28b5d187a6db78413b8174d5153d3422 *DESCRIPTION
101b78f6acd12b752cd5a18c45ac01e4 *NAMESPACE
ded72f0d4d811cf59385d79343000e34 *NEWS.md
45aa2e1e173feaa3a9e9e0adbecd0ab2 *R/RGlobals.R
2504cdc8c23ed853e4e335c379c32851 *R/app.R
2e6f7deb83eabe4eaff327f645f1bdde *R/create_ref.R
dadb684738f4b21028d3061474d071be *R/estimate_lineages.R
22c7c993974e01514dd6768f5e23d5df *R/get_codons.R
0802a1c6437076663bf014d61f367b15 *R/id_mutations.R
379945bcf3be432c58426113c5538eed *README.md
c196cf1c28ba7b164e8bf95a5a6ff8bc *build/vignette.rds
8b76d29c06aa91296aff580285a1fdbd *inst/doc/vignette.R
6e7938890e5c947d6ebf4346665283f7 *inst/doc/vignette.Rmd
36f69964a9ad1849e4e1660b03f4a6e5 *inst/doc/vignette.html
9f9f8b080db98d2693a669500886a981 *inst/extdata/example_lineage_muts.csv
d8757bc0d1f55ad3298f3bf6f81c7838 *inst/extdata/example_lineage_muts_w_sublins.csv
82bec94093ff6d8a4a20d97e605e9afd *inst/extdata/example_location_date.csv
0579a381035bd455e60b9b93d0a51761 *inst/extdata/sample_mutations.csv
01b434d6e9984b51460eb1510f4e57ec *inst/extdata/vcfs/Sample1_04182021.vcf.gz
c63884404dc52af53008776bb28799f4 *inst/extdata/vcfs/Sample2_05022021.vcf.gz
26b70344e5f952425bd16b29da05dab2 *inst/extdata/vcfs/Sample3_08152021.vcf.gz
234bff3949affb6d33c45fe7489c4da8 *man/add_depths_to_ref.Rd
a742b4885514b10b30fd6bb075eac3d5 *man/call_mutations.Rd
58cb78adcd0af9585a9d9b540465374f *man/create_ref.Rd
8f6da9cc8884febfc6003e8059bc30c2 *man/estimate_lineages.Rd
f328156563d0fca6cbf48fb3db790ba6 *man/explore_mutations.Rd
f935f7ecfa7bf1b7894832f207e101c9 *man/get_codons.Rd
25dc493302a9c901929190b9dd5793bc *man/id_indels.Rd
7e1e93b7b00f94613a1e38bbe1f16101 *man/id_snps.Rd
74ff571fdcedee39a0690bbc187d793e *man/vcf_to_mixvir.Rd
6e7938890e5c947d6ebf4346665283f7 *vignettes/vignette.Rmd
