R Under development (unstable) (2024-03-22 r86169 ucrt) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(vcfppR)
> 
> test_check("vcfppR")
please call the `output(filename)` function first
please call the `output(filename)` function first
[1] "##fileformat=VCF4.3\n##FILTER=<ID=PASS,Description=\"All filters passed\">\n##contig=<ID=chr20>\n##INFO=<ID=AF,Number=A,Type=Float,Description=\"Estimated allele frequency in the range (0,1)\">\n##FORMAT=<ID=GP,Number=3,Type=Float,Description=\"Posterior genotype probability of 0/0, 0/1, and 1/1\">\n##INFO=<ID=INFO,Number=1,Type=Float,Description=\"INFO score of imputation\">\n##FORMAT=<ID=DS,Number=1,Type=Float,Description=\"Diploid dosage\">\n##FORMAT=<ID=AC,Number=1,Type=Integer,Description=\"Allele counts\">\n##FORMAT=<ID=STR,Number=1,Type=String,Description=\"Test String type\">\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA12878\tNA12879\n"
the length of s must be divisable by nsamples()[1] "chr20\t2006060\trs146931526\tG\tC\t100\tPASS\tAF=0.000998403\tGP:DS:AC:STR\t0.966,0.034,0:0.034:3:HHH\t0.003,0.872,0.125:1.122:4:JJJ\n"
[1] "AF=0.000616523;AN=3244;DP=2498;FS=0;MLEAC=1;MLEAF=0.0003083;MQ=17.07;MQ0=0;QD=17.52;SOR=3.258;VQSLOD=-32.6;culprit=MQ;AN_EUR=658;AN_EAS=548;AN_AMR=520;AN_SAS=624;AN_AFR=894;AF_EUR=0;AF_EAS=0;AF_AMR=0.00384615;AF_SAS=0;AF_AFR=0;AC_EUR=0;AC_EAS=0;AC_AMR=2;AC_SAS=0;AC_AFR=0;AC_Het_EUR=0;AC_Het_EAS=0;AC_Het_AMR=0;AC_Het_SAS=0;AC_Het_AFR=0;AC_Het=0;AC_Hom_EUR=0;AC_Hom_EAS=0;AC_Hom_AMR=2;AC_Hom_SAS=0;AC_Hom_AFR=0;AC_Hom=2;HWE_EUR=1;ExcHet_EUR=1;HWE_EAS=1;ExcHet_EAS=1;HWE_AMR=0.00192678;ExcHet_AMR=1;HWE_SAS=1;ExcHet_SAS=1;HWE_AFR=1;ExcHet_AFR=1;HWE=0.000308356;ExcHet=1;ME=0;AN_EUR_unrel=508;AN_EAS_unrel=448;AN_AMR_unrel=330;AN_SAS_unrel=484;AN_AFR_unrel=666;AF_EUR_unrel=0;AF_EAS_unrel=0;AF_AMR_unrel=0;AF_SAS_unrel=0;AF_AFR_unrel=0;AC_EUR_unrel=0;AC_EAS_unrel=0;AC_AMR_unrel=0;AC_SAS_unrel=0;AC_AFR_unrel=0;AC_Het_EUR_unrel=0;AC_Het_EAS_unrel=0;AC_Het_AMR_unrel=0;AC_Het_SAS_unrel=0;AC_Het_AFR_unrel=0;AC_Hom_EUR_unrel=0;AC_Hom_EAS_unrel=0;AC_Hom_AMR_unrel=0;AC_Hom_SAS_unrel=0;AC_Hom_AFR_unrel=0"
[1] 2
there is no AA in the FORMAT
[1] "##fileformat=VCF4.3\n##FILTER=<ID=PASS,Description=\"All filters passed\">\n##ALT=<ID=NON_REF,Description=\"Represents any possible alternative allele at this location\">\n##contig=<ID=chr20>\n##INFO=<ID=AF,Number=A,Type=Float,Description=\"Estimated allele frequency in the range (0,1)\">\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 123 ]
> 
> proc.time()
   user  system elapsed 
   2.90    0.28    3.15