c2972a653dcb5b4972b7dd1999a69e1e *DESCRIPTION
101b78f6acd12b752cd5a18c45ac01e4 *NAMESPACE
e9f7cf46fb1a5955238952fe74f85760 *NEWS.md
c188b44db705b3bac05f699dea5143af *R/RGlobals.R
97aedf5750b778e3e5da83ba5380ea7c *R/app.R
2e6f7deb83eabe4eaff327f645f1bdde *R/create_ref.R
737e47857fe16b646234664112384f7c *R/estimate_lineages.R
22c7c993974e01514dd6768f5e23d5df *R/get_codons.R
b51960abd7d68ff8c8012656f16f713a *R/id_mutations.R
ea1da991e5533ed079e04398c6032fcb *README.md
97e578cd4a92faf098dc7d4a5e25dac6 *build/vignette.rds
718527902e6cfc197f86a22f94e20f80 *inst/doc/vignette.R
0e38951c196e9a3b4ee7bc17821b17b4 *inst/doc/vignette.Rmd
0e04bae993372c249141b6f1e49893dc *inst/doc/vignette.html
718527902e6cfc197f86a22f94e20f80 *inst/doc/vignette_mixvir.R
649f503f3598e243d9ae4d8f3ca36a7c *inst/doc/vignette_mixvir.Rmd
f007424772c864fa5c9dcb65c8c9b5cd *inst/doc/vignette_mixvir.pdf
9f9f8b080db98d2693a669500886a981 *inst/extdata/example_lineage_muts.csv
82bec94093ff6d8a4a20d97e605e9afd *inst/extdata/example_location_date.csv
b865a14f9f4bd5a673149f034f8307ed *inst/extdata/sample_mutations.tsv
a2629a1bbd6e1c59d5f9d0b974eed410 *inst/extdata/vcf/Sample1_04182021.vcf.gz
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
cb4fe488e3328b767600fdcef6c48c5d *man/call_mutations.Rd
58cb78adcd0af9585a9d9b540465374f *man/create_ref.Rd
bc86877a2263ae5358655cae127cfee8 *man/estimate_lineages.Rd
6c5b75e5c0df5bbe25704b02f90b39a9 *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
de12e901a59072b756d7f07cfdb7ae94 *vignettes/vignette.Rmd
0e04bae993372c249141b6f1e49893dc *vignettes/vignette.html
