コード例 #1
0
 public string GetMpileupChromosomes()
 {
     if (ChromosomeNames != null && ChromosomeNames.Count > 0)
     {
         return(ChromosomeNames.Merge(","));
     }
     return(null);
 }
コード例 #2
0
        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);
        }
コード例 #3
0
        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);
        }