ref-solver 0.3.0

Solve reference genome identification from BAM/SAM headers
Documentation 
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{
  "version": "2.0.0",
  "created_at": "2026-01-13T00:00:00Z",
  "assemblies": [
    {
      "id": "grch38",
      "name": "GRCh38",
      "organism": "Homo sapiens",
      "versions": [
        {
          "id": "grch38_p14",
          "version": "p14",
          "source": {
            "type": "ncbi",
            "accession": "GCF_000001405.40",
            "url": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_assembly_report.txt",
            "date": "2024-03-12"
          },
          "report_contigs": [
            {
              "id": 1,
              "sequence_name": "1",
              "length": 248956422,
              "md5": null,
              "refseq_accn": "NC_000001.11",
              "genbank_accn": "CM000663.2",
              "ucsc_name": "chr1",
              "sequence_role": "assembled-molecule",
              "assigned_molecule": "1"
            },
            {
              "id": 2,
              "sequence_name": "2",
              "length": 242193529,
              "md5": null,
              "refseq_accn": "NC_000002.12",
              "genbank_accn": "CM000664.2",
              "ucsc_name": "chr2",
              "sequence_role": "assembled-molecule",
              "assigned_molecule": "2"
            }
          ],
          "fasta_distributions": [
            {
              "id": "hg38_ucsc_sample",
              "display_name": "hg38 (UCSC) - Sample",
              "source": "ucsc",
              "download_url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz",
              "tags": ["primary", "sample"],
              "contigs": [
                {
                  "name": "chr1",
                  "length": 248956422,
                  "md5": "2648ae1bacce4ec4b6cf337dcae37816",
                  "sort_order": 0,
                  "report_contig_id": 1,
                  "aliases": ["1", "CM000663.2", "NC_000001.11"]
                },
                {
                  "name": "chr2",
                  "length": 242193529,
                  "md5": "4bb4f82880a14111eb7327169ffb729b",
                  "sort_order": 1,
                  "report_contig_id": 2,
                  "aliases": ["2", "CM000664.2", "NC_000002.12"]
                }
              ]
            },
            {
              "id": "hs38DH_sample",
              "display_name": "hs38DH (1KG) - Sample",
              "source": "one_thousand_genomes",
              "download_url": "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa",
              "tags": ["analysis_set", "decoy", "hla", "sample"],
              "contigs": [
                {
                  "name": "chr1",
                  "length": 248956422,
                  "md5": "6aef897c3d6ff0c78aff06ac189178dd",
                  "sort_order": 0,
                  "report_contig_id": 1,
                  "aliases": []
                },
                {
                  "name": "chr2",
                  "length": 242193529,
                  "md5": "f98db672eb0993dcfdabafe2a882905c",
                  "sort_order": 1,
                  "report_contig_id": 2,
                  "aliases": []
                },
                {
                  "name": "chr1_decoy",
                  "length": 5000,
                  "md5": "decoy_md5_sample_placeholder",
                  "sort_order": 2,
                  "report_contig_id": null,
                  "aliases": []
                }
              ]
            }
          ]
        }
      ]
    },
    {
      "id": "grch37",
      "name": "GRCh37",
      "organism": "Homo sapiens",
      "versions": [
        {
          "id": "grch37_p13",
          "version": "p13",
          "source": {
            "type": "ncbi",
            "accession": "GCF_000001405.25",
            "url": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_report.txt",
            "date": null
          },
          "report_contigs": [
            {
              "id": 1,
              "sequence_name": "1",
              "length": 249250621,
              "md5": null,
              "refseq_accn": "NC_000001.10",
              "genbank_accn": "CM000663.1",
              "ucsc_name": "chr1",
              "sequence_role": "assembled-molecule",
              "assigned_molecule": "1"
            }
          ],
          "fasta_distributions": [
            {
              "id": "hg19_ucsc_sample",
              "display_name": "hg19 (UCSC) - Sample",
              "source": "ucsc",
              "download_url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz",
              "tags": ["sample"],
              "contigs": [
                {
                  "name": "chr1",
                  "length": 249250621,
                  "md5": "1b22b98cdeb4a9304cb5d48026a85128",
                  "sort_order": 0,
                  "report_contig_id": 1,
                  "aliases": ["1", "NC_000001.10"]
                }
              ]
            }
          ]
        }
      ]
    }
  ],
  "standalone_distributions": []
}