(16&v)){if(64&v){if(32&v){i.mode=12;break e}e.msg="invalid literal/length code",i.mode=30;break e}p=g[(65535&p)+(u&(1<<v)-1)];continue t}for(k=65535&p,(v&=15)&&(_<v&&(u+=S[n++]<<_,_+=8),k+=u&(1<<v)-1,u>>>=v,_-=v),_<15&&(u+=S[n++]<<_,_+=8,u+=S[n++]<<_,_+=8),p=b[u&m];;){if(u>>>=v=p>>>24,_-=v,16&(v=p>>>16&255)){if(y=65535&p,_<(v&=15)&&(u+=S[n++]<<_,(_+=8)<v&&(u+=S[n++]<<_,_+=8)),(y+=u&(1<<v)-1)>l){e.msg="invalid distance too far back",i.mode=30;break e}if(u>>>=v,_-=v,y>(v=r-s)){if((v=y-v)>d&&i.sane){e.msg="invalid distance too far back",i.mode=30;break 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f(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new n.Buf16(320),this.work=new n.Buf16(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}function u(e){var t;return e&&e.state?(t=e.state,e.total_in=e.total_out=t.total=0,e.msg="",t.wrap&&(e.adler=1&t.wrap),t.mode=1,t.last=0,t.havedict=0,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new n.Buf32(852),t.distcode=t.distdyn=new n.Buf32(592),t.sane=1,t.back=-1,0):l}function _(e){var t;return e&&e.state?((t=e.state).wsize=0,t.whave=0,t.wnext=0,u(e)):l}function g(e,t){var i,n;return 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e;b--,m+=f[_++]<<p,p+=8}if(2&i.wrap&&35615===m){i.check=0,M[0]=255&m,M[1]=m>>>8&255,i.check=r(i.check,M,2,0),m=0,p=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&m)<<8)+(m>>8))%31){e.msg="incorrect header check",i.mode=d;break}if(8!=(15&m)){e.msg="unknown compression method",i.mode=d;break}if(p-=4,O=8+(15&(m>>>=4)),0===i.wbits)i.wbits=O;else if(O>i.wbits){e.msg="invalid window size",i.mode=d;break}i.dmax=1<<O,e.adler=i.check=1,i.mode=512&m?10:h,m=0,p=0;break;case 2:for(;p<16;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(i.flags=m,8!=(255&i.flags)){e.msg="unknown compression method",i.mode=d;break}if(57344&i.flags){e.msg="unknown header flags set",i.mode=d;break}i.head&&(i.head.text=m>>8&1),512&i.flags&&(M[0]=255&m,M[1]=m>>>8&255,i.check=r(i.check,M,2,0)),m=0,p=0,i.mode=3;case 3:for(;p<32;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}i.head&&(i.head.time=m),512&i.flags&&(M[0]=255&m,M[1]=m>>>8&255,M[2]=m>>>16&255,M[3]=m>>>24&255,i.check=r(i.check,M,4,0)),m=0,p=0,i.mode=4;case 4:for(;p<16;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}i.head&&(i.head.xflags=255&m,i.head.os=m>>8),512&i.flags&&(M[0]=255&m,M[1]=m>>>8&255,i.check=r(i.check,M,2,0)),m=0,p=0,i.mode=5;case 5:if(1024&i.flags){for(;p<16;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}i.length=m,i.head&&(i.head.extra_len=m),512&i.flags&&(M[0]=255&m,M[1]=m>>>8&255,i.check=r(i.check,M,2,0)),m=0,p=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&((z=i.length)>b&&(z=b),z&&(i.head&&(O=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Array(i.head.extra_len)),n.arraySet(i.head.extra,f,_,z,O)),512&i.flags&&(i.check=r(i.check,f,z,_)),b-=z,_+=z,i.length-=z),i.length))break e;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===b)break e;z=0;do{O=f[_+z++],i.head&&O&&i.length<65536&&(i.head.name+=String.fromCharCode(O))}while(O&&z<b);if(512&i.flags&&(i.check=r(i.check,f,z,_)),b-=z,_+=z,O)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=8;case 8:if(4096&i.flags){if(0===b)break e;z=0;do{O=f[_+z++],i.head&&O&&i.length<65536&&(i.head.comment+=String.fromCharCode(O))}while(O&&z<b);if(512&i.flags&&(i.check=r(i.check,f,z,_)),b-=z,_+=z,O)break e}else i.head&&(i.head.comment=null);i.mode=9;case 9:if(512&i.flags){for(;p<16;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(m!