feat: het indel product calling — ref-length FASTA + dual-track products#6
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jbrestel wants to merge 8 commits into
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feat: het indel product calling — ref-length FASTA + dual-track products#6jbrestel wants to merge 8 commits into
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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…rence length - Hom and het indels now emit ref_seq[pos:pos+len(REF)] instead of ALT allele or N masks - Ensures consensus FASTA always matches reference length; indel info tracked in DB - Also fixed SNP detection to check that allele length matches REF length - Added test_makeConsensusFastaFromGvcf.py with 4 test cases covering hom/het indels and low coverage Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…hema with zygosity/alleles Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…is now reference-length
… het indels now emit products Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
Nis reserved exclusively for low/no-coverage positions.genomic_indelstable withzygosity,ref_allele,alt_allelecolumns replaces the prior hom-only approach.findValues.plnow parses GT fields and emits the full 7-column TSV.processSequenceVariations.jlapplies indels to CDS sequences at product-calling time — hom indels emit one product (ALT-applied), het indels emit two products (REF + ALT), consistent with how het SNPs are handled today.Files Changed
bin/findValues.plmodules/mergeExperiments.nfgenomic_indelstable extended to 7 columnsbin/makeConsensusFastaFromGvcf.pybin/makeCodingData.jlfasta_offset; extendcodingIndels.dbschemabin/processSequenceVariations.jlget_indel_shift; addlookup_cds_indel,apply_indel_to_cds; indel product pathtesting/t/findValues.ttesting/t/test_makeConsensusFastaFromGvcf.pytesting/t/makeCodingData.jltesting/t/processSequenceVariations.jlTest Plan
python3 testing/t/test_makeConsensusFastaFromGvcf.py(4/4)julia testing/t/makeCodingData.jlandjulia testing/t/processSequenceVariations.jlPERL5LIB=... prove testing/t/findValues.tmergeExperimentsworkflow with a sample that has het indels and verifyproduct.datcontains both REF and ALT products🤖 Generated with Claude Code