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Send info on undercovered genes in HL7 message #5

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Send info on undercovered genes in HL7 message #5

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e6e9084
Send heme under-covered genes
iatol1 Nov 4, 2025
3e0351d
Add bfx pipeline to heme headers
iatol1 Nov 4, 2025
e07b5e2
Use correct pipeline version header name from varseq json
iatol1 Nov 10, 2025
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2 changes: 2 additions & 0 deletions mappings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,8 @@ def get_variant_id(idx):
"7102424": ["200x Depth Percentage", "ST"],
"7102425": ["500x Depth Percentage", "ST"],
"7102426": ["Mean Depth", "ST"],
"7102447": ["Under-covered Genes", "ST"],
"7102448": ["Bfx Pipeline Version", "ST"],
}

# Maps Sequence Ontology Terms to EPIC molecular consequence and DNA change type
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9 changes: 8 additions & 1 deletion varseq_hl7.py
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Expand Up @@ -241,7 +241,7 @@ def get_vaf(self, variant):
return round(variant["vaf"], 2)
elif variant.get("sv_vaf"):
return round(variant["sv_vaf"], 2)
# If no VAF is given, calculate it from altReadCount and readDepth
# If no VAF is given, calculate it from altReadCount and readDepth
elif variant["altReadCount"] and variant["readDepth"]:
return round(variant["altReadCount"] / variant["readDepth"], 2)
else:
Expand Down Expand Up @@ -336,6 +336,13 @@ def get_tumor_msg_header(self):
if self.panel == "UCLA Pan-Cancer All v1":
header += f"""{self.create_obx_segment("2a", "81695-9", f"^{self.get_msi()}")}\r"""
header += f"""{self.create_obx_segment("2a", "94076-7", f"{self.get_tmb()}")}\r"""
elif self.panel == "UCLA Heme v2":
under_covered_genes = self.get_custom_field("underCoveredGenes")
if under_covered_genes:
header += f"""{self.create_obx_segment("2a", "7102447", under_covered_genes)}\r"""
pipeline_version = self.get_custom_field("Pipeline_version")
if pipeline_version:
header += f"""{self.create_obx_segment("2a", "7102448", pipeline_version)}\r"""
return header

def get_normal_msg_header(self):
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