==(65535&i.check)){e.msg="header crc mismatch",i.mode=d;break}m=0,p=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=h;break;case 10:for(;p<32;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}e.adler=i.check=c(m),m=0,p=0,i.mode=11;case 11:if(0===i.havedict)return e.next_out=g,e.avail_out=w,e.next_in=_,e.avail_in=b,i.hold=m,i.bits=p,2;e.adler=i.check=1,i.mode=h;case h:if(5===t||6===t)break e;case 13:if(i.last){m>>>=7&p,p-=7&p,i.mode=27;break}for(;p<3;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}switch(i.last=1&m,p-=1,3&(m>>>=1)){case 0:i.mode=14;break;case 1:if(v(i),i.mode=20,6===t){m>>>=2,p-=2;break e}break;case 2:i.mode=17;break;case 3:e.msg="invalid block type",i.mode=d}m>>>=2,p-=2;break;case 14:for(m>>>=7&p,p-=7&p;p<32;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if((65535&m)!=(m>>>16^65535)){e.msg="invalid stored block lengths",i.mode=d;break}if(i.length=65535&m,m=0,p=0,i.mode=15,6===t)break e;case 15:i.mode=16;case 16:if(z=i.length){if(z>b&&(z=b),z>w&&(z=w),0===z)break e;n.arraySet(u,f,_,z,g),b-=z,_+=z,w-=z,g+=z,i.length-=z;break}i.mode=h;break;case 17:for(;p<14;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(i.nlen=257+(31&m),m>>>=5,p-=5,i.ndist=1+(31&m),m>>>=5,p-=5,i.ncode=4+(15&m),m>>>=4,p-=4,i.nlen>286||i.ndist>30){e.msg="too many length or distance symbols",i.mode=d;break}i.have=0,i.mode=18;case 18:for(;i.have<i.ncode;){for(;p<3;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}i.lens[U[i.have++]]=7&m,m>>>=3,p-=3}for(;i.have<19;)i.lens[U[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,N={bits:i.lenbits},R=o(0,i.lens,0,19,i.lencode,0,i.work,N),i.lenbits=N.bits,R){e.msg="invalid code lengths set",i.mode=d;break}i.have=0,i.mode=19;case 19:for(;i.have<i.nlen+i.ndist;){for(;I=(D=i.lencode[m&(1<<i.lenbits)-1])>>>16&255,T=65535&D,!((E=D>>>24)<=p);){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(T<16)m>>>=E,p-=E,i.lens[i.have++]=T;else{if(16===T){for(F=E+2;p<F;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(m>>>=E,p-=E,0===i.have){e.msg="invalid bit length repeat",i.mode=d;break}O=i.lens[i.have-1],z=3+(3&m),m>>>=2,p-=2}else if(17===T){for(F=E+3;p<F;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}p-=E,O=0,z=3+(7&(m>>>=E)),m>>>=3,p-=3}else{for(F=E+7;p<F;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}p-=E,O=0,z=11+(127&(m>>>=E)),m>>>=7,p-=7}if(i.have+z>i.nlen+i.ndist){e.msg="invalid bit length repeat",i.mode=d;break}for(;z--;)i.lens[i.have++]=O}}if(i.mode===d)break;if(0===i.lens[256]){e.msg="invalid code -- missing end-of-block",i.mode=d;break}if(i.lenbits=9,N={bits:i.lenbits},R=o(1,i.lens,0,i.nlen,i.lencode,0,i.work,N),i.lenbits=N.bits,R){e.msg="invalid literal/lengths set",i.mode=d;break}if(i.distbits=6,i.distcode=i.distdyn,N={bits:i.distbits},R=o(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,N),i.distbits=N.bits,R){e.msg="invalid distances set",i.mode=d;break}if(i.mode=20,6===t)break e;case 20:i.mode=21;case 21:if(b>=6&&w>=258){e.next_out=g,e.avail_out=w,e.next_in=_,e.avail_in=b,i.hold=m,i.bits=p,s(e,x),g=e.next_out,u=e.output,w=e.avail_out,_=e.next_in,f=e.input,b=e.avail_in,m=i.hold,p=i.bits,i.mode===h&&(i.back=-1);break}for(i.back=0;I=(D=i.lencode[m&(1<<i.lenbits)-1])>>>16&255,T=65535&D,!