public void PopulateBAMPaths()
{
BAMPaths = Directory.GetFiles(BAMFolder, "*.bam");
if (!BAMPaths.Any())
{
throw new ArgumentException(string.Format("No BAM files found in {0}", BAMFolder));
}
}
public void Validate()
{
var bamPathsSpecified = BAMPaths != null && BAMPaths.Length > 0;
var bamFolderSpecified = !string.IsNullOrWhiteSpace(BAMFolder);
//Either BAMPath(s) or BAMFolder should be specified.
if (!bamPathsSpecified && !bamFolderSpecified)
{
throw new ArgumentException("Specify either BAMPath(s) or BAMFolder");
}
if (bamPathsSpecified && bamFolderSpecified)
{
throw new ArgumentException("Specify either BAMPath(s) or BAMFolder");
}
if (GenomePaths == null || GenomePaths.Length == 0)
{
throw new ArgumentException("No GenomePaths specified.");
}
if (bamPathsSpecified)
{
if (BAMPaths.Length > 96)
{
throw new ArgumentException("Number of BAMPaths specified exceeds maximum of 96.");
}
if (BAMPaths.Distinct().Count() != BAMPaths.Count())
{
throw new ArgumentException("Duplicate BAMPaths detected.");
}
if (BAMPaths.Length != GenomePaths.Length && GenomePaths.Length > 1)
{
throw new ArgumentException(
"Multiple GenomePaths specified, but number does not correspond with number of BAMPaths.");
}
if (IntervalPaths != null && BAMPaths.Length != IntervalPaths.Length && IntervalPaths.Length > 1)
{
throw new ArgumentException(
"Multiple IntervalPaths specified, but number does not correspond with number of BAMPaths.");
}
// check files and directories exist
foreach (var bamPath in BAMPaths)
{
if (!File.Exists(bamPath))
{
throw new ArgumentException(string.Format("BAMPath '{0}' does not exist.", bamPath));
}
}
}
if (bamFolderSpecified)
{
if (!Directory.Exists(BAMFolder))
{
throw new ArgumentException(string.Format("BAMFolder {0} not found", BAMFolder));
}
if (GenomePaths.Length > 1)
{
throw new ArgumentException("Only 1 Genome Path should be specified when BAMFolder is specified.");
}
if (IntervalPaths != null && IntervalPaths.Length > 1)
{
throw new ArgumentException("At most 1 Interval Path should be specified when BAMFolder is specified.");
}
}
foreach (var genomePath in GenomePaths)
{
if (!Directory.Exists(genomePath))
{
throw new ArgumentException(string.Format("GenomePath '{0}' does not exist.", genomePath));
}
}
if (IntervalPaths != null)
{
foreach (var intervalPath in IntervalPaths)
{
if (!File.Exists(intervalPath))
{
throw new ArgumentException(string.Format("IntervalPath '{0}' does not exist.", intervalPath));
}
}
}
ValidationHelper.VerifyRange(MinimumVariantQScore, 0, int.MaxValue, "MinimumVariantQscore");
ValidationHelper.VerifyRange(MaximumVariantQScore, 0, int.MaxValue, "MaximumVariantQScore");
if (MaximumVariantQScore < MinimumVariantQScore)
{
throw new ArgumentException("MinimumVariantQScore must be less than or equal to MaximumVariantQScore.");
}
ValidationHelper.VerifyRange(MinimumBaseCallQuality, 0, int.MaxValue, "MinimumBaseCallQuality");
ValidationHelper.VerifyRange(MinimumFrequency, 0f, 1f, "MinimumFrequency");
ValidationHelper.VerifyRange(FilteredVariantQScore, MinimumVariantQScore, MaximumVariantQScore, "FilteredVariantQScore");
