public void ValidateSAMParserHeader()
{
string filePath = Utility._xmlUtil.GetTextValue(
Constants.SmallSAMFileNode, Constants.FilePathNode);
string[] expectedHeaderTagValues = Utility._xmlUtil.GetTextValue(
Constants.SmallSAMFileNode, Constants.RecordTagValuesNode).Split(',');
string[] expectedHeaderTagKeys = Utility._xmlUtil.GetTextValue(
Constants.SmallSAMFileNode, Constants.RecordTagKeysNode).Split(',');
string[] expectedHeaderTypes = Utility._xmlUtil.GetTextValue(
Constants.SmallSAMFileNode, Constants.HeaderTyepsNodes).Split(',');
SAMAlignmentHeader aligntHeader =
SAMParser.ParserSAMHeader(filePath);
int tagKeysCount = 0;
int tagValuesCount = 0;
for (int index = 0; index < aligntHeader.RecordFields.Count; index++)
{
Assert.AreEqual(expectedHeaderTypes[index].Replace("/", ""),
aligntHeader.RecordFields[index].Typecode.ToString().Replace("/", ""));
for (int tags = 0; tags < aligntHeader.RecordFields[index].Tags.Count; tags++)
{
Assert.AreEqual(
expectedHeaderTagKeys[tagKeysCount].Replace("/", ""),
aligntHeader.RecordFields[index].Tags[tags].Tag.ToString().Replace("/", ""));
Assert.AreEqual(
expectedHeaderTagValues[tagValuesCount].Replace("/", ""),
aligntHeader.RecordFields[index].Tags[tags].Value.ToString().Replace("/", "").Replace("\r", "").Replace("\n", ""));
tagKeysCount++;
tagValuesCount++;
}
}
}
/// <summary>
/// Genaral method to Invalidate ISequence Alignment
/// <param name="method">enum type to execute different overload</param>
/// </summary>
void ValidateISeqAlignParser(ParseOrFormatTypes method)
{
ISequenceAlignmentParser parser = new SAMParser();
try
{
switch (method)
{
case ParseOrFormatTypes.ParseOrFormatText:
parser.Parse(null as TextReader);
break;
case ParseOrFormatTypes.ParseOrFormatTextWithFlag:
parser.Parse(null as TextReader, true);
break;
case ParseOrFormatTypes.ParseOrFormatFileName:
parser.Parse(null as string);
break;
case ParseOrFormatTypes.ParseOrFormatFileNameWithFlag:
parser.Parse(null as string, true);
break;
case ParseOrFormatTypes.ParseOneOrFormatHeader:
SAMParser.ParserSAMHeader(null as TextReader);
break;
case ParseOrFormatTypes.ParseOneOrFormatHeaderFn:
SAMParser.ParserSAMHeader(null as string);
break;
default:
break;
}
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"SAM Parser P2 : Successfully validated the exception");
Console.WriteLine(
"SAM Parser P2 : Successfully validated the exception");
}
}
public void InvalidateSAMParseHeaderMBFReader()
{
string filePath = Utility._xmlUtil.GetTextValue(
Constants.InvalidSamMBFReaderNode,
Constants.FilePathNode);
try
{
using (TextReader reader = new StreamReader(filePath))
{
SAMParser.ParserSAMHeader(reader);
}
Assert.Fail();
}
catch (FormatException)
{
ApplicationLog.WriteLine(
"SAM Parser P2 : Successfully validated the exception");
Console.WriteLine(
"SAM Parser P2 : Successfully validated the exception");
}
}
