Merge Dev changes

Dockerfile

@@ -1,4 +1,4 @@
-FROM debian:13.4-slim AS downloader
+FROM debian:13.7-slim AS downloader
 
 # Tool versions and pinned SHA-256 checksums. Bumping a version is a
 # two-line edit (version + hash) in this block.
@@ -17,8 +17,8 @@ ARG VG_VERSION=1.73.0
 ARG VG_SHA256=d5752977237e801d971f0d044f43fde4f3005da35f0451b4f452d1c1c9b8414b
 # Sentieon's KMC fork adds the `-fa /dev/stdin` patch used by the pangenome pipeline.
 ARG KMC_VERSION=3.2.4
-ARG KMC_RELEASE_TAG=v3.2.4-pipe2
-ARG KMC_SHA256=d8bdf8edcd0577dba32e86e8f194b2eb04eb168c75a3e6d46721d5bef515ac96
+ARG KMC_RELEASE_TAG=v3.2.4-pipe3
+ARG KMC_SHA256=6ae37ac28c215919a67bd77edf004f9e323013bba5700bc44ad23c0b59da9a91
 ARG EXPANSIONHUNTER_VERSION=5.0.0
 ARG EXPANSIONHUNTER_SHA256=ebf3ec0ace6e6e3bbce12c26463da5d9f8e16374eff1ad10f0f1a9123050fa86
 # T1K and segdup-caller are built from git; pin the tag and verify the
@@ -155,7 +155,7 @@ RUN /opt/poetry-venv/bin/pip install --no-cache-dir \
 
 # Build the Python environment in an isolated stage. The venv is
 # later COPY'd over as-is.
-FROM debian:13.4-slim AS python-builder
+FROM debian:13.7-slim AS python-builder
 ARG SENTIEON_VERSION
 
 COPY --from=downloader /opt/sentieon-cli/dist /opt/sentieon-cli/dist
@@ -185,7 +185,7 @@ RUN apt-get update && \
       -depth -type d -name __pycache__ -exec rm -rf {} +
 
 # Build the container
-FROM debian:13.4-slim
+FROM debian:13.7-slim
 ARG SENTIEON_VERSION
 ARG BEDTOOLS_VERSION=2.30.0
 ARG MOSDEPTH_VERSION=0.3.9
@@ -205,7 +205,7 @@ LABEL org.opencontainers.image.title="sentieon-cli" \
       org.opencontainers.image.url="https://www.sentieon.com/" \
       org.opencontainers.image.source="https://github.com/Sentieon/sentieon-cli" \
       org.opencontainers.image.licenses="BSD-2-Clause" \
-      org.opencontainers.image.base.name="debian:13.4-slim" \
+      org.opencontainers.image.base.name="debian:13.7-slim" \
       org.opencontainers.image.version="${SENTIEON_VERSION}" \
       org.opencontainers.image.revision="${VCS_REF}" \
       org.opencontainers.image.created="${BUILD_DATE}"

README.md

@@ -15,9 +15,9 @@ pip install sentieon_cli
 
 Install the sentieon-cli through a container image:
 ```sh
-docker pull sentieon/sentieon_cli:latest
+docker pull sentieon/sentieon-cli:latest
 docker run --rm -v "$PWD:/data" -w /data \
-    sentieon/sentieon_cli:latest \
+    sentieon/sentieon-cli:latest \
     sentieon-cli dnascope-pangenome --help
 ```
 

pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "sentieon_cli"
-version = "2.0.0"
+version = "2.0.1"
 description = "Pipeline implementations for the Sentieon software"
 authors = [
     {name = "Don Freed", email = "don.freed@sentieon.com"},

sentieon_cli/base_pangenome.py

@@ -244,6 +244,8 @@ def __init__(self) -> None:
         self.t1k_kir_coord: Optional[pathlib.Path] = None
         self.t1k_kir_locus: str = DEFAULT_T1K_KIR_LOCUS
         self.has_cnv_model = False
+        # The bundle has a `combine_cnv.json` preset for `combine_cnv.py`
+        self.has_combine_preset = False
         # The pangenome reference, resolved from the graph's metadata by
         # `resolve_pangenome_reference`. The two arguments are hidden
         # overrides, so they stay `None` unless the user supplies them.
@@ -789,10 +791,22 @@ def add_pangenome_cnv(
             sv_vcf=sv_vcf,
             sample_sex=self.sample_sex,
             par_bed=self.cnv_par_bed,
+            combine_preset=self.cnv_combine_preset(),
             interval=interval,
             replace_rg=replace_rg,
         ).add_to(dag)
 
+    def cnv_combine_preset(self) -> Optional[pathlib.Path]:
+        """The `combine_cnv.py` preset for the bundle's CNVscope model.
+
+        The bundle's `combine_cnv.json` when it has one. Without it,
+        `combine_cnv.py` uses its defaults, the paired-end values.
+        """
+        if not self.has_combine_preset:
+            return None
+        bundle = self.required(self.model_bundle, "model_bundle")
+        return bundle.joinpath("combine_cnv.json")
+
     def build_kmc_job(
         self, kmer_prefix: pathlib.Path, job_threads: int
     ) -> Job: