@fishka/seqio 0.6.0 → 0.6.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/abif/index.d.mts +18 -3
- package/dist/abif/index.d.ts +18 -3
- package/dist/abif/index.js +1 -1
- package/dist/abif/index.js.map +1 -1
- package/dist/abif/index.mjs +1 -1
- package/dist/abif/index.mjs.map +1 -1
- package/dist/index.d.mts +1 -1
- package/dist/index.d.ts +1 -1
- package/dist/index.js +7 -7
- package/dist/index.js.map +1 -1
- package/dist/index.mjs +7 -7
- package/dist/index.mjs.map +1 -1
- package/package.json +1 -1
package/dist/index.js
CHANGED
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@@ -1,12 +1,12 @@
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1
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-
'use strict';function E(e){let t="";for(let n=0;n<e.length;n++)t+=String.fromCharCode(e[n]);return t}function F(e){let t=new Uint8Array(e.length);for(let n=0;n<e.length;n++)t[n]=e.charCodeAt(n)&255;return t}function w(e){return new DataView(e.buffer,e.byteOffset,e.byteLength)}function x(e,t,n){return e.subarray(t,t+n)}function X(e){return String.fromCharCode(e>>>24&255,e>>>16&255,e>>>8&255,e&255)}var z=128,N=28;function j(e){if(e.byteLength<z)throw new Error(`ABIF too small: ${e.byteLength} bytes`);let t=0;if(E(x(e,0,4))!=="ABIF")if(e.byteLength>=132&&E(x(e,128,4))==="ABIF")t=128;else throw new Error('Not an ABIF file: missing "ABIF" magic.');let n=t;if(e.byteLength-n<z)throw new Error(`ABIF too small: ${e.byteLength-n} bytes after offset ${n}`);let r=w(e),a=r.getInt16(n+4,false),i=_(e,r,n+6,n);if(i.tagName!=="tdir")throw new Error(`Expected "tdir" header entry, got "${i.tagName}"`);if(i.elementSize!==N)throw new Error(`Expected dir element size ${N}, got ${i.elementSize}`);let c=i.raw?.elementCount??i.elementCount,m=Math.max(0,c),u=r.getInt32(n+6+20,false);if(u<0||u+m*N>e.byteLength-n)throw new Error(`Directory out of bounds: offset=${u}, entries=${m}, file=${e.byteLength-n}`);let d=[];for(let T=0;T<m;T++)d.push(_(e,r,n+u+T*N,n));let y=i.raw?.dataSize??m*N,f=n+u+m*N,h=Math.min(Math.max(0,y-m*N),Math.max(0,e.byteLength-f)),o={entryCount:m,rawEntryCount:c,elementType:i.elementType,tagNumber:i.tagNumber,entrySize:i.elementSize,dataSize:y,dataOffset:u,dataOffsetBytes:i.raw?.dataOffsetBytes??new Uint8Array(4),dataHandle:i.dataHandle,paddingBytes:new Uint8Array(x(e,f,h))},g=new Uint8Array(x(e,n+6+N,z-6-N)),A=t===128?new Uint8Array(x(e,0,128)):void 0,C=Y(e,n,u,y,d,t);return {version:a,tdir:o,entries:d,macBinaryOffset:t,macBinaryHeader:A,headerReserved:g,unreferencedRanges:C}}function Y(e,t,n,r,a,i){let c=e.byteLength,m=[];i===128&&m.push([0,128]),m.push([t,t+z]);let u=Math.max(a.length*N,Math.max(0,r));m.push([t+n,t+n+u]);for(let o of a)if(o.raw&&!o.raw.inline){let 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4
4
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${r}
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5
5
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6
6
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${i}
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7
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-
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8
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-
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7
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8
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9
9
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`;let n="";for(let r=0;r<e.length;r+=t)n+=`${e.slice(r,r+t)}
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10
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-
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11
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-
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10
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11
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