83230c48e143d70e7bed6c557a004485 *DESCRIPTION
2fc9ae9291615dc62ba9c17ec1a773ce *LICENSE
24573e27fd4b3103a591178408d863b1 *NAMESPACE
637d788fc1e65ee1580de2f2e5f5f749 *NEWS.md
98a12f222cd27cd6454851903c9b7acc *R/guided_helpers.r
0ee91242c7726614991dcaa1655a8cb6 *R/merge.R
b7bfea1f95fbd2511e92cb16534411ef *R/output.R
352555bbf6259fdaa821e23a59221283 *R/process.R
f73179436dc79a7e5e69b2fa6ca79983 *R/search.R
41084559cbc9000c23617b235b5134d9 *R/zzz.R
422d31584494606d4dd53f174296fd66 *README.md
5b165b5bea66e967444014359e26f534 *build/vignette.rds
3271f3134b66cb7e88699361bfc5b564 *inst/doc/MinSNPs_Workflow.R
9f4734102a06278a1cc3f3c5b6e218b3 *inst/doc/MinSNPs_Workflow.Rmd
352fcda7d04490162b427ac073a0570c *inst/doc/MinSNPs_Workflow.html
418494447d78713c575f4d82a66c1094 *inst/extdata/Chlamydia_1.fasta
a912cfb8fb27e412022f2f39f585dd44 *inst/extdata/Chlamydia_2.fasta
cc8f4f58496d75c56a20378d6f2a1222 *inst/extdata/Chlamydia_mapped.fasta
cd7fb698255f3cb44b7edacc02e918c7 *man/branch_and_search.Rd
2bc6189875da06d55d25be55ca1765f5 *man/cal_fn.Rd
9bdef9fbf123fc47fe75d2d90d1b91ae *man/cal_fp.Rd
f9f7b81003b9521c0d2c5d34fec6602e *man/cal_met_snp.Rd
516b2f74fbe53bfddaa18bf3de24145a *man/calculate_percent.Rd
db52471b773f299f09ab835bb11f057f *man/calculate_simpson.Rd
c69b34bae2a081252e64b8a279146190 *man/check_fasta_meta_mapping.Rd
d363651d0ad6066f196a1e1e672f3ea6 *man/check_multistate.Rd
d7874ed29fe17bf799a7f1f894b7d00a *man/check_percent.Rd
07b69c36c5568e512bef889cf4eeb1ca *man/find_optimised_snps.Rd
d51ec7ac6becb3207a9907c09d8483bf *man/flag_allele.Rd
a1c83c572ff1956def6d8e09a14ce7d3 *man/flag_position.Rd
64148995d5b4d0568d3b771cfd7d6855 *man/full_merge.Rd
3b036bc1cec623b195d198a63db12d3c *man/full_merge_1.Rd
1c44a2e747824a28b4d2a787dd8981aa *man/generate_pattern.Rd
3365303d457e5bf2463a7df3acbcef95 *man/get_metric_fun.Rd
96089ae1678a4f7931eeb6dbff444ae4 *man/get_positions_to_search.Rd
6058ac3dab8ec9c1c3e2f12e59b56a23 *man/get_usual_length.Rd
ef3a9f57ac9dd640c0f7c33769ae870f *man/iterate_merge.Rd
d061efb0224b91258ecb69b956fe7327 *man/merge_fasta.Rd
70601a2fd9529e746f4237c55dde8a8d *man/output_parsed.Rd
e0c77cd1af2e8b22a58dc014060fd2c0 *man/output_result.Rd
39be32cd2b9c84fb11f4f786418feb3f *man/output_to_files.Rd
f641eaa42619d40106f6d74327018b92 *man/process_allele.Rd
a76a78b378fd2ba398cecd3565f574ca *man/read_fasta.Rd
69b59b3f14f01607d64a72bc0394107c *man/remove_dup_isolate.Rd
32df5f737fa4f72706010f00f69a4243 *man/resolve_IUPAC_missing.Rd
03a15d1b704045aec77d56d10c4e7b80 *man/view_percent.Rd
34e281153c81f74617eb0ba4675a34b0 *man/view_simpson.Rd
fad823b4adadd9dc32af5dd38688ecae *man/write_fasta.Rd
74949e8501a0f303bfc6da399d6f70fa *tests/testthat.R
d9a3b961c7c5e188a88c1d8413489059 *tests/testthat/test-process.R
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-search.R
9f4734102a06278a1cc3f3c5b6e218b3 *vignettes/MinSNPs_Workflow.Rmd