((E=D>>>24)<=p);){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(I&&!(240&I)){for(C=E,A=I,P=T;I=(D=i.lencode[P+((m&(1<<C+A)-1)>>C)])>>>16&255,T=65535&D,!(C+(E=D>>>24)<=p);){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}m>>>=C,p-=C,i.back+=C}if(m>>>=E,p-=E,i.back+=E,i.length=T,0===I){i.mode=26;break}if(32&I){i.back=-1,i.mode=h;break}if(64&I){e.msg="invalid literal/length code",i.mode=d;break}i.extra=15&I,i.mode=22;case 22:if(i.extra){for(F=i.extra;p<F;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}i.length+=m&(1<<i.extra)-1,m>>>=i.extra,p-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;I=(D=i.distcode[m&(1<<i.distbits)-1])>>>16&255,T=65535&D,!((E=D>>>24)<=p);){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(!(240&I)){for(C=E,A=I,P=T;I=(D=i.distcode[P+((m&(1<<C+A)-1)>>C)])>>>16&255,T=65535&D,!(C+(E=D>>>24)<=p);){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}m>>>=C,p-=C,i.back+=C}if(m>>>=E,p-=E,i.back+=E,64&I){e.msg="invalid distance code",i.mode=d;break}i.offset=T,i.extra=15&I,i.mode=24;case 24:if(i.extra){for(F=i.extra;p<F;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}i.offset+=m&(1<<i.extra)-1,m>>>=i.extra,p-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg="invalid distance too far back",i.mode=d;break}i.mode=25;case 25:if(0===w)break e;if(z=x-w,i.offset>z){if((z=i.offset-z)>i.whave&&i.sane){e.msg="invalid distance too far back",i.mode=d;break}z>i.wnext?(z-=i.wnext,S=i.wsize-z):S=i.wnext-z,z>i.length&&(z=i.length),B=i.window}else B=u,S=g-i.offset,z=i.length;z>w&&(z=w),w-=z,i.length-=z;do{u[g++]=B[S++]}while(--z);0===i.length&&(i.mode=21);break;case 26:if(0===w)break e;u[g++]=i.length,w--,i.mode=21;break;case 27:if(i.wrap){for(;p<32;){if(0===b)break e;b--,m|=f[_++]<<p,p+=8}if(x-=w,e.total_out+=x,i.total+=x,x&&(e.adler=i.check=i.flags?r(i.check,u,x,g-x):a(i.check,u,x,g-x)),x=w,(i.flags?m:c(m))!==i.check){e.msg="incorrect data check",i.mode=d;break}m=0,p=0}i.mode=28;case 28:if(i.wrap&&i.flags){for(;p<32;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(m!==(4294967295&i.total)){e.msg="incorrect length check",i.mode=d;break}m=0,p=0}i.mode=29;case 29:R=1;break e;case d:R=-3;break e;case 31:return-4;default:return l}return e.next_out=g,e.avail_out=w,e.next_in=_,e.avail_in=b,i.hold=m,i.bits=p,(i.wsize||x!==e.avail_out&&i.mode<d&&(i.mode<27||4!==t))&&k(e,e.output,e.next_out,x-e.avail_out)?(i.mode=31,-4):(y-=e.avail_in,x-=e.avail_out,e.total_in+=y,e.total_out+=x,i.total+=x,i.wrap&&x&&(e.adler=i.check=i.flags?r(i.check,u,x,e.next_out-x):a(i.check,u,x,e.next_out-x)),e.data_type=i.bits+(i.last?64:0)+(i.mode===h?128:0)+(20===i.mode||15===i.mode?256:0),(0===y&&0===x||4===t)&&0===R&&(R=-5),R)},t.inflateEnd=function(e){if(!e||!e.state)return l;var t=e.state;return t.window&&(t.window=null),e.state=null,0},t.inflateGetHeader=function(e,t){var i;return e&&e.state&&2&(i=e.state).wrap?