Fix failure to export haplo GTs (#374)

* fix failure to export haplo GTs to VCF
* Bump version: 3.2.0 → 3.2.1

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.2.0
+current_version = 3.2.1
 commit = True
 tag = False
 

.github/workflows/clinvar_runner.yaml

@@ -32,5 +32,5 @@ jobs:
           curl --fail --silent --show-error -X POST \
               -H "Authorization: Bearer $TOKEN" \
               -H "Content-Type:application/json" \
-              -d '{"output": "generate_clinvar_${{ steps.date.outputs.date }}", "dataset": "talos", "accessLevel": "full", "repo": "automated-interpretation-pipeline", "commit": "${{ github.sha }}", "cwd": "reanalysis", "script": ["./clinvar_runner.py"], "description": "Generate Latest Clinvar Summaries", "image": "australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:3.2.0", "config": {"workflow": {"sequencing_type": "genome"}, "cohorts": {"talos": {"clinvar_filter": ["victorian clinical genetics services, murdoch childrens research institute"]}}}, "wait": false}' \
+              -d '{"output": "generate_clinvar_${{ steps.date.outputs.date }}", "dataset": "talos", "accessLevel": "full", "repo": "automated-interpretation-pipeline", "commit": "${{ github.sha }}", "cwd": "reanalysis", "script": ["./clinvar_runner.py"], "description": "Generate Latest Clinvar Summaries", "image": "australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:3.2.1", "config": {"workflow": {"sequencing_type": "genome"}, "cohorts": {"talos": {"clinvar_filter": ["victorian clinical genetics services, murdoch childrens research institute"]}}}, "wait": false}' \
               https://server-a2pko7ameq-ts.a.run.app

.github/workflows/docker.yaml

@@ -14,7 +14,7 @@ permissions:
   contents: read
 
 env:
-  VERSION: 3.2.0
+  VERSION: 3.2.1
 
 jobs:
   docker:

reanalysis/hail_filter_sv.py

@@ -126,6 +126,28 @@ def rearrange_filters(mt: hl.MatrixTable) -> hl.MatrixTable:
     )
 
 
+def fix_hemi_calls(mt: hl.MatrixTable) -> hl.MatrixTable:
+    """
+    Hail's MT -> VCF export doesn't handle hemizygous calls
+    adjust the relevant single allele calls to a biallelic representation
+    going with Hom-Alt/Hom-Ref
+
+    if GT == 1, recast as [1, 1]
+    if GT == 0, recast as [0, 0]
+
+    Args:
+        mt ():
+    """
+
+    return mt.annotate_entries(
+        GT=hl.if_else(
+            mt.GT.is_diploid(),
+            mt.GT,
+            hl.if_else(mt.GT.is_non_ref(), hl.call(1, 1), hl.call(0, 0)),
+        )
+    )
+
+
 def main(
     mt_path: str,
     panelapp_path: str,
@@ -186,6 +208,9 @@ def main(
     # filter to labelled entries
     mt = mt.filter_rows(mt.info.categorybooleansv1 == ONE_INT)
 
+    # Hail's MT -> VCF export doesn't handle hemizygous calls
+    mt = fix_hemi_calls(mt)
+
     # now write that badboi
     hl.export_vcf(mt, vcf_out, tabix=True)
 

reanalysis/reanalysis_global.toml

@@ -71,7 +71,7 @@ default_memory = 'highmem'
 
 [images]
 gatk = 'australia-southeast1-docker.pkg.dev/cpg-common/images/gatk:4.2.6.1'
-aip = 'australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:3.2.0'
+aip = 'australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:3.2.1'
 vep_110 = "australia-southeast1-docker.pkg.dev/cpg-common/images/vep_110:release_110.1"
 cpg_workflows = "australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_workflows:latest"
 

reanalysis/version.py

@@ -3,4 +3,4 @@
 """
 
 # Do not edit this file manually
-__version__ = '3.2.0'
+__version__ = '3.2.1'

setup.py

@@ -31,7 +31,7 @@ def read_reqs(filename: str) -> list[str]:
     name='automated-interpretation-pipeline',
     description='CPG Variant Prioritisation',
     long_description=readme,
-    version='3.2.0',
+    version='3.2.1',
     author='Matthew Welland, CPG',
     author_email=(
         '[email protected], '