Release v1.0.1 (#10)

CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## [1.0.1] — 2026-04-28
+
+### Fixed
+
+- `gen-pair` now produces a two-sample somatic VCF (#7).
+- VCF output is now tabix-indexable; previously inter-chromosomal BND records broke sort order (#6).
+- README DOI and license badges (#8, #9).
+
+### Changed
+
+- **BREAKING**: `gen-pair` replaces `--out-tumor` / `--out-normal` with a single `--out` flag.
+
 ## [1.0.0] — 2026-04-25
 
 Initial release.
@@ -17,4 +29,4 @@ Initial release.
 - Writer plugin system: third-party callers can register via `svforge.writers` entry point
 - Non-configurable `##svforgeWarning=SYNTHETIC_DATA_DO_NOT_USE_FOR_CLINICAL_DIAGNOSIS` injected in every VCF header
 - `sanitize_command()` strips absolute paths from the logged command line so user home directories and cluster paths never leak into generated VCFs
-- Python 3.10+, hg38 only
+- Python 3.10+, hg38 only

CITATION.cff

@@ -4,8 +4,8 @@ title: "svForge"
 authors:
   - family-names: "Natiez"
     given-names: "Pierre"
-version: "1.0.0"
-date-released: "2026-04-25"
+version: "1.0.1"
+date-released: "2026-04-28"
 license: MIT
 repository-code: "https://github.com/pieetie/svforge"
 identifiers:

README.md

@@ -9,12 +9,12 @@
 ### Generate synthetic SV VCFs to stress-test your pipelines with confidence
 
 [![PyPI version](https://img.shields.io/pypi/v/svforge.svg)](https://pypi.org/project/svforge/)
-[![License](https://img.shields.io/pypi/l/svforge)](https://pypi.org/project/svforge/)
-[![DOI](https://zenodo.org/badge/1218168425.svg)](https://doi.org/10.5281/zenodo.19762333)
+[![License](https://img.shields.io/pypi/l/svforge)](https://github.com/pieetie/svforge/blob/main/LICENSE)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.19762333-blue)](https://doi.org/10.5281/zenodo.19762333)
 
 ---
 
-**svForge** produces caller-specific VCFs (Manta, DELLY) in VCF / VCF.gz / BCF format with fine-grained control over variability (HOMLEN, SVLEN, VAF) and realistic artefact injection (SVs in ENCODE blacklist regions, gnomAD germline SVs).
+**svForge** produces caller-shaped VCFs (Manta, DELLY) in VCF / VCF.gz / BCF format with fine-grained control over variability (HOMLEN, SVLEN, VAF) and realistic artefact injection (SVs in ENCODE blacklist regions, gnomAD germline SVs).
 
 Designed to be modular, it is easy to adapt to your own use case. 
 You can tune generation parameters, plug in new callers, and customize the workflow without reworking the whole tool.
@@ -35,7 +35,7 @@ pip install -e ".[dev,test]"
 
 ## Quick start
 
-For ready-to-run command lines (single sample, tumor/normal pair, validation, banks, and dev checks), see [`docs/ready-to-use.md`](docs/ready-to-use.md).
+For ready-to-run command lines (single-sample `gen`, paired somatic `gen-pair`, validation, banks, and dev checks), see [`docs/ready-to-use.md`](docs/ready-to-use.md).
 
 ## Typical use cases
 
@@ -50,7 +50,7 @@ For ready-to-run command lines (single sample, tumor/normal pair, validation, ba
 
 ```
 svforge gen          # one VCF for one sample
-svforge gen-pair     # tumor + normal VCFs for somatic pipelines
+svforge gen-pair     # one 2-sample somatic VCF (NORMAL + TUMOR)
 svforge validate     # self-consistency check of injected SVs
 svforge bank list    # list built-in banks
 svforge bank show    # dump a bank as YAML

docs/ready-to-use.md

@@ -129,15 +129,16 @@ svforge gen --caller manta --out data_local/gen-test/out.vcf.gz --n 100 --sample
 
 ---
 
-## 4. Tumor + normal pair (`gen-pair`)
+## 4. Paired somatic VCF (`gen-pair`)
+
+Produces **one** VCF with **two sample columns** (NORMAL + TUMOR for Manta, TUMOR + NORMAL for DELLY), like real `somaticSV.vcf.gz`.
 
 **Example:**
 
 ```bash
 svforge gen-pair \
   --caller manta \
-  --out-tumor data_local/gen-test/tumor.vcf.gz \
-  --out-normal data_local/gen-test/normal.vcf.gz \
+  --out data_local/gen-test/somaticSV.vcf.gz \
   --n-somatic 30 \
   --n-germline 10 \
   --tumor-sample-name TUMOR_01 \

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "svforge"
-version = "1.0.0"
+version = "1.0.1"
 description = "Synthetic VCF generator for structural variants (Manta, DELLY) with controlled variability and realistic artefact injection"
 readme = "README.md"
 requires-python = ">=3.10"

src/svforge/cli.py

@@ -4,7 +4,7 @@
 Subcommands:
 