(i.head=t,t.done=!1,0):l},t.inflateSetDictionary=function(e,t){var i,n=t.length;return e&&e.state?0!==(i=e.state).wrap&&11!==i.mode?l:11===i.mode&&a(1,t,n,0)!==i.check?-3:k(e,t,n,n)?(i.mode=31,-4):(i.havedict=1,0):l},t.inflateInfo="pako inflate (from Nodeca project)"},998:(e,t,i)=>{"use strict";var n=i(805),a=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],r=[16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78],s=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0],o=[16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64];e.exports=function(e,t,i,l,h,d,c,f){var u,_,g,b,w,m,p,v,k,y=f.bits,x=0,z=0,S=0,B=0,E=0,I=0,T=0,C=0,A=0,P=0,O=null,R=0,N=new n.Buf16(16),F=new n.Buf16(16),D=null,M=0;for(x=0;x<=15;x++)N[x]=0;for(z=0;z<l;z++)N[t[i+z]]++;for(E=y,B=15;B>=1&&0===N[B];B--);if(E>B&&(E=B),0===B)return h[d++]=20971520,h[d++]=20971520,f.bits=1,0;for(S=1;S<B&&0===N[S];S++);for(E<S&&(E=S),C=1,x=1;x<=15;x++)if(C<<=1,(C-=N[x])<0)return-1;if(C>0&&(0===e||1!==B))return-1;for(F[1]=0,x=1;x<15;x++)F[x+1]=F[x]+N[x];for(z=0;z<l;z++)0!==t[i+z]&&(c[F[t[i+z]]++]=z);if(0===e?(O=D=c,m=19):1===e?(O=a,R-=257,D=r,M-=257,m=256):(O=s,D=o,m=-1),P=0,z=0,x=S,w=d,I=E,T=0,g=-1,b=(A=1<<E)-1,1===e&&A>852||2===e&&A>592)return 1;for(;;){p=x-T,c[z]<m?(v=0,k=c[z]):c[z]>m?(v=D[M+c[z]],k=O[R+c[z]]):(v=96,k=0),u=1<<x-T,S=_=1<<I;do{h[w+(P>>T)+(_-=u)]=p<<24|v<<16|k}while(0!==_);for(u=1<<x-1;P&u;)u>>=1;if(0!==u?(P&=u-1,P+=u):P=0,z++,0==--N[x]){if(x===B)break;x=t[i+c[z]]}if(x>E&&(P&b)!==g){for(0===T&&(T=E),w+=S,C=1<<(I=x-T);I+T<B&&!((C-=N[I+T])<=0);)I++,C<<=1;if(A+=1<<I,1===e&&A>852||2===e&&A>592)return 1;h[g=P&b]=E<<24|I<<16|w-d}}return 0!==P&&(h[w+P]=x-T<<24|64<<16),f.bits=E,0}},674:e=>{"use strict";e.exports={2:"need dictionary",1:"stream end",0:"","-1":"file error","-2":"stream error","-3":"data 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C(e,t,i){var n,a,o,l,h=0;if(0!==e.last_lit)do{n=e.pending_buf[e.d_buf+2*h]<<8|e.pending_buf[e.d_buf+2*h+1],a=e.pending_buf[e.l_buf+h],h++,0===n?x(e,a,t):(x(e,(o=f[a])+256+1,t),0!==(l=r[o])&&y(e,a-=u[o],l),x(e,o=v(--n),i),0!==(l=s[o])&&y(e,n-=w[o],l))}while(h<e.last_lit);x(e,256,t)}function A(e,t){var i,n,a,r=t.dyn_tree,s=t.stat_desc.static_tree,o=t.stat_desc.has_stree,l=t.stat_desc.elems,h=-1;for(e.heap_len=0,e.heap_max=573,i=0;i<l;i++)0!==r[2*i]?(e.heap[++e.heap_len]=h=i,e.depth[i]=0):r[2*i+1]=0;for(;e.heap_len<2;)r[2*(a=e.heap[++e.heap_len]=h<2?++h:0)]=1,e.depth[a]=0,e.opt_len--,o&&(e.static_len-=s[2*a+1]);for(t.max_code=h,i=e.heap_len>>1;i>=1;i--)T(e,r,i);a=l;do{i=e.heap[1],e.heap[1]=e.heap[e.heap_len--],T(e,r,1),n=e.heap[1],e.heap[--e.heap_max]=i,e.heap[--e.heap_max]=n,r[2*a]=r[2*i]+r[2*n],e.depth[a]=(e.depth[i]>=e.depth[n]?e.depth[i]:e.depth[n])+1,r[2*i+1]=r[2*n+1]=a,e.heap[1]=a++,T(e,r,1)}while(e.heap_len>=2);e.heap[--e.heap_max]=e.heap[1],function(e,t){var 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4===s?(i=n.deflateEnd(this.strm),this.onEnd(i),this.ended=!0,0===i):2!