Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
The added test here fails under TreeTime 0.11.1 but has been fixed as part of <neherlab/treetime#263>. Description of the bug (as it relates to the test added in `vcf.t`): The SNPs at nt 33 are encoded in the VCF as: 1 33 . A C,G . . . GT 1 2 0 where ALT 1 ("C") is on Sample_A and ALT 2 ("G") is on Sample_B. The ALT 2 is not being parsed by `read_vcf`, which results in a changed mutation profile at pos 33: . **FASTA input** **VCF input** . |---G33C-- sample_A |---A33C-- sample_A . --A33G-| -------| . |--------- sample_B |--------- sample_B . Because of this bug, the following test fails. The `read_vcf` function is used in augur commands ancestral, refine, sequence-traits, translate and tree.
- Loading branch information