@fishka/seqio 0.7.0 → 0.8.0
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/index.d.mts +61 -2
- package/dist/index.d.ts +61 -2
- package/dist/index.js +10 -10
- package/dist/index.js.map +1 -1
- package/dist/index.mjs +10 -10
- package/dist/index.mjs.map +1 -1
- package/package.json +1 -1
package/dist/index.mjs
CHANGED
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@@ -1,14 +1,14 @@
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1
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`))}var O=class{constructor(){this.order=[];this.blocks=new Map;}add(t,n){let r=this.blocks.get(t);r?r.push(n):(this.blocks.set(t,[n]),this.order.push(t));}toRecords(){return this.order.map(t=>F(t,"",E((this.blocks.get(t)??[]).join(""))))}},Ge=/^[A-Za-z0-9.*?~-]+$/;function gn(e){let t=new O,n=false;for(let r of x(e)){if(L(r)||/^\s/.test(r)||!n&&(n=true,/multiple (sequence )?alignment/i.test(r)||/^(CLUSTAL|MUSCLE|MAFFT|T-?COFFEE|PROBCONS|KALIGN|MVIEW|PROMALS)/i.test(r)))continue;let i=/^(\S+)\s+(\S+)/.exec(r);i&&Ge.test(i[2])&&t.add(i[1],i[2]);}return t.toRecords()}function pn(e){let t=[],n=new O;for(let r of x(e)){if(r.startsWith("//")){t.push(...n.toRecords()),n=new O;continue}if(L(r)||r.startsWith("#"))continue;let i=/^(\S+)\s+(\S+)/.exec(r);i&&n.add(i[1],i[2]);}return t.push(...n.toRecords()),t}function hn(e){let t=x(e),n=0;for(;n<t.length&&L(t[n]);)n++;let r=(t[n]??"").trim().split(/\s+/),i=Number.parseInt(r[0]??"",10),o=Number.parseInt(r[1]??"",10);if(!Number.isFinite(i)||i<=0)return [];n++;let a=[],s=[];for(;n<t.length&&a.length<i;n++){if(L(t[n]))continue;let d=/^(\S+)\s+(.*)$/.exec(t[n]);d&&(a.push(d[1]),s.push(d[2].replace(/\s+/g,"")));}let c=a.length;if(c===0)return [];let m=Number.isFinite(o)&&o>0?o:Number.POSITIVE_INFINITY;for(let d=0;n<t.length;n++){if(L(t[n]))continue;let u=d%c;s[u].length<m&&(s[u]+=t[n].replace(/\s+/g,"")),d++;}return a.map((d,u)=>F(d,"",m===Number.POSITIVE_INFINITY?s[u]:s[u].slice(0,m)))}function bn(e){let t=z(e).replace(/\[[^\]]*\]/g,""),n=new O,r=false;for(let i of t.split(/\r\n|\r|\n/)){if(!r){/^\s*matrix\b/i.test(i)&&(r=true);continue}let o=i.trim();if(o===";")break;if(L(o))continue;let a=o.endsWith(";"),s=a?o.slice(0,-1).trim():o,c=/^("[^"]+"|'[^']+'|\S+)\s+(.+)$/.exec(s);if(c&&n.add(c[1].replace(/^['"]|['"]$/g,""),c[2].replace(/\s+/g,"")),a)break}return n.toRecords()}function An(e){let t=new O,n=false;for(let r of x(e)){if(!n){r.trimStart().startsWith("//")&&(n=true);continue}if(L(r))continue;let i=/^\s*(\S+)\s+(.+)$/.exec(r);i&&t.add(i[1],i[2].replace(/\s+/g,""));}return t.toRecords()}function Cn(e){let t=[],n,r="",i=[],o=false,a=()=>{if(n===void 0)return;let s=E(i.join(""));s.endsWith("*")&&(s=s.slice(0,-1)),t.push(F(n,r,s)),n=void 0,r="",i=[],o=false;};for(let s of x(e))if(s.startsWith(">")){a();let c=s.slice(1),m=c.indexOf(";");n=(m>=0?c.slice(m+1):c).trim(),o=true;}else {if(n===void 0)continue;o?