public IEnumerable <UnphasedExpansion> Unphased()
{
foreach (var unphaseAndLogProb in UnphaseToLogProb)
{
yield return(UnphasedExpansion.GetInstance(unphaseAndLogProb.Key, Math.Exp(unphaseAndLogProb.Value - LogTotal), UsedLowerResModel, BadHlaMsr1NameOrNull));
}
}
internal static UnphasedExpansion GetInstance(LinkedList1 <UOPair <HlaMsr1> > unphase, double prob, bool usedLowerResModel, string badHlaNameOrNull)
{
UnphasedExpansion unphasedExpansion = new UnphasedExpansion();
unphasedExpansion.Unphrase = unphase;
unphasedExpansion.Prob = prob;
unphasedExpansion.UsedLowerResModel = usedLowerResModel;
unphasedExpansion.BadHlaNameOrNull = badHlaNameOrNull;
return(unphasedExpansion);
}
static void Main(string[] args)
{
//HlaMsr1Factory.UnitTest();
try
{
ArgCollection argCollection = ArgCollection.GetInstance(args);
string ethnicityName = argCollection.ExtractOptional <string>("ethnicity", "").ToLowerInvariant();
SpecialFunctions.CheckCondition(Linkdis.EthnicityNameLowerList().Contains(ethnicityName), string.Format("'-ethnicity ETHNICITY' is required, where ETHNICITY is " + Linkdis.EthnicityNameMixedList().StringJoin(", ")));
int outputLineLimit = argCollection.ExtractOptional <int>("outputLineLimit", 100000);
int combinationLimit = argCollection.ExtractOptional <int>("combinationLimit", 10000);
bool isSparse = argCollection.ExtractOptionalFlag("sparse");
argCollection.CheckNoMoreOptions(3);
string inputFileName = argCollection.ExtractNext <string>("inputFile");
string phasedOutputFileName = argCollection.ExtractNext <string>("phasedOutputFile");
string unphasedOutputFileName = argCollection.ExtractNext <string>("unphasedOutputFile");
argCollection.CheckThatEmpty();
Linkdis linkdis = Linkdis.GetInstance(ethnicityName, combinationLimit);
string versionName = string.Format("MSCompBio HLA Completion v. {0}", GetVersionString());
CounterWithMessages pidCounter = CounterWithMessages.GetInstance("Pid index = {0}", 1, null);
int outputLineIndex = -1;
using (TextWriter phasedTextWriter = File.CreateText(phasedOutputFileName),
unphasedTextWriter = File.CreateText(unphasedOutputFileName))
{
phasedTextWriter.WriteLine(versionName + "\n");
unphasedTextWriter.WriteLine(versionName + "\n");
phasedTextWriter.WriteLine("pid" + "\t" + PhasedExpansion.Header);
unphasedTextWriter.WriteLine("pid" + "\t" + UnphasedExpansion.Header);
outputLineIndex += 6;
HashSet <string> warningSet = new HashSet <string>();
using (TextReader textReader = File.OpenText(inputFileName))
{
foreach (PidAndHlaSet pidAndHlaSet in isSparse ? PidAndHlaSet.GetEnumerationSparse(textReader) : PidAndHlaSet.GetEnumerationDense(textReader))
{
pidCounter.Increment();
warningSet.UnionWith(pidAndHlaSet.WarningSet);
ExpansionCollection expansionCollectionOrNull = linkdis.ExpandOrNullIfTooMany(pidAndHlaSet);
if (null == expansionCollectionOrNull)
{
phasedTextWriter.WriteLine(pidAndHlaSet.Pid + "\t" + PhasedExpansion.TooManyCombinationsMessage());
unphasedTextWriter.WriteLine(pidAndHlaSet.Pid + "\t" + UnphasedExpansion.TooManyCombinationsMessage());
warningSet.Add(string.Format("Error: Too many combinations, case {0} skipped", pidAndHlaSet.Pid));
outputLineIndex += 2;
if (outputLineIndex > outputLineLimit)
{
goto TOOMANYLINES;
}
}
else
{
foreach (PhasedExpansion phasedExpansion in expansionCollectionOrNull.Phased())
{
string phasedLine = pidAndHlaSet.Pid + "\t" + phasedExpansion.ToString();
phasedTextWriter.WriteLine(phasedLine);
if (phasedExpansion.BadHlaNameOrNull != null)
{
warningSet.Add(phasedLine);
}
++outputLineIndex;
if (outputLineIndex > outputLineLimit)
{
goto TOOMANYLINES;
}
}
foreach (UnphasedExpansion unphasedExpansion in expansionCollectionOrNull.Unphased())
{
string unphasedLine = pidAndHlaSet.Pid + "\t" + unphasedExpansion.ToString();
unphasedTextWriter.WriteLine(unphasedLine);
if (unphasedExpansion.BadHlaNameOrNull != null)
{
warningSet.Add(unphasedLine);
}
++outputLineIndex;
if (outputLineIndex > outputLineLimit)
{
goto TOOMANYLINES;
}
}
}
}
}
goto INANYCASE;
TOOMANYLINES:
string tooManyLinesMessage = string.Format("ERROR: The line limit of {0} was reached and output was ended early", outputLineLimit);
phasedTextWriter.WriteLine(tooManyLinesMessage);
unphasedTextWriter.WriteLine(tooManyLinesMessage);
warningSet.Add(tooManyLinesMessage);
INANYCASE:
Console.Error.WriteLine(warningSet.StringJoin("\n"));
}
}
catch (Exception exception)
{
Console.WriteLine(exception.Message);
if (exception.InnerException != null)
{
Console.WriteLine(exception.InnerException.Message);
}
Console.Error.WriteLine(@"
USAGE
HlaCompletion -ethnicity ETHNICITY [-outputLineLimit 100000] [-sparse] [-combinationLimit 10000] inputFile phaseFile unphaseFile
where ETHNICITY is {0}
'outputLineLimit' limits the total lines of output. If it is reached, a warning message is written as the last line of the output.
'combinationLimit' limits the number of combinations of HLAs consider in one phase for one case.
It is is reached, an error message is output for that case in place of results.
'-sparse' reads files in sparse format
", Linkdis.EthnicityNameMixedList().StringJoin(", "));
System.Environment.Exit(-1);
}
}
