/// <summary>
/// Creates BAMIndex object from the specified BAM file and writes to specified BAMIndex file.
/// </summary>
/// <param name="compressedBAMStream"></param>
/// <param name="indexFile"></param>
private static void CreateIndexFile(Stream compressedBAMStream, BAMIndexFile indexFile)
{
BAMParser parser = new BAMParser();
BAMIndex bamIndex;
try
{
bamIndex = parser.GetIndexFromBAMFile(compressedBAMStream);
}
finally
{
parser.Dispose();
}
parser = null;
indexFile.Write(bamIndex);
}
public void InvalidateGetIndexFromBAMFileUsingStream()
{
// Create BAM Parser object
using (var bamParserObj = new BAMParser())
{
try
{
bamParserObj.GetIndexFromBAMFile(null as Stream);
Assert.Fail();
}
catch (ArgumentNullException ex)
{
string exceptionMessage = ex.Message;
ApplicationLog.WriteLine(string.Format(null,
"BAM Parser P2 : Validated Exception {0} successfully",
exceptionMessage));
}
}
}