Gbz name validation - #38
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A wrong `--pangenome_ref_name` was silent: `vg haplotypes --set-reference` only warns, the sampled graph loses its reference paths, `vg convert -Q` writes no rGFA tags and `pgutil lift` exits 0 with every read unmapped. Read the reference name and contig prefix from the GBWT metadata in the GBZ header instead (new `pangenome_meta` module, well under a second per graph). The backbone reference is the unfragmented reference sample. Make `--pangenome_ref_name` and `--pangenome_contig_prefix` hidden overrides that must agree with the graph, check the backbone contigs and build against the reference FASTA, replace the `grch38.gbz` filename-suffix check, apply the GRCh38 contig-length check only to GRCh38 backbones, and add `check-sample-gbz` / `check-sample-gfa` jobs to both DAGs so a sampled graph or GFA without the reference fails the run. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Lo4R3WSNwCYMcKzvGKCqSs
`validate_grch38_contigs` compared the reference index and the `--pop_vcf` with a hard-coded table of the 25 GRCh38 chromosome lengths, so it only ran for a GRCh38 backbone and never looked at the 170 unplaced contigs the HPRC graph also carries. Drop the table and compare the two files instead: every contig of the backbone reference detected in the GBZ must carry the same length in the `--pop_vcf` header as in the reference FASTA index. A CHM13 graph is now checked the same way a GRCh38 one is, a contig absent from the pop VCF or without a length is an error, and the message names the first ten offenders with both lengths. Only the hidden `--skip_contig_checks` flag bypasses the check; `--skip_pangenome_name_checks` does not. The pop VCF header is now parsed in pure Python. `vcf_contigs` and `vcf_id` shelled out to `bcftools view -h`, and `vcf_contigs` returned a fake three-contig dictionary in dry runs, which left the dry run checking nothing and the real run checking everything. `read_vcf_header` opens the file with `gzip` when its first two bytes say so -- the extension is not trusted -- and stops at the first line that is not a header line, so the body is never read: the header of the 10 GB population VCF parses in about 1 ms. Dry runs now parse it too, and fall back only when the file cannot be read at all, which is what the unit tests and the placeholder files behind them need. The `SentieonVcfID` comparison follows the same rule, so a dry run catches a pop VCF that does not belong with the model bundle. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01RWPD3suVQRpMZbJHijXhao
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Improve pangenome validation