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Improve warnings for BAF requirements #14

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19 changes: 11 additions & 8 deletions src/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -384,15 +384,18 @@ int main(int argc, char *argv[])
cout << "..since you mateFile is not in SAMtools pileup format, the BAF values will not be calculated\n";
has_BAF=false;
}
string SNPinfoFile = std::string(cf.Value("BAF","SNPfile",""));

if (makePileup != "false" && SNPinfoFile=="") {
if (makePileup.substr(makePileup.size()-3,3)=="vcf" || makePileup.substr(makePileup.size()-6,6)=="vcf.gz") {
SNPinfoFile=makePileup;
} else {
cerr << "Warning: you have to provide a filename with the \"SNPfile\" option if you wish to calculate BAF profiles\n";
cerr << "SNPfile can be in .txt, .txt.gz, .vcf. or .vcf.gz format\n";
}
string SNPinfoFile = std::string(cf.Value("BAF","SNPfile",""));
if (SNPinfoFile == "" && makePileup != "false") {
SNPinfoFile = makePileup;
}
if (SNPinfoFile != ""
&& SNPinfoFile.substr(SNPinfoFile.size() - 3, 3) != "vcf"
&& SNPinfoFile.substr(SNPinfoFile.size() - 6, 6) != "vcf.gz"
&& SNPinfoFile.substr(SNPinfoFile.size() - 3, 3) != "txt"
&& SNPinfoFile.substr(SNPinfoFile.size() - 6, 6) != "txt.gz") {
cerr << "Warning: you have to provide a filename with the \"SNPfile\" or \"makePileup\" option if you wish to calculate BAF profiles\n";
cerr << "SNPfile can be in .txt, .txt.gz, .vcf. or .vcf.gz format\n";
}

std::string targetBed = std::string(cf.Value("target","captureRegions",""));
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