private void CheckParameter(string optionName, ProgramConfig program, ParameterConfig paramset, string paramname, Func <AnnotationProcessorOptions, string> getFunc, Action <AnnotationProcessorOptions, string> setFunc)
{
var value = getFunc(this);
value = paramset.GetParameter(paramname, value);
if (string.IsNullOrEmpty(value))
{
ParsingErrors.Add(string.Format("{0} {1}. Or you can define the default value at {2}::{3}::{4} in configuration file {5}.",
optionName,
BaseSentenceBuilder.CreateBuiltIn().RequiredOptionMissingText,
program.Name,
paramset.Name,
paramname,
this.Config.ConfigFilename));
}
else
{
setFunc(this, value);
}
}
public override bool PrepareOptions()
{
if (this.Annovar)
{
if (string.IsNullOrEmpty(this.AnnovarBuildVersion))
{
ParsingErrors.Add("--annovar_buildver " + BaseSentenceBuilder.CreateBuiltIn().RequiredOptionMissingText + ".");
}
var annovar = this.Config.FindOrCreate("annovar", "table_annovar.pl");
this.AnnovarCommand = annovar.Command;
if (!annovar.HasParameterSet(this.AnnovarBuildVersion))
{
var paramset = new ParameterConfig(this.AnnovarBuildVersion);
paramset.Parameters["databasedir"] = string.IsNullOrEmpty(this.AnnovarDatabaseDirectory) ? string.Empty : this.AnnovarDatabaseDirectory;
paramset.Parameters["protocol"] = string.IsNullOrEmpty(this.AnnovarProtocol) ? string.Empty : this.AnnovarProtocol;
paramset.Parameters["operation"] = string.IsNullOrEmpty(this.AnnovarOperation) ? string.Empty : this.AnnovarOperation;
annovar.ParameterSet[paramset.Name] = paramset;
this.Config.Save();
Console.WriteLine(string.Format("annovar buildver {0} is not defined at configuration file {1}, you can modify the configuration file for default parameters!", paramset.Name, this.Config.ConfigFilename));
}
var set = annovar.ParameterSet[this.AnnovarBuildVersion];
CheckParameter("annovar_databasedir", annovar, set, "databasedir", m => m.AnnovarDatabaseDirectory, (m, n) => m.AnnovarDatabaseDirectory = n);
CheckParameter("annovar_protocol", annovar, set, "protocol", m => m.AnnovarProtocol, (m, n) => m.AnnovarProtocol = n);
CheckParameter("annovar_operation", annovar, set, "operation", m => m.AnnovarOperation, (m, n) => m.AnnovarOperation = n);
if (!Directory.Exists(this.AnnovarDatabaseDirectory))
{
ParsingErrors.Add(string.Format("--annovar_databasedir : directory not exists : {0}", this.AnnovarDatabaseDirectory));
}
else
{
var files = Directory.GetFiles(this.AnnovarDatabaseDirectory, this.AnnovarBuildVersion + "*");
if (files.Length == 0)
{
ParsingErrors.Add(string.Format("--annovar_databasedir : there is no annovar database {0} in directory {1}", this.AnnovarBuildVersion, this.AnnovarDatabaseDirectory));
}
if (this.AnnovarSetDefault)
{
set.Parameters["databasedir"] = this.AnnovarDatabaseDirectory;
set.Parameters["protocol"] = this.AnnovarProtocol;
set.Parameters["operation"] = this.AnnovarOperation;
annovar.DefaultParameterSet = this.AnnovarBuildVersion;
this.Config.Save();
}
}
}
if (this.Rnaediting)
{
if (!File.Exists(this.RnaeditingDatabase))
{
ParsingErrors.Add(string.Format("--rnaediting_db : file not exists : {0}", this.RnaeditingDatabase));
}
}
if (this.Distance)
{
int count = 0;
if (!string.IsNullOrEmpty(this.DistanceInsertionBed))
{
if (!File.Exists(this.DistanceInsertionBed))
{
ParsingErrors.Add(string.Format("--distance_insertion_bed : file not exists : {0}", this.DistanceInsertionBed));
}
else
{
count++;
}
}
if (!string.IsNullOrEmpty(this.DistanceDeletionBed))
{
if (!File.Exists(this.DistanceInsertionBed))
{
ParsingErrors.Add(string.Format("--distance_deletion_bed : file not exists : {0}", this.DistanceDeletionBed));
}
else
{
count++;
}
}
if (!string.IsNullOrEmpty(this.DistanceJunctionBed))
{
if (!File.Exists(this.DistanceInsertionBed))
{
ParsingErrors.Add(string.Format("--distance_junction_bed : file not exists : {0}", this.DistanceJunctionBed));
}
else
{
count++;
}
}
if (!string.IsNullOrEmpty(this.GtfFile))
{
if (!File.Exists(this.GtfFile))
{
ParsingErrors.Add(string.Format("--distance_exon_gtf : file not exists : {0}", this.GtfFile));
}
else
{
count++;
}
}
if (count == 0)
{
ParsingErrors.Add(string.Format("--distance : no bed file defined"));
}
}
if (!this.IsPileup)
{
if (!File.Exists(this.InputFile))
{
ParsingErrors.Add(string.Format("-i : input file not exists : {0}", this.InputFile));
}
if (this.Annovar && !Directory.Exists(this.AnnotationDirectory))
{
try
{
Directory.CreateDirectory(this.AnnotationDirectory);
}
catch (Exception ex)
{
ParsingErrors.Add(string.Format("create directory {0} failed : {1}.", this.AnnotationDirectory, ex.Message));
}
}
}
if (string.IsNullOrEmpty(this.OutputFile))
{
this.OutputFile = Path.ChangeExtension(this.InputFile, ".annotation.tsv");
}
return(ParsingErrors.Count == 0);
}