ValidationHelper.VerifyRange((float)FilteredVariantFrequency, 0, 1f, "FilteredVariantFrequency");
if (LowGenotypeQualityFilter != null)
{
ValidationHelper.VerifyRange((float)LowGenotypeQualityFilter, 0, int.MaxValue, "FilteredLowGenomeQuality");
}
if (IndelRepeatFilter != null)
{
ValidationHelper.VerifyRange((int)IndelRepeatFilter, 0, 10, "FilteredIndelRepeats");
}
if (LowDepthFilter != null)
{
ValidationHelper.VerifyRange((int)LowDepthFilter, MinimumDepth, int.MaxValue, "FilteredLowDepth");
}
if ((LowDepthFilter == null) || (LowDepthFilter < MinimumDepth))
{
LowDepthFilter = MinimumDepth;
}
if (AppliedNoiseLevel != -1)
{
ValidationHelper.VerifyRange(AppliedNoiseLevel, 0, int.MaxValue, "AppliedNoiseLevel");
}
if (CallMNVs)
{
ValidationHelper.VerifyRange(MaxSizeMNV, 1, GlobalConstants.RegionSize, "MaxPhaseSNPLength");
ValidationHelper.VerifyRange(MaxGapBetweenMNV, 0, int.MaxValue, "MaxGapPhasedSNP");
}
ValidationHelper.VerifyRange(MinimumMapQuality, 0, int.MaxValue, "MinimumMapQuality");
ValidationHelper.VerifyRange(StrandBiasAcceptanceCriteria, 0f, int.MaxValue, "Strand bias cutoff");
ValidationHelper.VerifyRange(MaxNumThreads, 1, int.MaxValue, "MaxNumThreads");
ValidationHelper.VerifyRange(CollapseFreqThreshold, 0f, float.MaxValue, "CollapseFreqThreshold");
ValidationHelper.VerifyRange(CollapseFreqRatioThreshold, 0f, float.MaxValue, "CollapseFreqRatioThreshold");
if (!string.IsNullOrEmpty(PriorsPath))
{
if (!File.Exists(PriorsPath))
{
throw new ArgumentException(string.Format("PriorsPath '{0}' does not exist.", PriorsPath));
}
}
if (PloidyModel == PloidyModel.Diploid)
{
MinimumFrequency = DiploidThresholdingParameters.MinorVF;
}
if (FilteredVariantFrequency < MinimumFrequency)
{
FilteredVariantFrequency = MinimumFrequency;
}
if (RMxNFilterMaxLengthRepeat != null || RMxNFilterMinRepetitions != null)
{
if (RMxNFilterMaxLengthRepeat == null || RMxNFilterMinRepetitions == null)
{
throw new ArgumentException(string.Format("If specifying RMxN filter thresholds, you must supply both RMxNFilterMaxLengthRepeat and RMxNFilterMinRepetitions."));
}
ValidationHelper.VerifyRange((int)RMxNFilterMaxLengthRepeat, 0, 100, "RMxNFilterMaxLengthRepeat");
ValidationHelper.VerifyRange((int)RMxNFilterMinRepetitions, 0, 100, "RMxNFilterMinRepetitions");
}
if (ThreadByChr && !InsideSubProcess && !string.IsNullOrEmpty(ChromosomeFilter))
{
throw new ArgumentException("Cannot thread by chromosome when filtering on a particular chromosome.");
}
if (!string.IsNullOrEmpty(OutputFolder) && bamPathsSpecified && (BAMPaths.Length > 1))
{
//make sure none of the input BAMS have the same name. Or else we will have an output collision.
for (int i = 0; i < BAMPaths.Length; i++)
{
for (int j = i + 1; j < BAMPaths.Length; j++)
{
if (i == j)
{
continue;
}
var fileA = Path.GetFileName(BAMPaths[i]);
var fileB = Path.GetFileName(BAMPaths[j]);
if (fileA == fileB)
{
throw new ArgumentException(string.Format("VCF file name collision. Cannot process two different bams with the same name {0} into the same output folder {1}.", fileA, OutputFolder));
}
}
}
}
}
