P6: gtc-to-vcf (VCF/BCF + indexes), harmonisation, exports (plink, bedgraph, finalreport)
- formats/fasta: plain/BGZF FASTA, .fai/.gzi built identical to htslib, index check, build detection, contig aliases, mmap genome cache (IN-060..064) - formats/bgzf, formats/bcf: pure-Python BGZF, tabix .tbi, BCF 2.2 and CSI (OUT-010, OUT-038, OUT-040) - harmonize/sites: plus-strand mapping with audit rows, indel resolution from SourceSeq (port of GTCtoVCF, Apache-2.0) and left normalisation (OUT-014..021, OUT-030, OUT-042) - harmonize/combine: OUT-031 genotype combination (ploidy-aware, Infinium I/II signal classes, OUT-037) - pipeline/vcf: `simurg gtc-to-vcf` (per-sample VCF.gz+tbi, --merge cohort BCF+csi, audit parquet) - pipeline/export: `simurg export bedgraph|finalreport|plink|locus-summary` (OUT-043, OUT-050..052, OUT-071) - validation: 36 GSA samples vs gtc2vcf: 23.66 M identical calls, 0 unexplained differences; PLINK identical to plink2 on 637,397 variants; bcftools validates VCF/BCF and our indexes answer region queries correctly - fetch_data.sh p6 (Ensembl GRCh38 with checksum), make_oracle_vcf.sh, validate_p6_vcf.py; K-022/K-023
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@@ -370,6 +370,153 @@ def genotype_cmd(
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run_guarded(rep, lambda: run_genotype(opts, rep))
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# --------------------------------------------------------------------------------------------------------
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@app.command("gtc-to-vcf")
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def gtc_to_vcf_cmd(
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bpm: Annotated[Path, typer.Option("--bpm", help="BPM manifest (required).")],
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fasta: Annotated[Path, typer.Option("--fasta", help="Reference FASTA (plain or bgzip; required).")],
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out: Annotated[Path, typer.Option("--out", help="Output folder (required).")],
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gtcs: Annotated[Path | None, typer.Option("--gtcs", help="Folder searched recursively for GTC files.")] = None,
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sheet: Annotated[Path | None, typer.Option("--sheet", help="Sample sheet (CSV).")] = None,
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csv: Annotated[Path | None, typer.Option("--csv", help="CSV manifest (SourceSeq; required for indels).")] = None,
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no_bgzip: Annotated[bool, typer.Option("--no-bgzip", help="Plain VCF, no index.")] = False,
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genome_cache: Annotated[bool, typer.Option("--genome-cache/--no-genome-cache", help="mmap genome cache.")] = True,
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exclude_loci: Annotated[
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Path | None, typer.Option("--exclude-loci", "--filter-loci", help="Probe names to drop (one per line).")
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] = None,
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include_loci: Annotated[Path | None, typer.Option("--include-loci", help="Only these probe names.")] = None,
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unsquash_duplicates: Annotated[bool, typer.Option("--unsquash-duplicates", help="One record per probe.")] = False,
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inf1_nocall_informative: Annotated[
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bool, typer.Option("--inf1-nocall-informative", help="Read Infinium I no-calls as allele absence.")
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] = False,
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drop_ambiguous: Annotated[bool, typer.Option("--drop-ambiguous", help="Drop low-confidence strand loci.")] = False,
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filter_gs: Annotated[float | None, typer.Option("--filter-gs", help="FILTER LowGS when GS < X.")] = None,
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contig_alias: Annotated[str, typer.Option("--contig-alias", help="strict|auto|FILE")] = "strict",
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ploidy_policy: Annotated[str, typer.Option("--ploidy-policy", help="sex-aware|diploid")] = "sex-aware",
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threads: Annotated[int, typer.Option("--threads", min=0, max=1024, help="Worker processes (0 = auto).")] = 0,
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merge: Annotated[
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bool, typer.Option("--merge", help="One multi-sample BCF (+ .csi) instead of per-sample VCFs.")
