Replicate dnadiff output

The aim of `pyani dnadiff` subcommand is to replicate the exact `dnadiff` values for `AlignedBases` and `AvgIdentity`, since these values cannot be replicated using `delta` files alone. Here, I have sucessfully replicated the exact process implemented by `dnadiff` to obtain these values and have tested it on three separate test sets.
widdowquinn · Mar 19, 2024 · fa2e501 · fa2e501
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diff --git a/replicate_dnadiff/data/donovan_AF_bug/input/MGV-GENOME-0357962.fna b/replicate_dnadiff/data/donovan_AF_bug/input/MGV-GENOME-0357962.fna
diff --git a/replicate_dnadiff/data/donovan_AF_bug/input/MGV-GENOME-0358017.fna b/replicate_dnadiff/data/donovan_AF_bug/input/MGV-GENOME-0358017.fna
diff --git a/replicate_dnadiff/data/donovan_test/input/MGV-GENOME-0264574.fna b/replicate_dnadiff/data/donovan_test/input/MGV-GENOME-0264574.fna
diff --git a/replicate_dnadiff/data/donovan_test/input/MGV-GENOME-0266457.fna b/replicate_dnadiff/data/donovan_test/input/MGV-GENOME-0266457.fna
diff --git a/replicate_dnadiff/data/streptomyces_genomes/input/GCF_002802945.1_ASM280294v1_genomic.fna b/replicate_dnadiff/data/streptomyces_genomes/input/GCF_002802945.1_ASM280294v1_genomic.fna
diff --git a/replicate_dnadiff/data/streptomyces_genomes/input/GCF_003369795.1_ASM336979v1_genomic.fna b/replicate_dnadiff/data/streptomyces_genomes/input/GCF_003369795.1_ASM336979v1_genomic.fna