Accept AGC archives as sequence input - #144
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-s/--seqs now accepts an AGC (.agc) archive in addition to FASTA/FASTQ. SeqIndex ingests every sample/contig via ragc-core into the same concatenated store and FM-index used for FASTA, so contig names round-trip (a PanSN archive reproduces sample#haplotype#contig verbatim). Ingestion of archives above 32 MB is parallelized across -t threads via disjoint writes to the memory-mapped sequence file; output is byte-identical to the serial path and to the equivalent FASTA input.
AndreaGuarracino
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Ingesting tests/data/agc/small.agc (built with 'agc create' from tests/data/agc/small.fa) must yield the same names, lengths, and bases as ingesting the FASTA. Runs under cargo test (ragc-core is a normal dep).
AGC identifies a sequence by (sample, contig), seqwish by name alone. An archive built the canonical AGC way (agc create sampleA.fa sampleB.fa) repeats plain contig names across samples, which produced several sequences with the same name and made them unresolvable by name. A contig name that occurs in more than one sample is now qualified as contig@sample (AGC's query syntax, matching wfmash); already unique names, as in a PanSN archive, are unchanged. Duplicates that survive are a hard error rather than a silently broken index.
This was referenced Jul 24, 2026
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Adds native support for
-s/--seqsreading an AGC (.agc) archive in addition to FASTA/FASTQ.SeqIndex::build_indexdetects the.agcextension and ingests every sample/contig viaragc-core(a pure-Rust AGC decompressor) into the same concatenated sequence store and FM-index used for FASTA. Each contig is stored under its name verbatim, so a PanSN archive reproducessample#haplotype#contignames 1:1.For archives above 32 MB the decompression is parallelized across
-tthreads, each writing a disjoint range of the memory-mapped sequence file; smaller inputs keep the serial writer. Output is byte-identical to the serial path and to the equivalent FASTA input.Dependency:
ragc-corefromAndreaGuarracino/ragc(a fork ofekg/ragc, currently 4 commits ahead: addslist_contigs_names_onlyfor fast metadata scans, a fix for names-only loading, and a bounded segment cacheRAGC_CACHE_SIZE). Ideally those land upstream inekg/ragcso this can point there.Verified byte-identical: the induced seqwish graph is identical whether sequences come from FASTA or AGC, on LPA and yeast8 (96 Mbp, md5-identical GFA); serial and parallel ingest produce byte-identical output. Runtime and memory are at parity with FASTA; AGC ingest is sub-second and scales with archive size.