25a09538cfabec3ade20cba33dd353b5 *DESCRIPTION
2fc9ae9291615dc62ba9c17ec1a773ce *LICENSE
65194b81e6abb23564d8523560323a11 *NAMESPACE
53aa3dc2f55743249a343aa5f04f4feb *NEWS.md
5f9b2068339fbfe031d8aa4f255090f4 *R/guided_helpers.r
2e51b2fdfda291121b0d14a8a7c1ecf7 *R/merge.R
6e576538b750b9abd5f1323bbd0e4ab8 *R/output.R
e8a5e81cb4a5d96a9411a4394a2f451d *R/process.R
d7e06c61c55cc2d30178f87731362ca5 *R/search.R
a3f1f342d281b37dc10d56663e8acf90 *R/search_string_generation.R
6399b8353e77afe389a44bc7bd0ae06e *R/utility.R
8ed39662753567acd8ce432387e5974e *R/zzz.R
c7c7f1a8e7069914c9244db74ea925fe *README.md
bf899ea0294e9d6924e3cd697019d720 *build/vignette.rds
3295fff0fc6ff8952752a655be8b0cb7 *inst/doc/MinSNPs_Workflow.R
2dcb92ff64549dc821d2273c0cd92264 *inst/doc/MinSNPs_Workflow.Rmd
9277336c6edd907112d2808f07e07054 *inst/doc/MinSNPs_Workflow.html
418494447d78713c575f4d82a66c1094 *inst/extdata/Chlamydia_1.fasta
a912cfb8fb27e412022f2f39f585dd44 *inst/extdata/Chlamydia_2.fasta
cc8f4f58496d75c56a20378d6f2a1222 *inst/extdata/Chlamydia_mapped.fasta
c931b5ffa22fa57b4f7eb834a70d60fc *man/branch_and_search.Rd
61b9d470f71e912b0cf0d4aa5025ebb6 *man/cal_fn.Rd
a85b555eac6a83ccff1f943e84bd4eb4 *man/cal_fp.Rd
9ed06461d42f64ca5853c7f76435c154 *man/cal_met_snp.Rd
5dbc00df5fbe5ba7754d6b9aa3e42ed6 *man/calculate_percent.Rd
0bbd41b52dcc1240fbc49e0ebc24175c *man/calculate_simpson.Rd
2990ad1a1cf21c7f17ed166a1157a8fc *man/check_fasta_meta_mapping.Rd
51fe2848b024453ace7e461ebb3faeb1 *man/check_multistate.Rd
cfe8aba1c75405b04b43fbaed77fa42e *man/check_percent.Rd
d94bdce9773cc81ec28eeefd2abd5b38 *man/extend_length.Rd
2b96e7099c7b968a7f6f49fde5ffc3ec *man/find_optimised_snps.Rd
d9e61bf7fe5f153666f564079305089d *man/flag_allele.Rd
7f33b736c695f579028ef8f3b3e3d42e *man/flag_position.Rd
6b5572a622d0d9075d20cd92154e8a8b *man/full_merge.Rd
b1dd74b0affd927987dd945505b36bef *man/full_merge_1.Rd
36520d5084d8c91e3e2be472c5e2a94f *man/generate_kmer_search_string.Rd
16ddab5202dd88ebc78f620037d6ca5c *man/generate_kmers.Rd
ca51c5ef3e1cc894938979c29585c39d *man/generate_pattern.Rd
637e11c7110aa234797b5b31069ea0a4 *man/generate_snp_search_string.Rd
ad4642a5d67e3fac060ac0cd672c054e *man/get_metric_fun.Rd
106b227ad40594a52d98255eeac02dff *man/get_positions_to_search.Rd
9ab96abb6e64517d209fbe2456bb0176 *man/get_usual_length.Rd
e294421ab7fb61492eeff8c84528424f *man/identify_overlaps.Rd
c38322cf0ce54eae59ea878bbfd22b95 *man/iterate_merge.Rd
4ead268f4fb80825313898e409fe1ff6 *man/match_count.Rd
bb1ed077b26d4d628f573bff5680131e *man/merge_fasta.Rd
4952de5221d1c720479a54844aad6c09 *man/output_parsed.Rd
8d770ac8ad025ffc2492402b05109822 *man/output_result.Rd
84aef766c4e8a65a99f9930f7b1d2d3b *man/output_to_files.Rd
bb9450c32394082708627a9af2c8618f *man/process_allele.Rd
b2e7a7a523157b7d77d9eb21710b7729 *man/read_fasta.Rd
c9a3686102bb92f9bbbfbd8d8460b96f *man/read_sequences_from_fastq.Rd
9b1a82ccc2983ae389d370a357152407 *man/remove_dup_isolate.Rd
539fcb478b33ab36d236f105c928f8f4 *man/resolve_IUPAC_missing.Rd
6f031041acfac4257f7d2617af686e7f *man/reverse_complement.Rd
7b541f88dba0974c4f6a49b40c488690 *man/select_n_set_i_depth.Rd
f305279bf9f7340c6e8c75873dda9afb *man/view_percent.Rd
b63126219918d1a1c3387a7781961875 *man/view_simpson.Rd
6175a2e620fdbf759815833173a1fc46 *man/write_fasta.Rd
1e62e94ec949d8d657c572ead9cb98c9 *tests/testthat.R
5eee70fb4e2ac3a0a973f297931e9879 *tests/testthat/test-process.R
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-search.R
2dcb92ff64549dc821d2273c0cd92264 *vignettes/MinSNPs_Workflow.Rmd
