private static string DescribeAnnotationRegion(AnnotationRange ar)
{
if (ar == null)
{
return("Whole VCF");
}
string ret = $"{ar.Start.Chromosome}:{ar.Start.Position}-";
return(ar.End == null ? ret : $"{ret}{ar.End?.Chromosome}:{ar.End?.Position}");
}
internal static long GetTabixVirtualPosition(AnnotationRange annotationRange, Stream stream, IDictionary <string, IChromosome> refNameToChromosome)
{
// process the entire file if no range specified
if (annotationRange == null)
{
return(0);
}
var tabixIndex = Reader.GetTabixIndex(stream, refNameToChromosome);
return(tabixIndex.GetOffset(annotationRange.Start.Chromosome, annotationRange.Start.Position));
}
private static AnnotationConfig GetAnnotationConfig(NirvanaConfig config, AnnotationRange annotationRange, int jobIndex) => new AnnotationConfig
{
id = config.id + $"_job{jobIndex}",
genomeAssembly = config.genomeAssembly,
vcfUrl = config.vcfUrl,
tabixUrl = config.tabixUrl,
outputDir = config.outputDir,
outputPrefix = GetIndexedPrefix(config.vcfUrl, jobIndex),
supplementaryAnnotations = config.supplementaryAnnotations,
customAnnotations = config.customAnnotations,
customStrUrl = config.customStrUrl,
annotationRange = annotationRange
};
private static Task <AnnotationResultSummary> RunAnnotationJob(NirvanaConfig config, string annotationLambdaArn, ILambdaContext context, AnnotationRange range, int jobIndex)
{
var annotationConfig = GetAnnotationConfig(config, range, jobIndex);
Logger.WriteLine($"Job: {jobIndex}, Annotation region: {DescribeAnnotationRegion(range)}");
string configString = JsonUtilities.Stringify(annotationConfig);
var annotationJob = new AnnotationJob(context, jobIndex);
return(Task.Run(() => annotationJob.Invoke(annotationLambdaArn, configString)));
}