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] = False,
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force: Annotated[bool, typer.Option("--force", help="Replace existing outputs.")] = False,
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log_json: Annotated[bool, typer.Option("--log-json", "--json-log", help="JSON Lines log on stderr.")] = False,
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debug: Annotated[bool, typer.Option("--debug", help="Debug logging with tracebacks.")] = False,
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quiet: Annotated[bool, typer.Option("--quiet", "--no-progress", help="Suppress info messages.")] = False,
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) -> None:
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"""GTC files → one bgzipped, indexed SNV VCF per sample (plus-strand alleles, merged multi-probe sites)."""
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from simurg.pipeline.vcf import VcfOptions, run_gtc_to_vcf
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rep = Reporter(
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command="gtc-to-vcf",
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level="debug" if debug else "info",
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json_stderr=log_json,
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debug=debug,
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quiet=quiet,
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log_file=out / "logs" / "gtc-to-vcf.log",
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)
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opts = VcfOptions(
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out=out, bpm=bpm, fasta=fasta, gtcs=gtcs, sheet=sheet, csv=csv, bgzip=not no_bgzip, genome_cache=genome_cache,
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exclude_loci=exclude_loci, include_loci=include_loci, unsquash_duplicates=unsquash_duplicates,
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inf1_nocall_informative=inf1_nocall_informative, drop_ambiguous=drop_ambiguous, filter_gs=filter_gs,
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contig_alias=contig_alias, ploidy_policy=ploidy_policy, threads=threads, merge=merge, force=force,
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argv=sys.argv[1:],
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) # fmt: skip
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run_guarded(rep, lambda: run_gtc_to_vcf(opts, rep))
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# --------------------------------------------------------------------------------------------------------
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export_app = typer.Typer(help="Exports from GTCs or VCFs: bedgraph, finalreport, plink, locus-summary.")
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app.add_typer(export_app, name="export")
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def _plain_reporter(command: str, log_json: bool, debug: bool, quiet: bool) -> Reporter:
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return Reporter(command=command, level="debug" if debug else "info", json_stderr=log_json, debug=debug, quiet=quiet)
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@export_app.command("bedgraph")
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def export_bedgraph_cmd(
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bpm: Annotated[Path, typer.Option("--bpm", help="BPM manifest (required).")],
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out: Annotated[Path, typer.Option("--out", help="Output folder (required).")],
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gtcs: Annotated[Path | None, typer.Option("--gtcs", help="Folder searched recursively for GTC files.")] = None,
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sheet: Annotated[Path | None, typer.Option("--sheet", help="Sample sheet (CSV).")] = None,
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no_gzip: Annotated[bool, typer.Option("--no-gzip", help="Plain .bedgraph files.")] = False,
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chrom_style: Annotated[str, typer.Option("--chrom-style", help="manifest|ucsc")] = "manifest",
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smoothed_lrr: Annotated[int, typer.Option("--smoothed-lrr", min=0, help="Extra moving-median LRR track, K.")] = 0,
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force: Annotated[bool, typer.Option("--force", help="Replace existing outputs.")] = False,
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log_json: Annotated[bool, typer.Option("--log-json", "--json-log")] = False,
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debug: Annotated[bool, typer.Option("--debug")] = False,
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quiet: Annotated[bool, typer.Option("--quiet", "--no-progress")] = False,
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) -> None:
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"""BAF and LRR bedGraph tracks per sample (OUT-050 … OUT-052)."""
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from simurg.pipeline.export import BedgraphOptions, run_export_bedgraph
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rep = _plain_reporter("export bedgraph", log_json, debug, quiet)
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opts = BedgraphOptions(out=out, bpm=bpm, gtcs=gtcs, sheet=sheet, gzip=not no_gzip, chrom_style=chrom_style,
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smoothed_lrr=smoothed_lrr, force=force, argv=sys.argv[1:]) # fmt: skip
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run_guarded(rep, lambda: run_export_bedgraph(opts, rep))
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@export_app.command("finalreport")
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def export_finalreport_cmd(
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bpm: Annotated[Path, typer.Option("--bpm", help="BPM manifest (required).")],
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out: Annotated[Path, typer.Option("--out", help="Output folder (required).")],
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gtcs: Annotated[Path | None, typer.Option("--gtcs", help="Folder searched recursively for GTC files.")] = None,
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sheet: Annotated[Path | None, typer.Option("--sheet", help="Sample sheet (CSV).")] = None,
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csv: Annotated[Path | None, typer.Option("--csv", help="CSV manifest (source/reference strands).")] = None,
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egt: Annotated[Path | None, typer.Option("--egt", help="Cluster file (GT Score column).")] = None,
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matrix: Annotated[bool, typer.Option("--matrix", help="Loci × samples genotype matrix.")] = False,
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force: Annotated[bool, typer.Option("--force", help="Replace existing outputs.")] = False,
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log_json: Annotated[bool, typer.Option("--log-json", "--json-log")] = False,
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debug: Annotated[bool, typer.Option("--debug")] = False,
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quiet: Annotated[bool, typer.Option("--quiet", "--no-progress")] = False,
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) -> None:
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"""Long-format final report (one row per locus × sample), or a genotype matrix (OUT-071)."""
