@fishka/seqio 0.7.0 → 0.8.1

package/dist/index.d.mts

@@ -10,7 +10,7 @@ export { AbifBaseCallRole, AbifBaseCallVariant, AbifBaseCalls, AbifByteRange, Ab
  * file still resolves.
  */
 /** A format {@link detectFormat} can recognize. Some are detected before their reader ships. */
-type SeqFileFormat = 'abif' | 'scf' | 'fasta' | 'fastq' | 'genbank' | 'embl' | 'swissprot' | 'clustal' | 'stockholm' | 'phylip' | 'nexus' | 'msf' | 'pir' | 'gff' | 'unknown';
+type SeqFileFormat = 'abif' | 'scf' | 'fasta' | 'fastq' | 'genbank' | 'embl' | 'swissprot' | 'clustal' | 'stockholm' | 'phylip' | 'nexus' | 'msf' | 'pir' | 'gff' | 'sam' | 'bam' | 'gfa' | 'unknown';
 /**
  * Detect the sequencing file format from its content. Returns 'unknown' when no signature
  * matches (empty input, or a leading line that is neither a known magic nor a recognized
@@ -181,6 +181,23 @@ declare function hasUsableQuality(qualities?: readonly number[]): boolean;
 
 declare function parseGenbank(input: string | Uint8Array): SeqRecord[];
 
+/**
+ * GFA (Graphical Fragment Assembly, `.gfa`) reader — sequence extraction.
+ *
+ * Assembly / pangenome graphs. Only Segment (`S`) lines carry sequence; links, paths, jumps and
+ * containments are graph topology and hold none. Both dialects are supported by field position:
+ *
+ *   GFA1:  S <name> <sequence> [tags…]
+ *   GFA2:  S <sid>  <slen>     <sequence> [tags…]
+ *
+ * GFA2 inserts an integer segment length between the name and the sequence, so when the field after
+ * the name is a bare integer AND another field follows, the sequence is that next field; otherwise
+ * it's the field right after the name (GFA1). A `*` sequence (a segment declared without residues)
+ * is skipped — there's nothing to pick. Lenient: never throws; malformed lines are ignored.
+ */
+
+declare function parseGfa(input: string | Uint8Array): SeqRecord[];
+
 /**
  * GFF3 (`.gff`/`.gff3`) reader — sequence extraction.
  *
@@ -250,4 +267,46 @@ declare function parseMsf(input: string | Uint8Array): SeqRecord[];
 
 declare function parsePir(input: string | Uint8Array): SeqRecord[];
 
