public string GetMpileupChromosomes()
{
if (ChromosomeNames != null && ChromosomeNames.Count > 0)
{
return(ChromosomeNames.Merge(","));
}
return(null);
}
public override void PrintParameter(TextWriter tw)
{
tw.WriteLine("#type={0}", this.From);
if (this.From == DataSourceType.BAM)
{
tw.WriteLine("#normal={0}", this.NormalBam);
tw.WriteLine("#tumor={0}", this.TumorBam);
base.PrintParameter(tw);
}
else
{
if (this.From == DataSourceType.Mpileup)
{
tw.WriteLine("#mpileup={0}", this.TumorBam);
}
tw.WriteLine("#base_quality={0}", MinimumBaseQuality);
tw.WriteLine("#min_read_depth={0}", MinimumReadDepth);
tw.WriteLine("#max_read_depth={0}", MaximumReadDepth);
}
if (ChromosomeNames != null && ChromosomeNames.Count() > 0)
{
tw.WriteLine("#chromosomes={0}", this.ChromosomeNames.Merge(","));
}
tw.WriteLine("#fisher_pvalue={0}", this.FisherPvalue);
tw.WriteLine("#max_normal_percentage={0}", this.MaximumPercentageOfMinorAlleleInNormal);
tw.WriteLine("#min_tumor_percentage={0}", this.MinimumPercentageOfMinorAlleleInTumor);
tw.WriteLine("#min_tumor_read={0}", this.MinimumReadsOfMinorAlleleInTumor);
tw.WriteLine("#thread_count={0}", this.ThreadCount);
tw.WriteLine("#output={0}", this.OutputSuffix);
if (File.Exists(this.ExcludeBedFile))
{
tw.WriteLine("#exclude_bed={0}", this.ExcludeBedFile);
}
tw.WriteLine("#use_zero_minor_allele_strategy={0}", this.UseZeroMinorAlleleStrategy);
tw.WriteLine("#zero_minor_allele_strategy_fisher_pvalue={0}", this.ZeroMinorAlleleStrategyFisherPvalue);
}
public override bool PrepareOptions()
{
if (!PrepareOutputDirectory())
{
return(false);
}
if (!string.IsNullOrWhiteSpace(ExcludeBedFile) && !File.Exists(ExcludeBedFile))
{
ParsingErrors.Add("Exclude file not exists:" + ExcludeBedFile);
return(false);
}
switch (From)
{
case DataSourceType.Mpileup:
if (null == MpileupFile)
{
ParsingErrors.Add("Mpileup file not defined.");
return(false);
}
if (!File.Exists(MpileupFile))
{
ParsingErrors.Add(string.Format("Mpileup file not exists {0}.", MpileupFile));
return(false);
}
Console.WriteLine("#mpileup file: " + MpileupFile);
break;
case DataSourceType.BAM:
if (null == NormalBam)
{
ParsingErrors.Add("Bam file for normal sample not defined.");
}
else if (!File.Exists(NormalBam))
{
ParsingErrors.Add(string.Format("Bam file for normal sample not exists {0}", NormalBam));
}
if (null == TumorBam)
{
ParsingErrors.Add("Bam file for tumor sample not defined.");
}
else if (!File.Exists(TumorBam))
{
ParsingErrors.Add(string.Format("Bam file for tumor sample is not exists {0}", TumorBam));
}
if (ThreadCount >= 2)
{
Console.WriteLine("Checking chromosome names for thread mode ...");
if (ChromosomeNames == null || ChromosomeNames.Count == 0 && File.Exists(GenomeFastaFile))
{
var fai = GenomeFastaFile + ".fai";
if (File.Exists(fai))
{
var lines = File.ReadAllLines(fai);
ChromosomeNames = lines.ToList().ConvertAll(m =>
{
var pos = m.IndexOfAny(new[] { '\t', ' ' });
if (pos == -1)
{
return(m);
}
return(m.Substring(0, pos));
});
}
else
{
Console.WriteLine("Reading chromosome names from fasta file ...");
ChromosomeNames = SequenceUtils.ReadFastaNames(GenomeFastaFile);
if (ChromosomeNames.Count == 0)
{
ParsingErrors.Add(string.Format("Genome fasta file doesn't contain chromosome names, {0}.",
GenomeFastaFile));
return(false);
}
}
foreach (var chr in ChromosomeNames)
{
Console.WriteLine(chr);
}
}
}
else
{
if (ChromosomeNames != null && ChromosomeNames.Count > 0)
{
Console.WriteLine("#mpileup chromosome names: " + ChromosomeNames.Merge(","));
}
}
break;
case DataSourceType.Console:
Console.WriteLine("#mpileup from console.");
break;
}
return(true);
}