private static ExitCodes ProgramExecution()
{
string cachePath = CacheConstants.TranscriptPath(_inputPrefix);
var(refIndexToChromosome, _, _) = SequenceHelper.GetDictionaries(_compressedReferencePath);
var cache = TranscriptCacheHelper.GetCache(cachePath, refIndexToChromosome);
var geneToInternalId = InternalGenes.CreateDictionary(cache.Genes);
using (var writer = new GffWriter(GZipUtilities.GetStreamWriter(_outputFileName)))
{
var creator = new GffCreator(writer, geneToInternalId);
creator.Create(cache.TranscriptIntervalArrays);
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
Source transcriptSource = ParseVepCacheDirectoryMain.GetSource(_transcriptSource);
string cachePath = CacheConstants.TranscriptPath(_inputPrefix);
IDictionary <ushort, IChromosome> refIndexToChromosome =
SequenceHelper.GetDictionaries(_compressedReferencePath).refIndexToChromosome;
TranscriptCacheData cache = TranscriptCacheHelper.GetCache(cachePath, refIndexToChromosome);
IDictionary <IGene, int> geneToInternalId = InternalGenes.CreateDictionary(cache.Genes);
using (var writer = new GffWriter(GZipUtilities.GetStreamWriter(_outputFileName)))
{
var creator = new GffCreator(writer, geneToInternalId, transcriptSource);
creator.Create(cache.TranscriptIntervalArrays);
}
return(ExitCodes.Success);
}
