private static Dictionary <string, List <BedEntry> > ReadCommonRegions(string commonCNVsbedPath)
{
Dictionary <string, List <BedEntry> > commonRegions;
using (var reader = new BedReader(new GzipOrTextReader(commonCNVsbedPath)))
{
var commonTmpRegions = reader.LoadAllEntries();
commonRegions = Utilities.SortAndOverlapCheck(commonTmpRegions, commonCNVsbedPath);
}
return(commonRegions);
}
public void ParsingDoesntThrowException(string bedFileName)
{
var bedFile = Path.Combine(BedsFolder, bedFileName).ToFileInfo();
Assert.Equal(bedFile.FullName, IncludeBedFile.CreateFromBedFile(bedFile).BedFile.FullName);
var bedReader = BedReader.Create(bedFile);
var source = bedReader.Select(b => (b.Contig, b.Start, b.Stop)).ToList();
var actual = BedReader.Create(IncludeBedFile
.CreateFromContigIntervals(bedReader, Path.GetTempFileName().ToFileInfo()).BedFile)
.Select(b => (b.Contig, b.Start, b.Stop)).ToList();
// if source and count is equal, then the sequence should equal.
Assert.Equal(source.Count == actual.Count, source.SequenceEqual(actual));
}
public static IncludeBedFile CreateFromBedReader([NotNull] BedReader bedReader)
=> TypeCache <string, IncludeBedFile> .GetOrAdd(bedReader.FileSource.GetCompleteRealPath().FullName, () =>
new IncludeBedFile(CreateGenomeIntervalTree(bedReader),
new Lazy <FileInfo>(() => bedReader.FileSource)));
public static IncludeBedFile CreateFromBedFile([NotNull] FileInfo bedFile) => CreateFromBedReader(BedReader.Create(bedFile));
public static IncludeBedFile CreateFromBedFile([NotNull] FileInfo bedFile)
=> bedFile.ExistsNow()
? CreateFromBedReader(BedReader.Create(bedFile))
: TypeCache <string, IncludeBedFile> .GetOrAdd(bedFile.FullName,
() => CreateFromBedReader(BedReader.Create(bedFile)));