/// <summary>
/// executes the program
/// </summary>
protected override void ProgramExecution()
{
var bundle = GetDataBundle(ConfigurationSettings.InputReferencePath, ConfigurationSettings.InputPrefix);
var header = bundle.Cache.Header.Custom as GlobalCustomHeader;
if (header == null)
{
throw new InvalidCastException("Unable to cast the custom header as a GlobalCustomHeader");
}
IUpdater updater = null;
var outputFiles = new List <string>();
var transcriptDataSource = bundle.Cache.Header.TranscriptSource.ToString();
if (_useTranscriptUpdater)
{
var transcripts = GetDesiredTranscripts(bundle, ConfigurationSettings.TranscriptIds);
if (transcripts.Count == 0)
{
throw new UserErrorException($"Unable to find the desired transcript: {ConfigurationSettings.TranscriptIds}");
}
var transcriptId = ConfigurationSettings.TranscriptIds.First();
var transcript = transcripts[0];
updater = new TranscriptUpdater(transcriptId, transcript.ReferenceIndex, transcriptDataSource);
}
else if (_useMultiTranscriptUpdater)
{
var transcripts = GetDesiredTranscripts(bundle, ConfigurationSettings.TranscriptIds);
if (transcripts.Count < 2)
{
throw new UserErrorException($"Unable to find two or more transcripts: {ConfigurationSettings.TranscriptIds}");
}
var ids = new List <string>();
ids.AddRange(ConfigurationSettings.TranscriptIds);
updater = new MultiTranscriptUpdater(ids, transcriptDataSource);
}
else if (_usePositionUpdater)
{
var refIndex = bundle.Sequence.Renamer.GetReferenceIndex(ConfigurationSettings.ReferenceName);
updater = new PositionUpdater(refIndex, ConfigurationSettings.ReferencePosition,
ConfigurationSettings.ReferenceAllele, ConfigurationSettings.AlternateAllele, transcriptDataSource);
}
else if (_usePositionRangeUpdater)
{
var refIndex = bundle.Sequence.Renamer.GetReferenceIndex(ConfigurationSettings.ReferenceName);
updater = new PositionRangeUpdater(refIndex, ConfigurationSettings.ReferencePosition,
ConfigurationSettings.ReferenceEndPosition, transcriptDataSource);
}
if (updater == null)
{
throw new NullReferenceException("The IUpdater is null.");
}
var status = updater.Update(bundle, ConfigurationSettings.OutputDirectory, header.VepVersion, outputFiles);
UnitTestResourceCrawler.CleanupFiles(status, new List <string>(), outputFiles);
if (status != UpdateStatus.Current)
{
throw new UserErrorException($"Unable to create the mini-cache file. Status: {status}");
}
Console.WriteLine();
Console.WriteLine("- created the following files:");
foreach (var path in outputFiles)
{
Console.WriteLine(Path.GetFileNameWithoutExtension(path));
}
}
private static CacheFile TryMatchFilename(string ndbPath, Func <string, Match> matcher, MiniCacheType type,
ChromosomeRenamer renamer)
{
string filename = Path.GetFileName(ndbPath);
if (filename == null)
{
return(null);
}
var match = matcher(filename);
if (!match.Success)
{
return(null);
}
IUpdater updater;
string id, transcriptDataSource;
int position;
ushort refIndex;
switch (type)
{
case MiniCacheType.Transcript:
var tuple = FormatUtilities.SplitVersion(match.Groups[1].Value);
id = tuple.Item1;
refIndex = renamer.GetReferenceIndex(match.Groups[2].Value);
transcriptDataSource = match.Groups[3].Value;
updater = new TranscriptUpdater(id, refIndex, transcriptDataSource);
break;
case MiniCacheType.Regulatory:
id = match.Groups[1].Value;
refIndex = renamer.GetReferenceIndex(match.Groups[2].Value);
transcriptDataSource = match.Groups[3].Value;
updater = new RegulatoryUpdater(id, refIndex, transcriptDataSource);
break;
case MiniCacheType.Position:
refIndex = renamer.GetReferenceIndex(match.Groups[1].Value);
position = int.Parse(match.Groups[2].Value);
string refAllele = match.Groups[3].Value;
string altAllele = match.Groups[4].Value;
transcriptDataSource = match.Groups[5].Value;
updater = new PositionUpdater(refIndex, position, refAllele, altAllele, transcriptDataSource);
break;
case MiniCacheType.PositionRange:
refIndex = renamer.GetReferenceIndex(match.Groups[1].Value);
position = int.Parse(match.Groups[2].Value);
int endPosition = int.Parse(match.Groups[3].Value);
transcriptDataSource = match.Groups[4].Value;
updater = new PositionRangeUpdater(refIndex, position, endPosition, transcriptDataSource);
break;
default:
throw new GeneralException($"Unexpected mini-cache type encountered: {type}");
}
return(new CacheFile(ndbPath, updater.RefIndex, ConvertTranscriptDataSource(updater.TranscriptDataSource),
type, updater));
}