==s||(this.onEnd(0),o.avail_out=0,!0)},h.prototype.onData=function(e){this.chunks.push(e)},h.prototype.onEnd=function(e){0===e&&("string"===this.options.to?this.result=this.chunks.join(""):this.result=a.flattenChunks(this.chunks)),this.chunks=[],this.err=e,this.msg=this.strm.msg},t.Deflate=h,t.deflate=d,t.deflateRaw=function(e,t){return(t=t||{}).raw=!0,d(e,t)},t.gzip=function(e,t){return(t=t||{}).gzip=!0,d(e,t)}},392:e=>{"use strict";class t{constructor(e={}){if(!(e.maxSize&&e.maxSize>0))throw new TypeError("`maxSize` must be a number greater than 0");this.maxSize=e.maxSize,this.cache=new Map,this.oldCache=new Map,this._size=0}_set(e,t){this.cache.set(e,t),this._size++,this._size>=this.maxSize&&(this._size=0,this.oldCache=this.cache,this.cache=new Map)}get(e){if(this.cache.has(e))return this.cache.get(e);if(this.oldCache.has(e)){const t=this.oldCache.get(e);return this.oldCache.delete(e),this._set(e,t),t}}set(e,t){return this.cache.has(e)?this.cache.set(e,t):this._set(e,t),this}has(e){return this.cache.has(e)||this.oldCache.has(e)}peek(e){return this.cache.has(e)?this.cache.get(e):this.oldCache.has(e)?this.oldCache.get(e):void 0}delete(e){const t=this.cache.delete(e);return t&&this._size--,this.oldCache.delete(e)||t}clear(){this.cache.clear(),this.oldCache.clear(),this._size=0}*keys(){for(const[e]of this)yield e}*values(){for(const[,e]of this)yield e}*[Symbol.iterator](){for(const e of this.cache)yield e;for(const e of this.oldCache){const[t]=e;this.cache.has(t)||(yield e)}}get size(){let e=0;for(const t of this.oldCache.keys())this.cache.has(t)||e++;return this._size+e}}e.exports=t},411:(e,t,i)=>{"use strict";var n,a=i(805),r=i(665),s=i(269),o=i(823),l=i(674),h=-2,d=258,c=262,f=103,u=113,_=666;function g(e,t){return e.msg=l[t],t}function b(e){return(e<<1)-(e>4?9:0)}function w(e){for(var t=e.length;--t>=0;)e[t]=0}function m(e){var t=e.state,i=t.pending;i>e.avail_out&&(i=e.avail_out),0!==i&&(a.arraySet(e.output,t.pending_buf,t.pending_out,i,e.next_out),e.next_out+=i,t.pending_out+=i,e.total_out+=i,e.avail_out-=i,t.pending-=i,0===t.pending&&(t.pending_out=0))}function p(e,t){r._tr_flush_block(e,e.block_start>=0?e.block_start:-1,e.strstart-e.block_start,t),e.block_start=e.strstart,m(e.strm)}function v(e,t){e.pending_buf[e.pending++]=t}function k(e,t){e.pending_buf[e.pending++]=t>>>8&255,e.pending_buf[e.pending++]=255&t}function y(e,t){var i,n,a=e.max_chain_length,r=e.strstart,s=e.prev_length,o=e.nice_match,l=e.strstart>e.w_size-c?e.strstart-(e.w_size-c):0,h=e.window,f=e.w_mask,u=e.prev,_=e.strstart+d,g=h[r+s-1],b=h[r+s];e.prev_length>=e.good_match&&(a>>=2),o>e.lookahead&&(o=e.lookahead);do{if(h[(i=t)+s]===b&&h[i+s-1]===g&&h[i]===h[r]&&h[++i]===h[r+1]){r+=2,i++;do{}while(h[++r]===h[++i]&&h[++r]===h[++i]&&h[++r]===h[++i]&&h[++r]===h[++i]&&h[++r]===h[++i]&&h[++r]===h[++i]&&h[++r]===h[++i]&&h[++r]===h[++i]&&r<_);if(n=d-(_-r),r=_-d,n>s){if(e.match_start=t,s=n,n>=o)break;g=h[r+s-1],b=h[r+s]}}}while((t=u[t&f])>l&&0!