 - ``gen``        single-sample synthetic VCF
-- ``gen-pair``   tumor + normal paired VCFs
+- ``gen-pair``   single paired somatic VCF (two sample columns)
 - ``validate``   self-consistency check against bundled injection catalogs
 - ``bank``       list / show built-in banks
 - ``callers``    list every registered writer
@@ -158,9 +158,11 @@ def _add_gen_parser(sub: argparse._SubParsersAction[argparse.ArgumentParser]) ->
 
 
 def _add_gen_pair_parser(sub: argparse._SubParsersAction[argparse.ArgumentParser]) -> None:
-    p = sub.add_parser("gen-pair", help="Generate paired tumor/normal VCFs")
-    p.add_argument("--out-tumor", type=Path, required=True)
-    p.add_argument("--out-normal", type=Path, required=True)
+    p = sub.add_parser(
+        "gen-pair",
+        help="Generate a paired tumor/normal somatic SV VCF (2 sample columns)",
+    )
+    p.add_argument("--out", type=Path, required=True, help="Output .vcf / .vcf.gz / .bcf")
     p.add_argument("--n-somatic", type=int, required=True)
     p.add_argument("--n-germline", type=int, required=True)
     p.add_argument("--tumor-sample-name", required=True)
@@ -224,32 +226,24 @@ def _cmd_gen_pair(args: argparse.Namespace) -> int:
     pair = sample_pair(bank, args.n_somatic, args.n_germline, cfg)
     writer = get_writer(args.caller)
     provenance = build_svforge_tags(caller=args.caller, seed=effective_seed, argv=sys.argv)
-    _write_sample_vcf(
+
+    _write_paired_vcf(
         writer,
         pair.tumor,
-        args.tumor_sample_name,
-        args.out_tumor,
-        args.genome,
-        provenance,
-        header_template_override=args.header_template,
-    )
-    _write_sample_vcf(
-        writer,
-        pair.normal,
-        args.normal_sample_name,
-        args.out_normal,
-        args.genome,
-        provenance,
+        tumor_sample=args.tumor_sample_name,
+        normal_sample=args.normal_sample_name,
+        out_path=args.out,
+        genome=args.genome,
+        provenance_tags=provenance,
         header_template_override=args.header_template,
     )
+
     log.info(
-        "Tumor: %d SVs (%d somatic + %d germline), Normal: %d SVs -> %s, %s (seed=%d)",
+        "Wrote %d SVs (%d somatic + %d germline) to %s (seed=%d)",
         len(pair.tumor),
         len(pair.somatic_ids),
         len(pair.germline_ids),
-        len(pair.normal),
-        args.out_tumor,
-        args.out_normal,
+        args.out,
         effective_seed,
     )
     return 0
@@ -363,7 +357,31 @@ def _write_sample_vcf(
         provenance_tags=provenance_tags,
         template_override=header_template_override,
     )
-    records = writer.format_records(svs, sample_name)
+    records = writer.format_records_sorted(svs, sample_name, header)
+    write_vcf(out_path, header, records)
+
+
+def _write_paired_vcf(
+    writer: CallerWriter,
+    svs: list[SV],
+    *,
+    tumor_sample: str,
+    normal_sample: str,
+    out_path: Path,
+    genome: GenomeBuild,
+    provenance_tags: Sequence[str],
+    header_template_override: Path | None = None,
+) -> None:
+    header = writer.header_lines_paired(
+        tumor_sample=tumor_sample,
+        normal_sample=normal_sample,
+        genome=genome,
+        provenance_tags=provenance_tags,
+        template_override=header_template_override,
+    )
+    records = writer.format_records_paired_sorted(
+        svs, tumor_sample, normal_sample, header
+    )
     write_vcf(out_path, header, records)
 
 

src/svforge/io/vcf_writer.py

@@ -18,6 +18,8 @@
 
 import pysam
 
+from svforge.writers.base import VCFRecord
+
 
 def detect_mode(path: Path) -> str:
     """
@@ -39,7 +41,7 @@ def detect_mode(path: Path) -> str:
 def write_vcf(
     out_path: str | Path,
     header_lines: Iterable[str],
-    record_lines: Iterable[str],
+    record_lines: Iterable[VCFRecord],
 ) -> Path:
     """
     Materialise a text VCF to a file in the format implied by ``out_path``
@@ -54,7 +56,7 @@ def write_vcf(
     mode = detect_mode(out)
 
     header_text = _lines_to_text(header_lines)
-    record_text = _lines_to_text(record_lines)
+    record_text = _records_to_text(record_lines)
 
     if mode == "w":
         out.write_text(header_text + record_text, encoding="utf-8")
@@ -74,7 +76,7 @@ def write_vcf(
         staging.write_text(header_text + record_text, encoding="utf-8")
         with (
             pysam.VariantFile(str(staging)) as vin,
-            pysam.VariantFile(str(out), mode, header=vin.header) as vout,  # type: ignore[arg-type]
+            pysam.VariantFile(str(out), mode, header=vin.header) as vout,
         ):
             for rec in vin:
                 vout.write(rec)
@@ -87,3 +89,11 @@ def _lines_to_text(lines: Iterable[str]) -> str:
     for line in lines:
         parts.append(line if line.endswith("\n") else line + "\n")
     return "".join(parts)
+
+
+def _records_to_text(records: Iterable[VCFRecord]) -> str:
+    parts: list[str] = []
+    for rec in records:
+        line = rec.line
+        parts.append(line if line.endswith("\n") else line + "\n")
+    return "".join(parts)