@fishka/seqio 0.6.0 → 0.6.1

package/dist/abif/index.d.mts

@@ -390,8 +390,23 @@ declare function findEntry(file: AbifFile, name: string, number: number): AbifEn
 /** Find all entries with the given tag name. */
 declare function findEntries(file: AbifFile, name: string): AbifEntry[];
 /**
- * Replace the payload of an existing entry, or append a new one.
- * elementType/elementSize/elementCount must be supplied for new entries.
+ * Insert a new entry at the slot that keeps the directory sorted by
+ * (tagName, tagNumber) — the order genuine ABI instruments emit and the ABIF
+ * spec prescribes. Readers that binary-search the directory (e.g. Chromas)
+ * silently miss a tag appended out of order — a re-basecalled file loses its
+ * quality bars because PCON2 is not found. Existing entries are never reordered,
+ * so an unmodified file still round-trips byte-exact; only the freshly added tag
+ * lands in its sorted place.
+ *
+ * Prefer {@link upsertEntry}; use this directly only to add an entry whose
+ * payload intentionally desyncs from `elementCount * elementSize` (e.g. copying
+ * a tolerated malformed record verbatim), which upsertEntry rejects.
+ */
+declare function insertEntrySorted(entries: AbifEntry[], entry: AbifEntry): void;
+/**
+ * Replace the payload of an existing entry, or insert a new one in sorted
+ * directory order. elementType/elementSize/elementCount must be supplied for
+ * new entries.
  *
  * This is the required way to mutate an entry read from a file — it clears `.raw`
  * on replacement so writeAbif() never reuses a now-stale on-disk shape. Setting
@@ -636,4 +651,4 @@ declare function getPositionsForVersion(file: AbifFile, version: number): number
  */
 declare function getSamplingRate(file: AbifFile): number | undefined;
 
-export { type AbifBaseCallRole, type AbifBaseCallVariant, type AbifBaseCalls, type AbifByteRange, type AbifChromatogramBundle, type AbifDataChannelRole, type AbifDecodedValue, type AbifDirEntry, type AbifDirectory, type AbifEntry, type AbifEntryRaw, type AbifFile, type AbifMetadata, type ChannelSignals, type Chromatogram, type CropAbifOptions, type CropAbifRange, ENTRY_SIZE, HEADER_SIZE, type ParsedAbif, averagePeakSpacing, channelMaxLength, cropAbif, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getConfidencesForVersion, getDataChannel, getFwo, getPositions, getPositionsForVersion, getReverseComplemented, getSamplingRate, getSequence, getSequenceForVersion, hasData9To12Block, hasSignals, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif };
+export { type AbifBaseCallRole, type AbifBaseCallVariant, type AbifBaseCalls, type AbifByteRange, type AbifChromatogramBundle, type AbifDataChannelRole, type AbifDecodedValue, type AbifDirEntry, type AbifDirectory, type AbifEntry, type AbifEntryRaw, type AbifFile, type AbifMetadata, type ChannelSignals, type Chromatogram, type CropAbifOptions, type CropAbifRange, ENTRY_SIZE, HEADER_SIZE, type ParsedAbif, averagePeakSpacing, channelMaxLength, cropAbif, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getConfidencesForVersion, getDataChannel, getFwo, getPositions, getPositionsForVersion, getReverseComplemented, getSamplingRate, getSequence, getSequenceForVersion, hasData9To12Block, hasSignals, insertEntrySorted, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif };

package/dist/abif/index.d.ts

@@ -390,8 +390,23 @@ declare function findEntry(file: AbifFile, name: string, number: number): AbifEn
 /** Find all entries with the given tag name. */
 declare function findEntries(file: AbifFile, name: string): AbifEntry[];
 /**
- * Replace the payload of an existing entry, or append a new one.
- * elementType/elementSize/elementCount must be supplied for new entries.
+ * Insert a new entry at the slot that keeps the directory sorted by
+ * (tagName, tagNumber) — the order genuine ABI instruments emit and the ABIF
+ * spec prescribes. Readers that binary-search the directory (e.g. Chromas)
+ * silently miss a tag appended out of order — a re-basecalled file loses its
+ * quality bars because PCON2 is not found. Existing entries are never reordered,
+ * so an unmodified file still round-trips byte-exact; only the freshly added tag
+ * lands in its sorted place.
+ *
+ * Prefer {@link upsertEntry}; use this directly only to add an entry whose
+ * payload intentionally desyncs from `elementCount * elementSize` (e.g. copying
+ * a tolerated malformed record verbatim), which upsertEntry rejects.
+ */
+declare function insertEntrySorted(entries: AbifEntry[], entry: AbifEntry): void;
+/**
+ * Replace the payload of an existing entry, or insert a new one in sorted
+ * directory order. elementType/elementSize/elementCount must be supplied for
+ * new entries.
  *
  * This is the required way to mutate an entry read from a file — it clears `.raw`
  * on replacement so writeAbif() never reuses a now-stale on-disk shape. Setting
@@ -636,4 +651,4 @@ declare function getPositionsForVersion(file: AbifFile, version: number): number
  */
 declare function getSamplingRate(file: AbifFile): number | undefined;
 