=--a);return s<=e.lookahead?s:e.lookahead}function x(e){var t,i,n,r,l,h,d,f,u,_,g=e.w_size;do{if(r=e.window_size-e.lookahead-e.strstart,e.strstart>=g+(g-c)){a.arraySet(e.window,e.window,g,g,0),e.match_start-=g,e.strstart-=g,e.block_start-=g,t=i=e.hash_size;do{n=e.head[--t],e.head[t]=n>=g?n-g:0}while(--i);t=i=g;do{n=e.prev[--t],e.prev[t]=n>=g?n-g:0}while(--i);r+=g}if(0===e.strm.avail_in)break;if(h=e.strm,d=e.window,f=e.strstart+e.lookahead,u=r,_=void 0,(_=h.avail_in)>u&&(_=u),i=0===_?0:(h.avail_in-=_,a.arraySet(d,h.input,h.next_in,_,f),1===h.state.wrap?h.adler=s(h.adler,d,_,f):2===h.state.wrap&&(h.adler=o(h.adler,d,_,f)),h.next_in+=_,h.total_in+=_,_),e.lookahead+=i,e.lookahead+e.insert>=3)for(l=e.strstart-e.insert,e.ins_h=e.window[l],e.ins_h=(e.ins_h<<e.hash_shift^e.window[l+1])&e.hash_mask;e.insert&&(e.ins_h=(e.ins_h<<e.hash_shift^e.window[l+3-1])&e.hash_mask,e.prev[l&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=l,l++,e.insert--,!(e.lookahead+e.insert<3)););}while(e.lookahead<c&&0!==e.strm.avail_in)}function z(e,t){for(var i,n;;){if(e.lookahead<c){if(x(e),e.lookahead<c&&0===t)return 1;if(0===e.lookahead)break}if(i=0,e.lookahead>=3&&(e.ins_h=(e.ins_h<<e.hash_shift^e.window[e.strstart+3-1])&e.hash_mask,i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),0!==i&&e.strstart-i<=e.w_size-c&&(e.match_length=y(e,i)),e.match_length>=3)if(n=r._tr_tally(e,e.strstart-e.match_start,e.match_length-3),e.lookahead-=e.match_length,e.match_length<=e.max_lazy_match&&e.lookahead>=3){e.match_length--;do{e.strstart++,e.ins_h=(e.ins_h<<e.hash_shift^e.window[e.strstart+3-1])&e.hash_mask,i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart}while(0!=--e.match_length);e.strstart++}else e.strstart+=e.match_length,e.match_length=0,e.ins_h=e.window[e.strstart],e.ins_h=(e.ins_h<<e.hash_shift^e.window[e.strstart+1])&e.hash_mask;else n=r._tr_tally(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++;if(n&&(p(e,!1),0===e.strm.avail_out))return 1}return e.insert=e.strstart<2?e.strstart:2,4===t?(p(e,!0),0===e.strm.avail_out?3:4):e.last_lit&&(p(e,!1),0===e.strm.avail_out)?1:2}function S(e,t){for(var i,n,a;;){if(e.lookahead<c){if(x(e),e.lookahead<c&&0===t)return 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if(e.match_available){if((n=r._tr_tally(e,0,e.window[e.strstart-1]))&&p(e,!1),e.strstart++,e.lookahead--,0===e.strm.avail_out)return 1}else e.match_available=1,e.strstart++,e.lookahead--}return e.match_available&&(n=r._tr_tally(e,0,e.window[e.strstart-1]),e.match_available=0),e.insert=e.strstart<2?e.strstart:2,4===t?(p(e,!0),0===e.strm.avail_out?3:4):e.last_lit&&(p(e,!1),0===e.strm.avail_out)?1:2}function B(e,t,i,n,a){this.good_length=e,this.max_lazy=t,this.nice_length=i,this.max_chain=n,this.func=a}function 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a.Buf16(573),w(this.depth),this.l_buf=0,this.lit_bufsize=0,this.last_lit=0,this.d_buf=0,this.opt_len=0,this.static_len=0,this.matches=0,this.insert=0,this.bi_buf=0,this.bi_valid=0}function I(e){var t;return e&&e.state?(e.total_in=e.total_out=0,e.data_type=2,(t=e.state).pending=0,t.pending_out=0,t.wrap<0&&(t.wrap=-t.wrap),t.status=t.wrap?42:u,e.adler=2===t.wrap?0:1,t.last_flush=0,r._tr_init(t),0):g(e,h)}function T(e){var t,i=I(e);return 0===i&&((t=e.state).window_size=2*t.w_size,w(t.head),t.max_lazy_match=n[t.level].max_lazy,t.good_match=n[t.level].good_length,t.nice_match=n[t.level].nice_length,t.max_chain_length=n[t.level].max_chain,t.strstart=0,t.block_start=0,t.lookahead=0,t.insert=0,t.match_length=t.prev_length=2,t.match_available=0,t.ins_h=0),i}function C(e,t,i,n,r,s){if(!e)return h;var o=1;if(-1===t&&(t=6),n<0?