Finished most tests. Fixed siglist filter functions. #8
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fernandogelin
suggested changes
Nov 2, 2018
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Hi @gtollefson, please take a look at the comments here and address the issues before I can merge.
src/ViVa.jl
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| @@ -4,7 +4,7 @@ using DataFrames #use CSV.jl ? depwarnings | |||
| using PlotlyJS | |||
| using Rsvg | |||
| using Blink | |||
| using CSV | |||
| #using CSV | |||
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Suggested change
| #using CSV |
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if you're not using CSV, just remove that line
test/new_vcf_utils.jl
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| @@ -26,189 +26,167 @@ sample_names = get_sample_names(reader) | |||
| @test df[3,1] == 2 | |||
| end | |||
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| #functions for variant filters | |||
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| @testset "io_chromosome_range_vcf_filter" begin | |||
| sub = io_chromosome_range_vcf_filter("chr4:0-400000000",reader) | |||
| println(sub[1:2]) | |||
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remove print statements from tests and add @test macros.
test/new_vcf_utils.jl
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| @testset "io_chromosome_range_vcf_filter" begin | ||
| sub = io_chromosome_range_vcf_filter("chr4:0-400000000",reader) | ||
| println(sub[1:2]) | ||
| println(size(sub,2)) | ||
| end | ||
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| @testset "io_sig_list_vcf_filter" begin | ||
| #= |
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why is this commented out?
| #functions for converting vcf record array to numerical array | ||
| @testset "combined_all_genotype_array_functions" begin |
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the next few test sets have no test, only print statements. Make sure all test sets are actually testing something. Also, it looks like there are nested test sets here, is this necessary. Try to use indentation to match begin and end statements.
…list filter functions to iterate over VCF.Reader object first then siglist to make faster. Allowed inputing vcf filename as path to filename.
fernandogelin
approved these changes
Nov 5, 2018
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Fixed siglist filter function and wrote most tests. Still working on last 1/3 of tests.