4e36f316a588a20658ecf835ca4df804 *DESCRIPTION
a67b2bae97e1d6d416f773cb3f897596 *LICENSE
92a9c42e8c837bdcec7e5648d961afce *NAMESPACE
ab66dcace749116172cbd2ca24f0e47e *NEWS
285c9bf55c1210f6c987eeb572d17d3f *R/get_lineage_report.R
6eaf8dc6649af4e928a4f142acfa11f4 *R/input_checking.R
d66970566789b1d81fbba3a337d4a68c *R/lineagespot.R
53e1c68ab44689db12517ff965f95ac0 *R/lineagespot_hits.R
82a5fd72eab8bd0531ceeb5a30ddd35f *R/merge_vcf.R
ca8e5b6fb67565fd15168d4e71399419 *R/uniq_variants.R
505be48b4416a98d14abd06602607b81 *README.md
4c14a7d71a87c686419573b9971a22cb *build/vignette.rds
235f3f5f235d3d3d1a056d2d02054afe *inst/CITATION
a93bdc3a9b7f87d8952bea985041176e *inst/doc/lineagespot.R
e8c040fb4a7658ecd5dab9d21dcf8ecc *inst/doc/lineagespot.Rmd
787ce797fac93cd0cc716a1dd810d705 *inst/doc/lineagespot.html
f5e0a3774b7342f30933a6a6096b87d8 *inst/extdata/NC_045512.2_annot.gff3
75d5f9e5aa25e8295175be3f01e5c801 *inst/extdata/ref/AY.1.txt
a63320752bc2b7751296b4449f6e97c7 *inst/extdata/ref/AY.2.txt
d4411d1c25b50414e66bc84fa561ad82 *inst/extdata/ref/AY.3.1.txt
9cadcd3d11009852ef56b367f85192c2 *inst/extdata/ref/AY.3.txt
6c30d353b0b6943653fcf8ddd4191f27 *inst/extdata/ref/B.1.1.7+S_E484K.txt
9ea0bb2f409d7477cd4fce4f6961e883 *inst/extdata/ref/B.1.1.7.txt
37988678fe4feeb5615208b395df7761 *inst/extdata/ref/B.1.351.2.txt
bf8aba1c30257ea58a10556a1e990a98 *inst/extdata/ref/B.1.351.3.txt
34a840993d5217bac537fe1d586887ad *inst/extdata/ref/B.1.351.txt
8856c72b91d113b8ba7ae808637c44e3 *inst/extdata/ref/B.1.617.2.txt
baba26946cb2b1592e81f3d031af4ab6 *inst/extdata/ref/P.1.1.txt
09d79737395c6c69482e93cd753ba4ab *inst/extdata/ref/P.1.2.txt
09d79737395c6c69482e93cd753ba4ab *inst/extdata/ref/P.1.txt
55367e21ab319d455b1f86c15f770c6f *inst/extdata/srep-article-code/README.md
7d232ebab2293db3c3157327af2c4bb1 *inst/extdata/vcf-files/SampleA_freebayes_ann.vcf
e99b4f3fc50668b0f4f8ab04eb00d0e3 *inst/extdata/vcf-files/SampleB_freebayes_ann.vcf
71c9b4573e3e3f830fd4f2ff2f0e2b46 *inst/extdata/vcf-files/SampleC_freebayes_ann.vcf
9c4d7c29f3d4c520b036f6468d6f53d5 *inst/scripts/README.md
c312f2fdbc6e364b727fbed8b26623fb *inst/scripts/raw-data-analysis.md
55e7ead4438248a24e5f66b50b0b01b8 *man/get_lineage_report.Rd
97fa3ebf05d956427738101784787084 *man/is_gff3.Rd
f59a521bd293b6a7230a57e46acd1b8f *man/lineagespot.Rd
ed5b163b9f4c12bbb8f68112aa5c9d80 *man/lineagespot_hits.Rd
38156ec40984f697bc172c7631b11afc *man/list_input.Rd
4c338806cb58bc1a165173f05e92c676 *man/list_vcf.Rd
0b780ede9331d4e9c459b0f7bc007ef5 *man/merge_vcf.Rd
420a7bde4f2784d7cee2e1591599b2b6 *man/uniq_variants.Rd
6a00a25391f617d0493a76540cb54456 *tests/testthat.R
d61cc2fbf1a9712aab66e1cd07f73d40 *tests/testthat/test_get_lineage_report.R
01e0e1d6a5667c7d399310d0b7d4dba0 *tests/testthat/test_input.R
af173269df0ce5f90288c2e36c88402e *tests/testthat/test_lineagespot.R
c2dc86b1543f1945a4696929aa65b3f7 *tests/testthat/test_merge_vcf.R
49b1a4a632313994871bf0d0471a329a *tests/testthat/test_uniVariants_lineagespotHits.R
e8c040fb4a7658ecd5dab9d21dcf8ecc *vignettes/lineagespot.Rmd