-export { type AbifBaseCallRole, type AbifBaseCallVariant, type AbifBaseCalls, type AbifByteRange, type AbifChromatogramBundle, type AbifDataChannelRole, type AbifDecodedValue, type AbifDirEntry, type AbifDirectory, type AbifEntry, type AbifEntryRaw, type AbifFile, type AbifMetadata, type ChannelSignals, type Chromatogram, type CropAbifOptions, type CropAbifRange, ENTRY_SIZE, HEADER_SIZE, type ParsedAbif, averagePeakSpacing, channelMaxLength, cropAbif, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getConfidencesForVersion, getDataChannel, getFwo, getPositions, getPositionsForVersion, getReverseComplemented, getSamplingRate, getSequence, getSequenceForVersion, hasData9To12Block, hasSignals, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif };
+export { type AbifBaseCallRole, type AbifBaseCallVariant, type AbifBaseCalls, type AbifByteRange, type AbifChromatogramBundle, type AbifDataChannelRole, type AbifDecodedValue, type AbifDirEntry, type AbifDirectory, type AbifEntry, type AbifEntryRaw, type AbifFile, type AbifMetadata, type ChannelSignals, type Chromatogram, type CropAbifOptions, type CropAbifRange, ENTRY_SIZE, HEADER_SIZE, type ParsedAbif, averagePeakSpacing, channelMaxLength, cropAbif, dataChannelRole, ensureRawDataChannels, findEntries, findEntry, getChannelMap, getConfidences, getConfidencesForVersion, getDataChannel, getFwo, getPositions, getPositionsForVersion, getReverseComplemented, getSamplingRate, getSequence, getSequenceForVersion, hasData9To12Block, hasSignals, insertEntrySorted, isFwoPermutation, parseAbif, readAbif, setAveragePeakSpacing, setConfidences, setPositions, setSequence, tagNameFromInt32, upsertEntry, writeAbif };