-export { type FastaRecord, type FastqRecord, MAX_PHRED, type QualRecord, type SeqFileFormat, type SeqRecord, type WrapOptions, detectFormat, formatFasta, formatFastq, formatQual, hasUsableQuality, makeSeqRecord, parseClustal, parseEmbl, parseFasta, parseFastq, parseGenbank, parseGff, parseMsf, parseNexus, parsePhylip, parsePir, parseStockholm, parseSwissprot };
+/**
+ * BAM (`.bam`) reader — read-sequence extraction from the binary alignment format.
+ *
+ * BAM is the binary twin of SAM. On disk it is BGZF-compressed (a gzip stream of concatenated
+ * blocks); this reader expects the INFLATED bytes — starting with the "BAM\1" magic. The caller
+ * peels the gzip/BGZF wrapper first (a gzip decompressor decodes BGZF's concatenated members), so
+ * this stays a synchronous, dependency-free binary parser.
+ *
+ * Semantics mirror the SAM reader exactly (see {@link parseSam}): one sequence per read (secondary
+ * 0x100 / supplementary 0x800 skipped), reverse-strand sequence stored verbatim (reference-forward),
+ * id = read name (+ /1,/2 for paired mates), description = "RNAME:POS (+/-)" or "unmapped". Records
+ * without a stored sequence (l_seq = 0) are skipped. Lenient: on any truncation or garble it stops
+ * and returns what it parsed cleanly, never throwing.
+ */
+
+declare function parseBam(bytes: Uint8Array): SeqRecord[];
+
+/**
+ * SAM (`.sam`) reader — read-sequence extraction.
+ *
+ * SAM is a read-alignment format: one record per alignment, tab-delimited, with 11 mandatory
+ * fields (QNAME FLAG RNAME POS MAPQ CIGAR RNEXT PNEXT TLEN SEQ QUAL). This reader returns each
+ * record's read sequence — field 10, `SEQ`. Records whose SEQ is `*` (sequence not stored) are
+ * skipped: there's nothing to pick.
+ *
+ * The sequence is returned VERBATIM as written. For a reverse-strand alignment (FLAG bit 0x10) SAM
+ * already stores the reverse complement (reference-forward orientation), so that reference-oriented
+ * sequence is what you get — it is deliberately not un-flipped to the original read orientation.
+ *
+ * One sequence per read: secondary (FLAG 0x100) and supplementary (0x800) alignments are skipped —
+ * they re-map the same read (a duplicate, or a hard-clipped split fragment), which would pollute a
+ * "pick the sequences" list. What's kept is the read's SEQ from its primary (or unmapped) record —
+ * i.e. the sequence as SAM stores it, which for a hard-clipped primary alignment omits the clipped
+ * flanks rather than reconstructing the original full read.
+ *
+ * `@`-prefixed lines are skipped as headers — the SAM spec's QNAME charset `[!-?A-~]` excludes '@'
+ * (0x40) precisely so a read name can never be confused with a header. Lenient: never throws; lines
+ * with fewer than 11 fields are ignored rather than rejected.
+ */
+
+declare function parseSam(input: string | Uint8Array): SeqRecord[];
+
+export { type FastaRecord, type FastqRecord, MAX_PHRED, type QualRecord, type SeqFileFormat, type SeqRecord, type WrapOptions, detectFormat, formatFasta, formatFastq, formatQual, hasUsableQuality, makeSeqRecord, parseBam, parseClustal, parseEmbl, parseFasta, parseFastq, parseGenbank, parseGfa, parseGff, parseMsf, parseNexus, parsePhylip, parsePir, parseSam, parseStockholm, parseSwissprot };

package/dist/index.d.ts

@@ -10,7 +10,7 @@ export { AbifBaseCallRole, AbifBaseCallVariant, AbifBaseCalls, AbifByteRange, Ab
  * file still resolves.
  */
 /** A format {@link detectFormat} can recognize. Some are detected before their reader ships. */
-type SeqFileFormat = 'abif' | 'scf' | 'fasta' | 'fastq' | 'genbank' | 'embl' | 'swissprot' | 'clustal' | 'stockholm' | 'phylip' | 'nexus' | 'msf' | 'pir' | 'gff' | 'unknown';
+type SeqFileFormat = 'abif' | 'scf' | 'fasta' | 'fastq' | 'genbank' | 'embl' | 'swissprot' | 'clustal' | 'stockholm' | 'phylip' | 'nexus' | 'msf' | 'pir' | 'gff' | 'sam' | 'bam' | 'gfa' | 'unknown';
 /**
  * Detect the sequencing file format from its content. Returns 'unknown' when no signature
  * matches (empty input, or a leading line that is neither a known magic nor a recognized
@@ -181,6 +181,23 @@ declare function hasUsableQuality(qualities?: readonly number[]): boolean;
 
 declare function parseGenbank(input: string | Uint8Array): SeqRecord[];
 
+/**
+ * GFA (Graphical Fragment Assembly, `.gfa`) reader — sequence extraction.
+ *
+ * Assembly / pangenome graphs. Only Segment (`S`) lines carry sequence; links, paths, jumps and
+ * containments are graph topology and hold none. Both dialects are supported by field position:
+ *
+ *   GFA1:  S <name> <sequence> [tags…]
+ *   GFA2:  S <sid>  <slen>     <sequence> [tags…]
+ *
+ * GFA2 inserts an integer segment length between the name and the sequence, so when the field after
+ * the name is a bare integer AND another field follows, the sequence is that next field; otherwise
+ * it's the field right after the name (GFA1). A `*` sequence (a segment declared without residues)
+ * is skipped — there's nothing to pick. Lenient: never throws; malformed lines are ignored.
+ */
+
+declare function parseGfa(input: string | Uint8Array): SeqRecord[];
+
 /**
  * GFF3 (`.gff`/`.gff3`) reader — sequence extraction.
  *
@@ -250,4 +267,46 @@ declare function parseMsf(input: string | Uint8Array): SeqRecord[];
 
 declare function parsePir(input: string | Uint8Array): SeqRecord[];
 
