Merge pull request #69 from oxfordmmm/feat/gvcf-support

fix: ensure all minos positions from merge-vcfs

bin/merge-vcfs

@@ -15,7 +15,7 @@ def fetch_minos_positions(minos_vcf: Path) -> set[int]:
     Returns:
         set[int]: The positions to exclude.
     """
-    vcf = gumpy.VCFFile(minos_vcf.as_posix())
+    vcf = gumpy.VCFFile(minos_vcf.as_posix(), ignore_filter=True)
     positions = set()
     for pos, m_type in vcf.calls:
         if m_type != "indel":
@@ -65,7 +65,7 @@ if __name__ == "__main__":
     # Pull out these positions from the GVCF
     gvcf_headers, subset = subset_vcf(gvcf_path.as_posix(), to_fetch)
 
-    minos_headers, minos_values = subset_vcf(minos_path.as_posix(), sorted(list(minos_positions)))
+    minos_headers, minos_values = subset_vcf(minos_path.as_posix(), [])
 
     # Pull out header parts to catch parts which need adding
     minos_format = [header for header in minos_headers if "##FORMAT" in header]

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = gnomonicus
-version = 2.6.0
+version = 2.6.1
 author = Philip W Fowler, Jeremy Westhead
 author_email = philip.fowler@ndm.ox.ac.uk
 description = Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants
@@ -18,6 +18,7 @@ python_requires = >=3.10
 install_requires = 
     gumpy>=1.3.0
     piezo>=0.8.3
+    vcf_subset>=1.1.1
     numpy
     pandas
     recursive_diff