public static PiscesOptionsParser GetOriginalPiscesOptions(List <string> vcfHeaderLines, string configFileDir)
{
var vcfConfigureFile = Path.Combine(configFileDir, "PiscesOptions.used.json");
PiscesOptionsParser piscesParser = new PiscesOptionsParser();
if (File.Exists(vcfConfigureFile))
{
piscesParser = GetOptionsFromConfigFile(vcfConfigureFile);
}
else
{
Logger.WriteToLog($"Pisces option file {vcfConfigureFile} does not exist. Reading defaults from the VCF header");
piscesParser = GetPiscesOptionsFromVcfHeader(vcfHeaderLines);
}
return(piscesParser);
}
private static PiscesOptionsParser GetOptionsFromConfigFile(string vcfConfigureFile)
{
var piscesParser = new PiscesOptionsParser();
try
{
piscesParser.Options = JsonUtil.Deserialize <PiscesApplicationOptions>(vcfConfigureFile);
Logger.WriteToLog($"Pisces option file {vcfConfigureFile} loaded");
return(piscesParser);
}
catch (Exception ex)
{
Logger.WriteExceptionToLog(ex);
Logger.WriteToLog($"Pisces option file {vcfConfigureFile} failed to load. Continuing without it ");
piscesParser.ParsingResult.Exception = ex;
piscesParser.ParsingResult.UpdateExitCode(ExitCodeType.InvalidFileFormat);
return(piscesParser);
}
}
public static PiscesOptionsParser GetPiscesOptionsFromVcfHeader(List <string> VcfHeaderLines)
{
var piscesParser = new PiscesOptionsParser();
var startString = "##Pisces_cmdline=";
if (VcfHeaderLines.Count != 0 && VcfHeaderLines.Exists(x => x.StartsWith(startString)))
{
try
{
var piscesCmd = VcfHeaderLines.FindLast(x => x.StartsWith(startString)).Replace(startString, "").Replace("\"", "").ToLower();
piscesCmd = piscesCmd.Replace("-v ", "-vffilter "); //"v" used to be vf filter, now it returns the version number. Be kind and help the user with this one. If th ey pass "-v" that will shut down all the parsing and output the version.
piscesCmd = piscesCmd.Replace("-bamfolder ", "-bam "); //being kind to another obsolete argument
//parse the original pisces options, but do not validate.
//We dont need to validate everything, just to get the vcf processing options.
piscesParser.ParseArgs(piscesCmd.Split(), false);
((PiscesApplicationOptions)piscesParser.Options).SetDerivedParameters();
return(piscesParser);
}
catch (Exception ex)
{
Logger.WriteToLog("Unable to parse the original Pisces commandline from the input vcf.");
Logger.WriteExceptionToLog(ex);
piscesParser.ParsingResult.Exception = ex;
piscesParser.ParsingResult.UpdateExitCode(ExitCodeType.BadFormat);
}
}
piscesParser.ParsingResult.Exception = new Exception("Pisces command line was not found in the input vcf");
piscesParser.ParsingResult.UpdateExitCode(ExitCodeType.BadFormat);
return(piscesParser);
}