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Adding VCF index

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This commit is contained in:
Noah L. Schrick 2022-11-30 19:05:11 -06:00
parent 3947a74936
commit c394312139
9 changed files with 49136 additions and 14976 deletions
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Code/Data/ebi-a-GCST006414.vcf.gz.tbi Normal file
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Code/Duality_Technologies/palisade-gwas-demos-master/build/CMakeFiles/demo-chi2.dir/demo-chi2.cpp.o
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Code/Duality_Technologies/palisade-gwas-demos-master/build/run.sh Executable file
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@ -0,0 +1,4 @@
#!/bin/bash
#
./demo-chi2 --SNPdir "../data" --SNPfilename "random_sample" --pvalue "pvalue.txt" --runtime "result.txt" --samplesize="200" --snps="16384"

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Code/Duality_Technologies/palisade-gwas-demos-master/data/chi2.txt
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Code/Duality_Technologies/palisade-gwas-demos-master/data/odds.txt
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Code/Duality_Technologies/palisade-gwas-demos-master/data/pvalue.txt
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Code/Duality_Technologies/palisade-gwas-demos-master/data/result.txt
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@ -1,5 +1,5 @@
Key Generation Time: 0.021 s Key Generation Time: 0.022 s
Encoding and Encryption Time: 5.168 s Encoding and Encryption Time: 5.388 s
Computation Time: 1.487 s Computation Time: 1.613 s
Decryption & Decoding Time: 0.098 s Decryption & Decoding Time: 0.101 s
End-to-end Runtime: 6.941 s End-to-end Runtime: 7.54 s

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Code/Duality_Technologies/palisade-gwas-demos-master/demo-chi2.cpp
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@ -181,6 +181,9 @@ void RunChi2(const string &SNPDir,
keyGenTime = TOC(t); keyGenTime = TOC(t);
std::cout << "\nKey Generation Time: \t\t" << keyGenTime/1000 << " s" << std::endl;
TIC(t); TIC(t);
size_t sizeS = (size_t)std::ceil((double)sData[0].size()/(m/4)); size_t sizeS = (size_t)std::ceil((double)sData[0].size()/(m/4));
@ -224,6 +227,8 @@ void RunChi2(const string &SNPDir,
} }
encryptionTime = TOC(t); encryptionTime = TOC(t);
std::cout << "Encoding and Encryption Time: \t" << encryptionTime/1000 << " s" << std::endl;
TIC(t); TIC(t);
@ -319,6 +324,8 @@ void RunChi2(const string &SNPDir,
} }
computationTime = TOC(t); computationTime = TOC(t);
std::cout << "Computation Time: \t\t" << computationTime/1000 << " s" << std::endl;
TIC(t); TIC(t);
@ -335,6 +342,8 @@ void RunChi2(const string &SNPDir,
} }
decryptionTime = TOC(t); decryptionTime = TOC(t);
std::cout << "Decryption & Decoding Time: \t" << decryptionTime/1000 << " s" << std::endl;
std::vector<double> chival(headersS.size()); std::vector<double> chival(headersS.size());
std::vector<double> pval(headersS.size()); std::vector<double> pval(headersS.size());
@ -384,11 +393,6 @@ void RunChi2(const string &SNPDir,
} }
myfile3.close(); myfile3.close();
std::cout << "\nKey Generation Time: \t\t" << keyGenTime/1000 << " s" << std::endl;
std::cout << "Encoding and Encryption Time: \t" << encryptionTime/1000 << " s" << std::endl;
std::cout << "Computation Time: \t\t" << computationTime/1000 << " s" << std::endl;
std::cout << "Decryption & Decoding Time: \t" << decryptionTime/1000 << " s" << std::endl;
endToEndTime = TOC(tAll); endToEndTime = TOC(tAll);
std::cout << "\nEnd-to-end Runtime: \t\t" << endToEndTime/1000 << " s" << std::endl; std::cout << "\nEnd-to-end Runtime: \t\t" << endToEndTime/1000 << " s" << std::endl;