4d8b5a7e3ca46ff3cf9bc4e8168971d0 *DESCRIPTION
2fc9ae9291615dc62ba9c17ec1a773ce *LICENSE
371600a9a730c6c979e52aea37d39ad3 *NAMESPACE
6956dfe2400d6ccf9e4bbab0ccaf774e *NEWS.md
5f9b2068339fbfe031d8aa4f255090f4 *R/guided_helpers.r
2e51b2fdfda291121b0d14a8a7c1ecf7 *R/merge.R
34538a7478da8dce337b58fe398f83c2 *R/output.R
c0dbc052622e85ace8814adb9547b003 *R/process.R
eca86174a4b2bf5b7779baa571436634 *R/search.R
4a27ff51b1902bf82c258cacd298ab14 *R/search_from_reads.R
5b1ec71b63ef30848595980a7b2f613b *R/search_string_generation.R
fbdeacd704b26bfef03f6ec162da489c *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
e302cd6051217b491334f3fd305c7cdf *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
d9c224d59e9ff4a9164324efc52c6392 *man/cal_met_snp.Rd
ffdfd87877e7cb73913847586b1fb950 *man/calculate_percent.Rd
bef7fd943bd18af44c554fb9eec56744 *man/calculate_simpson.Rd
b21421d854eff39b69586dbec2debdb1 *man/calculate_variant_within_group.Rd
2990ad1a1cf21c7f17ed166a1157a8fc *man/check_fasta_meta_mapping.Rd
7848b2c68b7e06617e06a8c3775badec *man/check_multistate.Rd
cfe8aba1c75405b04b43fbaed77fa42e *man/check_percent.Rd
97e7e6375a9cecb2c6ab63de5980c8cd *man/combine_fastq_search_result.Rd
e6a4eb9477c61d652d6d1ce900b1adb7 *man/combine_search_string_result.Rd
49bbdbce90d98ecd1149b13a253cafcc *man/combine_search_string_result_from_files.Rd
3d3c07df6daf28f31c5e2c5902f5dfa9 *man/combine_search_string_result_from_list.Rd
c762ce5bcde93540493540e15184717a *man/estimate_coverage.Rd
d94bdce9773cc81ec28eeefd2abd5b38 *man/extend_length.Rd
266de9d93a5e4a8df823e467ad605339 *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
b1e527c9912ed59aaf55d25fbccf0f91 *man/generate_snp_search_string.Rd
ef0ae499a0ca0052ce31c7abaedbbde3 *man/get_all_process_methods.Rd
ad4642a5d67e3fac060ac0cd672c054e *man/get_metric_fun.Rd
106b227ad40594a52d98255eeac02dff *man/get_positions_to_search.Rd
aba76bd54876f7f78a69d9b152aa1c68 *man/get_snps_set.Rd
9ab96abb6e64517d209fbe2456bb0176 *man/get_usual_length.Rd
e294421ab7fb61492eeff8c84528424f *man/identify_overlaps.Rd
e55145788e9b4c1f99eb45baf637edc9 *man/infer_from_combined.Rd
c38322cf0ce54eae59ea878bbfd22b95 *man/iterate_merge.Rd
e02c7140d37df1cbbee61ae1133ffbf7 *man/iterate_through.Rd
4ead268f4fb80825313898e409fe1ff6 *man/match_count.Rd
bb1ed077b26d4d628f573bff5680131e *man/merge_fasta.Rd
01020522fa168640f5349db24e3f8933 *man/output_parsed.Rd
8d770ac8ad025ffc2492402b05109822 *man/output_result.Rd
84aef766c4e8a65a99f9930f7b1d2d3b *man/output_to_files.Rd
bb9450c32394082708627a9af2c8618f *man/process_allele.Rd
dddd139039693d07b44d3f612158759d *man/process_kmer_result.Rd
936c1711aeb88d6c2126b1abdc0b2981 *man/process_result_file.Rd
2ae1b9a45983fba9793cff1a30e84162 *man/process_snp_result.Rd
b2e7a7a523157b7d77d9eb21710b7729 *man/read_fasta.Rd
e639ce4c3a3139bae88e95f9e22beac5 *man/read_sequences_from_fastq.Rd
9b1a82ccc2983ae389d370a357152407 *man/remove_dup_isolate.Rd
2142b91efb54b92f80147373228cec5c *man/remove_snp_conflict.Rd
539fcb478b33ab36d236f105c928f8f4 *man/resolve_IUPAC_missing.Rd
6f031041acfac4257f7d2617af686e7f *man/reverse_complement.Rd
469a99a5dcd8dec6413be174eb06fd55 *man/search_from_fastq_reads.Rd
7b541f88dba0974c4f6a49b40c488690 *man/select_n_set_i_depth.Rd
f017fceb333b096c85f3d7e3559cafd1 *man/sequence_reads_match_count.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
