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[test] Add misc tool tests
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@isinaltinkaya
isinaltinkaya committed Jan 8, 2024
1 parent c4e0294 commit c78454b
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14 changes: 0 additions & 14 deletions misc/Makefile
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CXX ?= g++


ifeq ($(DEV),1)
$(info Compiling in developer mode)
COMPILEMODE = -DDEV=1
# TODO disable clean and replace with ngsAMOVA style checks
all: clean
CXXFLAGS := -g -Wall -O0
else
$(info Compiling in release mode)
COMPILEMODE = -DDEV=0
# TODO disable clean and replace with ngsAMOVA style checks
all: clean
endif

LIBS = -lz -lm -lbz2 -llzma -lcurl -lpthread


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28 changes: 28 additions & 0 deletions misc/data/call2.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##source=tskit 0.4.1
##contig=<ID=chr22,length=51304566>
##fileDate=Tue Dec 19 11:21:41 2023
##source=vcfgl [version: v0.4] [build: Dec 18 2023 17:43:39] [htslib: 1.16]
##source=Command: vcfgl --verbose 0 --threads 1 --seed 1 --input sim/sim_vcfgl_2312/model_OutOfAfrica_3G09/contig_chr22/vcf/sim_vcfgl_2312-OutOfAfrica_3G09-chr22.vcf --output sim/sim_vcfgl_2312/model_OutOfAfrica_3G09/contig_chr22/vcfgl_gl1/sim_vcfgl_2312-OutOfAfrica_3G09-chr22-rep0-d1-e0.002_qs0_0 --output-mode b --depth 1.000000 --error-rate 0.002000 --error-qs 0 --beta-variance -1.000000e+00 --gl-model 1 --gl1-theta 0.830000 --platform 0 --precise-gl 0 --i16-mapq 20 --gvcf-dps (null) -explode 0 --rm-invar-sites 3 --rm-empty-sites 1 -doUnobserved 1 -doGVCF 0 -printPileup 1 -printTruth 1 -addGL 1 -addGP 0 -addPL 1 -addI16 0 -addQS 1 -addFormatDP 1 -addInfoDP 0 -addFormatAD 1 -addInfoAD 1 -addFormatADF 0 -addInfoADF 0 -addFormatADR 0 -addInfoADR 0
##ALT=<ID=*,Description="Symbolic alternate allele representing any possible alternative allele at this location">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Simulated per-sample read depth">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype likelihood in log10 likelihood ratio format">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the REF and ALT alleles">
##INFO=<ID=AD,Number=R,Type=Integer,Description="Total allelic depths for the REF and ALT alleles">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Phred-scaled Genotype Quality">
##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype posterior probabilities in the range 0 to 1">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##bcftools_callVersion=1.18+htslib-1.18
##bcftools_callCommand=call --annotate FORMAT/GQ,FORMAT/GP,INFO/PV4 -mv --prior 0.0011 -O b -o sim/sim_vcfgl_2312/model_OutOfAfrica_3G09/contig_chr22/genotype_calling_gl1/sim_vcfgl_2312-OutOfAfrica_3G09-chr22-rep0-d1-e0.002-qs0_0-snp.bcf sim/sim_vcfgl_2312/model_OutOfAfrica_3G09/contig_chr22/vcfgl_gl1/sim_vcfgl_2312-OutOfAfrica_3G09-chr22-rep0-d1-e0.002_qs0_0.bcf; Date=Tue Dec 19 11:59:11 2023
##bcftools_viewVersion=1.18-6-gc7cbe0b3+htslib-1.18-7-gac70212
##bcftools_viewCommand=view ../../../simulation/sim/sim_vcfgl_2312/model_OutOfAfrica_3G09/contig_chr22/genotype_calling_gl1/sim_vcfgl_2312-OutOfAfrica_3G09-chr22-rep0-d1-e0.002-qs0_0-snp.bcf; Date=Thu Dec 21 14:39:20 2023
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT popYRI_ind1 popYRI_ind2
chr22 42 . A C,T 515.208 PASS . GT:DP:GQ ./.:0:0 1/1:2:7
chr22 44 . A T 515.208 PASS . GT:DP:GQ 0/1:0:127 0/0:2:16
13 changes: 13 additions & 0 deletions misc/data/truth2.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##source=tskit 0.4.1
##contig=<ID=chr22,length=51304566>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##fileDate=Tue Dec 19 11:21:41 2023
##source=vcfgl [version: v0.4] [build: Dec 18 2023 17:43:39] [htslib: 1.16]
##source=Command: vcfgl --verbose 0 --threads 1 --seed 1 --input sim/sim_vcfgl_2312/model_OutOfAfrica_3G09/contig_chr22/vcf/sim_vcfgl_2312-OutOfAfrica_3G09-chr22.vcf --output sim/sim_vcfgl_2312/model_OutOfAfrica_3G09/contig_chr22/vcfgl_gl1/sim_vcfgl_2312-OutOfAfrica_3G09-chr22-rep0-d1-e0.002_qs0_0 --output-mode b --depth 1.000000 --error-rate 0.002000 --error-qs 0 --beta-variance -1.000000e+00 --gl-model 1 --gl1-theta 0.830000 --platform 0 --precise-gl 0 --i16-mapq 20 --gvcf-dps (null) -explode 0 --rm-invar-sites 3 --rm-empty-sites 1 -doUnobserved 1 -doGVCF 0 -printPileup 1 -printTruth 1 -addGL 1 -addGP 0 -addPL 1 -addI16 0 -addQS 1 -addFormatDP 1 -addInfoDP 0 -addFormatAD 1 -addInfoAD 1 -addFormatADF 0 -addInfoADF 0 -addFormatADR 0 -addInfoADR 0
##bcftools_viewVersion=1.18-6-gc7cbe0b3+htslib-1.18-7-gac70212
##bcftools_viewCommand=view ../../../simulation/sim/sim_vcfgl_2312/model_OutOfAfrica_3G09/contig_chr22/vcfgl_gl1/sim_vcfgl_2312-OutOfAfrica_3G09-chr22-rep0-d1-e0.002_qs0_0.truth.bcf; Date=Thu Dec 21 14:40:18 2023
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT popYRI_ind1 popYRI_ind2
chr22 42 . A C 515.208 PASS . GT 0/0 1/1
chr22 44 . A C 515.208 PASS . GT 1/0 0/0

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