(o=0,n=-n):n>15&&(o=2,n-=16),r<1||r>9||8!==i||n<8||n>15||t<0||t>9||s<0||s>4)return g(e,h);8===n&&(n=9);var l=new E;return 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e;z=0;do{O=f[_+z++],i.head&&O&&i.length<65536&&(i.head.name+=String.fromCharCode(O))}while(O&&z<b);if(512&i.flags&&(i.check=r(i.check,f,z,_)),b-=z,_+=z,O)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=8;case 8:if(4096&i.flags){if(0===b)break e;z=0;do{O=f[_+z++],i.head&&O&&i.length<65536&&(i.head.comment+=String.fromCharCode(O))}while(O&&z<b);if(512&i.flags&&(i.check=r(i.check,f,z,_)),b-=z,_+=z,O)break e}else i.head&&(i.head.comment=null);i.mode=9;case 9:if(512&i.flags){for(;p<16;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(m!==(65535&i.check)){e.msg="header crc mismatch",i.mode=d;break}m=0,p=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=h;break;case 10:for(;p<32;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}e.adler=i.check=c(m),m=0,p=0,i.mode=11;case 11:if(0===i.havedict)return e.next_out=g,e.avail_out=w,e.next_in=_,e.avail_in=b,i.hold=m,i.bits=p,2;e.adler=i.check=1,i.mode=h;case h:if(5===t||6===t)break e;case 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@@ -2,7 +2,6 @@ import { GenericFilehandle } from 'generic-filehandle2';
2
2
  import VirtualOffset from './virtualOffset';
3
3
  import Chunk from './chunk';
4
4
  export interface Options {
5
- [key: string]: unknown;
6
5
  signal?: AbortSignal;
7
6
  }
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  export interface IndexData {
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/tabix",
3
- "version": "2.0.4",
3
+ "version": "2.0.5",
4
4
  "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/tabix-js",
@@ -52,18 +52,18 @@
52
52
  "@types/node": "^20.11.16",
53
53
  "@typescript-eslint/eslint-plugin": "^8.0.1",
54
54
  "@typescript-eslint/parser": "^8.0.1",
55
- "@vitest/coverage-v8": "^2.0.5",
55
+ "@vitest/coverage-v8": "^3.0.1",
56
56
  "documentation": "^14.0.3",
57
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  "eslint": "^9.9.0",
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- "eslint-plugin-unicorn": "^56.0.0",
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+ "eslint-plugin-unicorn": "^57.0.0",
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  "prettier": "^3.3.3",
60
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  "rimraf": "^6.0.1",
61
61
  "standard-changelog": "^6.0.0",
62
62
  "typescript": "^5.7.0",
63
63
  "typescript-eslint": "^8.0.1",
64
- "vitest": "^2.0.5",
64
+ "vitest": "^3.0.1",
65
65
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66
- "webpack-cli": "^5.1.4"
66
+ "webpack-cli": "^6.0.1"
67
67
  },
68
68
  "publishConfig": {
69
69
  "access": "public"
package/src/indexFile.ts CHANGED
@@ -3,8 +3,6 @@ import VirtualOffset from './virtualOffset'
3
3
  import Chunk from './chunk'
4
4
 
5
5
  export interface Options {
6
- // support having some unknown parts of the options
7
- [key: string]: unknown
8
6
  signal?: AbortSignal
9
7
  }
10
8