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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,135 @@ | ||
| #include <Rcpp.h> | ||
| #include <fstream> | ||
| #include <zlib.h> | ||
| #include "vcfRCommon.h" | ||
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| // These are deprecated functions I hope to remove. | ||
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| Rcpp::StringMatrix DataFrame_to_StringMatrix( Rcpp::DataFrame df, int depr = 1 ){ | ||
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| Rcpp::StringVector sv = df(0); | ||
| Rcpp::StringMatrix sm(sv.size(), df.size()); | ||
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| sm.attr("col.names") = df.attr("col.names"); | ||
| sm.attr("row.names") = df.attr("row.names"); | ||
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| if( depr == 1 ){ | ||
| Rcpp::Rcerr << "The Rcpp function DataFrame_to_StringMatrix was deprecated in vcfR 1.6.0" << std::endl; | ||
| Rcpp::Rcerr << "If you use this function and you would like to advocate its persistence, please contact the maintainer." << std::endl; | ||
| Rcpp::Rcerr << "The maintainer of this package can be found with" << std::endl; | ||
| Rcpp::Rcerr << "maintainer('vcfR')" << std::endl; | ||
| return sm; | ||
| } | ||
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| for(int i=0; i < df.size(); i++){ | ||
| sv = df(i); | ||
| for(int j=0; j < sv.size(); j++){ | ||
| sm(j, i) = sv(j); | ||
| } | ||
| } | ||
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| return sm; | ||
| } | ||
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| /* Write data to fasta file */ | ||
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| // [[Rcpp::export]] | ||
| void write_fasta( Rcpp::CharacterVector seq, | ||
| std::string seqname, | ||
| std::string filename, | ||
| int rowlength=80, | ||
| int verbose=1, int depr = 1) { | ||
| // rowlength=rowlength-1; | ||
| FILE * pFile; | ||
| // pFile=fopen(filename.c_str(),"wt"); | ||
| pFile=fopen(filename.c_str(),"at"); | ||
| int i = 0; | ||
| // unsigned int i = 0; | ||
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| if( depr == 1 ){ | ||
| Rcpp::Rcerr << "The function write_fasta was deprecated in vcfR 1.6.0" << std::endl; | ||
| Rcpp::Rcerr << "If you use this function and you would like to advocate its persistence, please contact the maintainer." << std::endl; | ||
| Rcpp::Rcerr << "The maintainer of this package can be found with" << std::endl; | ||
| Rcpp::Rcerr << "maintainer('vcfR')" << std::endl; | ||
| Rcpp::stop(""); | ||
| } | ||
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| if(verbose == 1){ | ||
| Rcpp::Rcout << "Processing sample: " << seqname << "\n"; | ||
| } | ||
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| putc ('>' , pFile); | ||
| for(i=0; (unsigned)i<seqname.size(); i++){ | ||
| putc (seqname[i] , pFile); | ||
| } | ||
| putc ('\n' , pFile); | ||
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| // Number of records to report progress at. | ||
| const int nreport = 1000; | ||
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| putc (Rcpp::as< char >(seq[0]) , pFile); | ||
| for(i=1; i<seq.size(); i++){ | ||
| Rcpp::checkUserInterrupt(); | ||
| // putc (seq[i][0] , pFile); | ||
| if( i % rowlength == 0){ | ||
| putc('\n', pFile); | ||
| } | ||
| putc (Rcpp::as< char >(seq[i]) , pFile); | ||
| if(i % nreport == 0 && verbose == 1){ | ||
| Rcpp::Rcout << "\rNucleotide " << i << " processed"; | ||
| } | ||
| } | ||
| putc('\n', pFile); | ||
| fclose (pFile); | ||
| if(verbose == 1){ | ||
| Rcpp::Rcout << "\rNucleotide " << i << " processed\n"; | ||
| } | ||
| // return 0; | ||
| } | ||
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| double extractElementD(Rcpp::String x, int number=1, int depr = 1){ | ||
| // | ||
| // x is a string similar to: | ||
| // GT:GQ:DP:RO:QR:AO:QA:GL | ||
| // | ||
| // number is the position in the colon delimited | ||
| // string which needs to be extracted. | ||
| // | ||
| // int count = 0; | ||
| int start = 0; | ||
| int pos = 1; | ||
| std::string istring = x; | ||
| std::string teststring; | ||
| unsigned int i = 0; | ||
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| if( depr == 1 ){ | ||
| Rcpp::Rcerr << "The function extractElementD was deprecated in vcfR 1.6.0" << std::endl; | ||
| Rcpp::Rcerr << "If you use this function and you would like to advocate its persistence, please contact the maintainer." << std::endl; | ||
| Rcpp::Rcerr << "The maintainer of this package can be found with" << std::endl; | ||
| Rcpp::Rcerr << "maintainer('vcfR')" << std::endl; | ||
| Rcpp::stop(""); | ||
| } | ||
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| for(i=1; i <= istring.size(); i++){ | ||
| if(istring[i] == ':'){ | ||
| if(pos == number){ | ||
| teststring = istring.substr(start, i-start); | ||
| double teststring2 = atof(teststring.c_str()); | ||
| return teststring2; | ||
| // return std::stod(teststring); | ||
| } else { | ||
| start = i+1; | ||
| pos++; | ||
| i++; | ||
| } | ||
| } | ||
| } | ||
| // If we get here we did not find the element. | ||
| return(0); | ||
| } | ||
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