/// <summary>
/// constructor
/// </summary>
private CacheFile(string path, ushort refIndex, TranscriptDataSource ds, MiniCacheType type, IUpdater updater)
{
CachePath = path;
TranscriptDataSource = ds;
Type = type;
ReferenceIndex = refIndex;
Updater = updater;
AddInputFiles(FileOperations.GetFullPathWithoutExtension(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));
}
