private CheckpointRunnerAsync GetCheckpointRunner(ILogger logger, IDirectoryLocation outputDirectory, string startCheckpoint, string stopCheckpoint, IDirectoryLocation wholeGenomeFastaFolder)
{
var parentDirectories = new Dictionary <string, IDirectoryLocation>
{
{ "Output", outputDirectory },
};
// Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta
IDirectoryLocation genomeRoot = wholeGenomeFastaFolder?.Parent?.Parent?.Parent?.Parent?.Parent;
if (genomeRoot != null)
{
parentDirectories.Add("Genome", genomeRoot);
}
JsonConverter[] converters = { new FileSystemLocationConverter(parentDirectories) };
ICheckpointSerializerAsync serializer = new CheckpointJsonSerializerAsync(CheckpointManagerFactory.GetCheckpointFolder(outputDirectory), logger, converters);
return(CheckpointRunnerAsync.Create(serializer, logger, outputDirectory, startCheckpoint, stopCheckpoint, true));
}
private CheckpointRunnerAsync GetCheckpointRunner(ILogger logger, IDirectoryLocation outputDirectory, string startCheckpoint, string stopCheckpoint, IDirectoryLocation wholeGenomeFastaFolder)
{
var parentDirectories = new Dictionary<string, IDirectoryLocation>
{
{"Output", outputDirectory},
};
// Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta
IDirectoryLocation genomeRoot = wholeGenomeFastaFolder?.Parent?.Parent?.Parent?.Parent?.Parent;
if (genomeRoot != null) parentDirectories.Add("Genome", genomeRoot);
JsonConverter[] converters = { new FileSystemLocationConverter(parentDirectories) };
ICheckpointSerializerAsync serializer = new CheckpointJsonSerializerAsync(CheckpointManagerFactory.GetCheckpointFolder(outputDirectory), logger, converters);
return CheckpointRunnerAsync.Create(serializer, logger, outputDirectory, startCheckpoint, stopCheckpoint, true);
}