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from simurg.pipeline.export import FinalReportOptions, run_export_finalreport
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rep = _plain_reporter("export finalreport", log_json, debug, quiet)
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opts = FinalReportOptions(out=out, bpm=bpm, gtcs=gtcs, sheet=sheet, csv=csv, egt=egt, matrix=matrix, force=force,
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argv=sys.argv[1:]) # fmt: skip
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run_guarded(rep, lambda: run_export_finalreport(opts, rep))
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@export_app.command("plink")
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def export_plink_cmd(
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vcfs: Annotated[Path, typer.Option("--vcfs", help="Folder with SimurgArray per-sample *.snv.vcf.gz.")],
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out: Annotated[Path, typer.Option("--out", help="Output folder (required).")],
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sheet: Annotated[Path | None, typer.Option("--sheet", help="Sample sheet (reported sex).")] = None,
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gtcs: Annotated[Path | None, typer.Option("--gtcs", help="GTC folder (estimated sex).")] = None,
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multiallelic: Annotated[str, typer.Option("--multiallelic", help="split|drop")] = "split",
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prefix: Annotated[str, typer.Option("--prefix", help="Output file prefix.")] = "cohort",
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force: Annotated[bool, typer.Option("--force", help="Replace existing outputs.")] = False,
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log_json: Annotated[bool, typer.Option("--log-json", "--json-log")] = False,
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debug: Annotated[bool, typer.Option("--debug")] = False,
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quiet: Annotated[bool, typer.Option("--quiet", "--no-progress")] = False,
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) -> None:
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"""PLINK 1 .bed/.bim/.fam from SimurgArray VCFs (OUT-043)."""
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from simurg.pipeline.export import PlinkOptions, run_export_plink
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rep = _plain_reporter("export plink", log_json, debug, quiet)
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opts = PlinkOptions(out=out, vcfs=vcfs, sheet=sheet, gtcs=gtcs, multiallelic=multiallelic, prefix=prefix,
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force=force, argv=sys.argv[1:]) # fmt: skip
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run_guarded(rep, lambda: run_export_plink(opts, rep))
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@export_app.command("locus-summary")
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def export_locus_summary_cmd(
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bpm: Annotated[Path, typer.Option("--bpm", help="BPM manifest (required).")],
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egt: Annotated[Path, typer.Option("--egt", help="EGT cluster file (required).")],
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out: Annotated[Path, typer.Option("--out", help="Output folder (required).")],
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gtcs: Annotated[Path | None, typer.Option("--gtcs", help="Folder searched recursively for GTC files.")] = None,
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sheet: Annotated[Path | None, typer.Option("--sheet", help="Sample sheet (CSV).")] = None,
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threads: Annotated[int, typer.Option("--threads", min=0, max=1024)] = 0,
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force: Annotated[bool, typer.Option("--force", help="Replace existing outputs.")] = False,
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log_json: Annotated[bool, typer.Option("--log-json", "--json-log")] = False,
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debug: Annotated[bool, typer.Option("--debug")] = False,
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quiet: Annotated[bool, typer.Option("--quiet", "--no-progress")] = False,
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) -> None:
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"""Per-locus summary statistics (OUT-072); same as ``simurg qc loci``."""
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_qc_cohort("loci", out, bpm, gtcs, sheet, egt, threads, force, log_json, debug, quiet)
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# --------------------------------------------------------------------------------------------------------
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qc_app = typer.Typer(help="Quality control: controls, samples, contamination, relatedness, loci, thresholds.")
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app.add_typer(qc_app, name="qc")
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