Some files in /tests are not currently used. To keep clutter down, they should be removed. The files in question are:
all files in the reads_se dir. These are single-end test files, but single-end functionality is currently tested by simply omitting the second read file for paired end reads for some reads.
Some files in reads not currently used in tests. The only files used are: Test0_*, Test2_*, and Test5_*. The rest are unused.
sample_sheet_se.csv, unused sample sheet for reads in reads_se
test_data_variant_plot.csv, unused file which was supposed to be used in as of yet unimplemented regression tests.
WW_210219_KW1_snv.vcf_snv_empty.csv ???, see 7a536d3
coverage_gathering* very old output files giving overviews over past coverage results, used nowhere and likely outdated.
mutation_sheet*, except mutation_sheet_detailed.csv, unused mutations sheets. The actually used mutation sheet lives in sample_data.
sample_data/[Tt]est_* except Test_vep_sarscov2_parsed.txt and test_vep_parsing_input.txt. Everything besides the two exceptions which are actually used in the only implemented test, are unused and likely outdated.
sample_data/mutation_sheet_210927.csv and sample_data/mutation_sheet_21104_covidCG.csv, also unused mution sheets.
all files in coverage, old and likely outdated testing data for tests that are not implemented.
The dir sample_data/signature_mutations contains signature mutation info whose origin I can't comprehend, but one of which is used in Sample_prep_scripts/sigmuts_on_amplicons.Rmd, along with the mutation sheet mutation_sheet_detailed.csv. I am not sure if we still need the files in sample_data/signature_mutations and the notebooks, but I suppose they will stay for now.
Some files in
/testsare not currently used. To keep clutter down, they should be removed. The files in question are:reads_sedir. These are single-end test files, but single-end functionality is currently tested by simply omitting the second read file for paired end reads for some reads.readsnot currently used in tests. The only files used are:Test0_*,Test2_*, andTest5_*. The rest are unused.sample_sheet_se.csv, unused sample sheet for reads inreads_setest_data_variant_plot.csv, unused file which was supposed to be used in as of yet unimplemented regression tests.WW_210219_KW1_snv.vcf_snv_empty.csv???, see7a536d3coverage_gathering*very old output files giving overviews over past coverage results, used nowhere and likely outdated.mutation_sheet*, exceptmutation_sheet_detailed.csv, unused mutations sheets. The actually used mutation sheet lives insample_data.sample_data/[Tt]est_*exceptTest_vep_sarscov2_parsed.txtandtest_vep_parsing_input.txt. Everything besides the two exceptions which are actually used in the only implemented test, are unused and likely outdated.sample_data/mutation_sheet_210927.csvandsample_data/mutation_sheet_21104_covidCG.csv, also unused mution sheets.coverage, old and likely outdated testing data for tests that are not implemented.The dir
sample_data/signature_mutationscontains signature mutation info whose origin I can't comprehend, but one of which is used inSample_prep_scripts/sigmuts_on_amplicons.Rmd, along with the mutation sheetmutation_sheet_detailed.csv. I am not sure if we still need the files insample_data/signature_mutationsand the notebooks, but I suppose they will stay for now.