(r=s.trim(),o=false):i.push(s);}return a(),t}function _(e){return (e&2304)!==0}function H(e,t){if(t&1){if(t&64)return `${e}/1`;if(t&128)return `${e}/2`}return e}function W(e,t,n){return n&4||!e||e==="*"?"unmapped":`${e}:${t} (${n&16?"-":"+"})`}var Ve="=ACMGRSVTWYHKDBN",pe=32;function _e(e){let t=[];if(!(e[0]===66&&e[1]===65&&e[2]===77&&e[3]===1))return t;let n=new DataView(e.buffer,e.byteOffset,e.byteLength),r=new TextDecoder,i=(o,a)=>r.decode(e.subarray(o,o+Math.max(0,a-1)));try{let o=e.length,a=4;if(a+4>o)return t;let s=n.getInt32(a,!0);if(a+=4,s<0||a+s+4>o)return t;a+=s;let c=n.getInt32(a,!0);if(a+=4,c<0)return t;let m=[];for(let d=0;d<c;d++){if(a+4>o)return t;let u=n.getInt32(a,!0);if(a+=4,u<=0||a+u+4>o)return t;m.push(i(a,u)),a+=u+4;}for(;a+4<=e.length;){let d=n.getInt32(a,!0);if(a+=4,d<pe||a+d>e.length)break;let u=a+d,p=n.getInt32(a,!0),l=n.getInt32(a+4,!0),h=n.getUint8(a+8),y=n.getUint16(a+12,!0),S=n.getUint16(a+14,!0),w=n.getInt32(a+16,!0),f=a+pe,g=i(f,h);f+=h+y*4;let A=w+1>>1;if(w>0&&f+A<=u&&!_(S)){let b=p>=0&&p<m.length?m[p]:"*";t.push(F(H(g,S),W(b,l+1,S),He(e,f,w)));}a=u;}}catch{}return t}function He(e,t,n){let r="";for(let i=0;i<n;i++){let o=e[t+(i>>1)];r+=Ve[i&1?o&15:o>>4];}return r}function We(e){let t=[];for(let n of x(e)){if(n.length===0||n.charCodeAt(0)===64)continue;let r=n.split(" ");if(r.length<11)continue;let i=r[9];if(!i||i==="*")continue;let o=he(r[1]);_(o)||t.push(F(H(r[0],o),W(r[2],he(r[3]),o),i));}return t}function he(e){let t=Number.parseInt(e,10);return Number.isFinite(t)?t:0}
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export{R as ENTRY_SIZE,D as HEADER_SIZE,le as MAX_PHRED,Et as averagePeakSpacing,yt as channelMaxLength,mt as cropAbif,tt as dataChannelRole,kt as detectFormat,Lt as ensureRawDataChannels,Ke as findEntries,N as findEntry,_t as formatFasta,Ht as formatFastq,Wt as formatQual,rt as getChannelMap,ot as getConfidences,v as getConfidencesForVersion,et as getDataChannel,Q as getFwo,at as getPositions,P as getPositionsForVersion,nt as getReverseComplemented,st as getSamplingRate,it as getSequence,M as getSequenceForVersion,B as hasData9To12Block,At as hasSignals,jt as hasUsableQuality,Y as insertEntrySorted,K as isFwoPermutation,F as makeSeqRecord,bt as parseAbif,_e as parseBam,gn as parseClustal,vt as parseEmbl,de as parseFasta,Vt as parseFastq,Zt as parseGenbank,Be as parseGfa,cn as parseGff,An as parseMsf,bn as parseNexus,hn as parsePhylip,Cn as parsePir,We as parseSam,pn as parseStockholm,Pt as parseSwissprot,oe as readAbif,Tt as setAveragePeakSpacing,Rt as setConfidences,Ft as setPositions,wt as setSequence,be as tagNameFromInt32,I as upsertEntry,Qe as writeAbif};//# sourceMappingURL=index.mjs.map
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//# sourceMappingURL=index.mjs.map
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