-export { type FastaRecord, type FastqRecord, MAX_PHRED, type QualRecord, type SeqFileFormat, type SeqRecord, type WrapOptions, detectFormat, formatFasta, formatFastq, formatQual, hasUsableQuality, makeSeqRecord, parseClustal, parseEmbl, parseFasta, parseFastq, parseGenbank, parseGff, parseMsf, parseNexus, parsePhylip, parsePir, parseStockholm, parseSwissprot };
+/**
+ * BAM (`.bam`) reader — read-sequence extraction from the binary alignment format.
+ *
+ * BAM is the binary twin of SAM. On disk it is BGZF-compressed (a gzip stream of concatenated
+ * blocks); this reader expects the INFLATED bytes — starting with the "BAM\1" magic. The caller
+ * peels the gzip/BGZF wrapper first (a gzip decompressor decodes BGZF's concatenated members), so
+ * this stays a synchronous, dependency-free binary parser.
+ *
+ * Semantics mirror the SAM reader exactly (see {@link parseSam}): one sequence per read (secondary
+ * 0x100 / supplementary 0x800 skipped), reverse-strand sequence stored verbatim (reference-forward),
+ * id = read name (+ /1,/2 for paired mates), description = "RNAME:POS (+/-)" or "unmapped". Records
+ * without a stored sequence (l_seq = 0) are skipped. Lenient: on any truncation or garble it stops
+ * and returns what it parsed cleanly, never throwing.
+ */
+
+declare function parseBam(bytes: Uint8Array): SeqRecord[];
+
+/**
+ * SAM (`.sam`) reader — read-sequence extraction.
+ *
+ * SAM is a read-alignment format: one record per alignment, tab-delimited, with 11 mandatory
+ * fields (QNAME FLAG RNAME POS MAPQ CIGAR RNEXT PNEXT TLEN SEQ QUAL). This reader returns each
+ * record's read sequence — field 10, `SEQ`. Records whose SEQ is `*` (sequence not stored) are
+ * skipped: there's nothing to pick.
+ *
+ * The sequence is returned VERBATIM as written. For a reverse-strand alignment (FLAG bit 0x10) SAM
+ * already stores the reverse complement (reference-forward orientation), so that reference-oriented
+ * sequence is what you get — it is deliberately not un-flipped to the original read orientation.
+ *
+ * One sequence per read: secondary (FLAG 0x100) and supplementary (0x800) alignments are skipped —
+ * they re-map the same read (a duplicate, or a hard-clipped split fragment), which would pollute a
+ * "pick the sequences" list. What's kept is the read's SEQ from its primary (or unmapped) record —
+ * i.e. the sequence as SAM stores it, which for a hard-clipped primary alignment omits the clipped
+ * flanks rather than reconstructing the original full read.
+ *
+ * `@`-prefixed lines are skipped as headers — the SAM spec's QNAME charset `[!-?A-~]` excludes '@'
+ * (0x40) precisely so a read name can never be confused with a header. Lenient: never throws; lines
+ * with fewer than 11 fields are ignored rather than rejected.
+ */
+
+declare function parseSam(input: string | Uint8Array): SeqRecord[];
+
+export { type FastaRecord, type FastqRecord, MAX_PHRED, type QualRecord, type SeqFileFormat, type SeqRecord, type WrapOptions, detectFormat, formatFasta, formatFastq, formatQual, hasUsableQuality, makeSeqRecord, parseBam, parseClustal, parseEmbl, parseFasta, parseFastq, parseGenbank, parseGfa, parseGff, parseMsf, parseNexus, parsePhylip, parsePir, parseSam, parseStockholm, parseSwissprot };

package/dist/index.js

@@ -1,14 +1,14 @@
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