private static ExitCodes ProgramExecution()
{
using (var writer = GZipUtilities.GetStreamWriter(_outputFileName))
{
string cachePath = CacheConstants.TranscriptPath(_inputPrefix);
var sequenceData = SequenceHelper.GetDictionaries(_referencePath);
// load the cache
Console.Write("- reading {0}... ", Path.GetFileName(cachePath));
var cache = TranscriptCacheHelper.GetCache(cachePath, sequenceData.refIndexToChromosome);
Console.WriteLine("found {0:N0} reference sequences. ", cache.RegulatoryRegionIntervalArrays.Length);
Console.Write("- writing GFF entries... ");
foreach (var intervalArray in cache.RegulatoryRegionIntervalArrays)
{
if (intervalArray == null)
{
continue;
}
foreach (var interval in intervalArray.Array)
{
WriteRegulatoryFeature(writer, interval.Value);
}
}
Console.WriteLine("finished.");
}
return(ExitCodes.Success);
}
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);
}