package/dist/abif/index.js

@@ -1,2 +1,2 @@
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Uint8Array(x(e,t+20,4));return {tagName:a,tagNumber:i,elementType:c,elementSize:l,elementCount:g,payload:A,dataHandle:y,raw:{elementCount:u,dataSize:d,dataOffset:C,inline:o,dataOffsetBytes:T}}}function ae(e){let n=e.macBinaryOffset,t=e.entries.length,r=e.tdir.entryCount,a=e.entries.map(o=>o.raw&&o.payload.byteLength===o.raw.dataSize?o.raw:void 0),i=F;i=Math.max(i,e.tdir.dataOffset+Math.max(e.tdir.dataSize,r*N));for(let o of a)o&&!o.inline&&(i=Math.max(i,o.dataOffset+o.dataSize));for(let o of e.unreferencedRanges)i=Math.max(i,o.offset-n+o.bytes.length);let c=t>r,l=i,u=c?l:e.tdir.dataOffset,d=t===r?e.tdir.dataSize:t*N;c&&(l+=d);let y=new Array(t);for(let o=0;o<t;o++){let g=e.entries[o].payload.byteLength;if(a[o]||g<=4){y[o]=-1;continue}y[o]=l,l+=g;}let f=new 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m=r.entries[s],p=a[s].decoded;if(m.tagName==="DATA"){let b=I(p);b&&(c[m.tagNumber]=b,m.tagNumber>=1&&m.tagNumber<=4?l[o(m.tagNumber-1)]=b:m.tagNumber>=9&&m.tagNumber<=12&&(u[o(m.tagNumber-9)]=b));}else if(m.tagName==="PBAS"&&p.kind==="string")y[m.tagNumber]=p.value;else if(m.tagName==="PCON"){let b=m.elementSize===1?Array.from(m.payload.subarray(0,m.elementCount)):I(p);b&&(f[m.tagNumber]=b);}else if(m.tagName==="PLOC"){let b=I(p);b&&(h[m.tagNumber]=b.map(M=>M<0?M+65536:M));}else if(m.tagName==="SPAC")if(m.elementSize===4&&m.payload.byteLength>=4){let b=w(m.payload).getFloat32(0,false);Number.isFinite(b)&&b>0&&(d.samplingRate=b);}else p.kind==="number"&&(d.samplingRate=p.value);else if(m.tagName==="SMPL"&&p.kind==="string")d.sampleName=p.value;else if(m.tagName==="LANE"&&p.kind==="number")d.laneNumber=p.value;else if(m.tagName==="TUBE"&&p.kind==="string")d.tube=p.value;else if(m.tagName==="MCHN"&&p.kind==="string")d.machineName=p.value;else 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s=y[C].toUpperCase(),m=f[C]??[];m.length!==s.length&&(m=Object.keys(f).map(Number).map(b=>f[b]).find(b=>b.length===s.length)??[]);let p=h[C]??[];p.length!==s.length&&(p=Object.keys(h).map(Number).map(b=>h[b]).find(b=>b.length===s.length)??[]),A={sequence:s,confidences:m,positions:p,pbasVersion:C};}if(!Number.isFinite(d.samplingRate)||(d.samplingRate??0)<=0){let s=A?.positions,m=Math.max(u.A.length,u.C.length,u.G.length,u.T.length);s&&s.length>1?d.samplingRate=(s[s.length-1]-s[0])/(s.length-1):A&&A.sequence.length>0&&m>0&&(d.samplingRate=m/A.sequence.length);}let T={baseOrder:i,dataChannels:c,data1To4:l,data9To12:u};return {fileName:n,fileSize:t.byteLength,abifVersion:r.version,macBinaryOffset:r.macBinaryOffset,dirEntryCount:r.entries.length,metadata:d,chromatogram:T,baseCalls:A,baseCallVariants:g,entries:a}}function ve(e){return e.A.length>0||e.C.length>0||e.G.length>0||e.T.length>0}function Fe(e){return Math.max(e.A.length,e.C.length,e.G.length,e.T.length)}function Le(e,n){$(e,"PBAS",2,z(n),{elementType:2,elementSize:1,elementCount:n.length});}function Me(e,n){let t=new Uint8Array(n.length);for(let r=0;r<n.length;r++)t[r]=Math.max(0,Math.min(255,Math.round(n[r])));$(e,"PCON",2,t,{elementType:2,elementSize:1,elementCount:n.length});}function Oe(e,n){let t=new Uint8Array(n.length*2),r=w(t);for(let a=0;a<n.length;a++)r.setUint16(a*2,Math.max(0,Math.min(65535,n[a])),false);$(e,"PLOC",2,t,{elementType:4,elementSize:2,elementCount:n.length});}function Pe(e,n,t){let r=new Uint8Array(4);w(r).setFloat32(0,n,false),$(e,"SPAC",1,r,{elementType:7,elementSize:4,elementCount:1});let a=z(t),i=Math.min(255,a.length),c=new Uint8Array(1+i);c[0]=i,c.set(a.subarray(0,i),1),$(e,"SPAC",2,c,{elementType:18,elementSize:1,elementCount:1+i});let l=new Uint8Array(4);w(l).setFloat32(0,n,false),$(e,"SPAC",3,l,{elementType:7,elementSize:4,elementCount:1});}function Re(e){return e.length<2?0:(e[e.length-1]-e[0])/(e.length-1)}function Ie(e){if(!B(e))for(let n=1;n<=4;n++){let t=S(e,"DATA",n);if(!t)continue;let r=8+n;S(e,"DATA",r)||O(e.entries,{tagName:"DATA",tagNumber:r,elementType:t.elementType,elementSize:t.elementSize,elementCount:t.elementCount,payload:new Uint8Array(t.payload),dataHandle:0});}}exports.ENTRY_SIZE=N;exports.HEADER_SIZE=v;exports.averagePeakSpacing=Re;exports.channelMaxLength=Fe;exports.cropAbif=Ne;exports.dataChannelRole=ce;exports.ensureRawDataChannels=Ie;exports.findEntries=se;exports.findEntry=S;exports.getChannelMap=ge;exports.getConfidences=he;exports.getConfidencesForVersion=D;exports.getDataChannel=fe;exports.getFwo=P;exports.getPositions=pe;exports.getPositionsForVersion=k;exports.getReverseComplemented=de;exports.getSamplingRate=ye;exports.getSequence=be;exports.getSequenceForVersion=U;exports.hasData9To12Block=B;exports.hasSignals=ve;exports.insertEntrySorted=O;exports.isFwoPermutation=R;exports.parseAbif=$e;exports.readAbif=j;exports.setAveragePeakSpacing=Pe;exports.setConfidences=Me;exports.setPositions=Oe;exports.setSequence=Le;exports.tagNameFromInt32=W;exports.upsertEntry=$;exports.writeAbif=oe;//# sourceMappingURL=index.js.map
 //# sourceMappingURL=index.js.map