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fix: skip bcftools merge for single PCGR VCF chunk (#26) - #36
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run_somatic_chunk -> merging_pcgr_files unconditionally called util.merge_vcf_files, which shells out to `bcftools merge`. That command requires 2+ inputs, so a sample whose variants fit in a single chunk (no splitting needed) produced a bcftools merge Usage error instead of a valid annotated VCF. Guard on len(pcgr_vcf_files) == 1: copy the single chunk's VCF directly to the expected merged-output path and tabix-index it, matching the indexed .vcf.gz contract that merge_vcf_files normally produces. Two or more chunks still go through the existing bcftools merge -> sort -> index path unchanged.
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This was referenced Jul 17, 2026
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Summary
merging_pcgr_files()(bolt/common/pcgr.py) calledbcftools mergeunconditionally on the chunked PCGR VCF outputs.bcftools mergerequires 2+ input files — when a sample's variants fit in a single PCGR chunk (no splitting needed), this produced abcftools mergeusage error instead of a valid annotated VCF..vcf.gzcontractmerge_vcf_filesnormally produces. 2+ chunks are unaffected.Closes #26.
Test plan
test_single_chunk_skips_bcftools_merge,test_multiple_chunks_still_merge(tests/test_pcgr_hypermutated.py)python -m pytest tests/test_pcgr_hypermutated.py -v— 35 passedpython -m unittest discover tests/ --buffer— 49 tests, OK