public void CreateBamReader()
{
// Should return a fully functional bam reader
var tempPath = $"TemporaryBamFile_{Guid.NewGuid()}.bam";
if (File.Exists(tempPath))
{
File.Delete(tempPath);
}
using (var bamWriter = new BamWriter(tempPath, "header", new List <GenomeMetadata.SequenceMetadata>()))
{
var bamWriterHandle = new BamWriterHandle(bamWriter);
bamWriterHandle.WriteAlignment(TestHelpers.CreateBamAlignment("ATCG", 8, 10, 30, true));
bamWriterHandle.WriteAlignment(null);
}
Assert.True(File.Exists(tempPath));
var stitcherOptions = new StitcherOptions();
var factory = new GeminiDataSourceFactory(stitcherOptions, "fakeGenomePath", false);
using (var bamReader = factory.CreateBamReader(tempPath))
{
BamAlignment alignment = new BamAlignment();
var getNext = bamReader.GetNextAlignment(ref alignment, true);
Assert.True(getNext);
Assert.Equal(7, alignment.Position);
}
File.Delete(tempPath);
}
public void CreateReadPairSource()
{
var stitcherOptions = new StitcherOptions();
var factory = new GeminiDataSourceFactory(stitcherOptions, "fakeGenomePath", false);
var bamReader = new Mock <IBamReader>();
var readPairSource = factory.CreateReadPairSource(bamReader.Object, new ReadStatusCounter());
Assert.Equal(typeof(PairFilterReadPairSource), readPairSource.GetType());
// TODO maybe I can do some asserts on the configuration of the readpair source by passing through some reads and checking result? that's pretty indirect though.
}
private static string ProcessChromosome(Dictionary <string, int> chromRefIds, string outMultiPath, List <string> taskDirectories,
string chrom, GeminiMultiOptions options)
{
// TODO either officially deprecate non-multiprocess-processing and remove this, or consolidate this with the Gemini calling code from Gemini/Program.cs
var outdir = Path.Combine(outMultiPath, chrom);
var refId = chromRefIds[chrom];
var intermediate = string.IsNullOrEmpty(options.GeminiSampleOptions.IntermediateDir)
? null
: Path.Combine(options.GeminiSampleOptions.IntermediateDir, chrom);
var geminiSampleOptions = new GeminiSampleOptions
{
InputBam = options.InputBam,
OutputFolder = outdir,
OutputBam = Path.Combine(outdir, "out.bam"),
IntermediateDir = intermediate,
RefId = refId
};
// Gemini defaults different than stitcher defaults
options.StitcherOptions.NifyUnstitchablePairs = false;
// Set stitcher pair-filter-level duplicate filtering if skip and remove dups, to save time
options.StitcherOptions.FilterDuplicates = options.GeminiOptions.SkipAndRemoveDups;
var dataSourceFactory = new GeminiDataSourceFactory(options.StitcherOptions, options.GeminiOptions.GenomePath,
options.GeminiOptions.SkipAndRemoveDups, refId,
Path.Combine(outdir, "Regions.txt"), debug: options.GeminiOptions.Debug);
var dataOutputFactory = new GeminiDataOutputFactory(options.StitcherOptions.NumThreads);
var samtoolsWrapper = new SamtoolsWrapper(options.GeminiOptions.SamtoolsPath, options.GeminiOptions.IsWeirdSamtools);
var geminiWorkflow = new GeminiWorkflow(dataSourceFactory, dataOutputFactory,
options.GeminiOptions, geminiSampleOptions, options.RealignmentOptions, options.StitcherOptions, options.OutputDirectory, options.RealignmentAssessmentOptions, options.IndelFilteringOptions, samtoolsWrapper);
Directory.CreateDirectory(outdir);
geminiWorkflow.Execute();
//var logger = new Illumina.CG.Common.Logging.Logger(taskLogDir, $"GeminiTaskLog_{chrom}.txt");
//var task = _taskCreator.GetCliTask(cmdLineList.ToArray(), chrom, exePath, outdir, chromRefIds[chrom], logger,
// string.IsNullOrEmpty(_options.GeminiSampleOptions.IntermediateDir)
// ? null
// : Path.Combine(_options.GeminiSampleOptions.IntermediateDir, chrom));
//tasks.Add(task);
Console.WriteLine($"Completed Gemini Workflow for {chrom}");
var path = (Path.Combine(outdir, "merged.bam.sorted.bam"));
taskDirectories.Add(outdir);
//paths[refId] = path;
return(path);
}
//wrapper should now handle all throwing and catching..
protected override void ProgramExecution()
{
_options.GeminiSampleOptions.InputBam = _options.InputBam;
_options.GeminiSampleOptions.OutputFolder = _options.OutputDirectory;
_options.GeminiSampleOptions.OutputBam = Path.Combine(_options.OutputDirectory, "out.bam");
_options.GeminiOptions.Debug = _options.StitcherOptions.Debug;
// Gemini defaults different than stitcher defaults
_options.StitcherOptions.NifyUnstitchablePairs = false;
// Set stitcher pair-filter-level duplicate filtering if skip and remove dups, to save time
_options.StitcherOptions.FilterDuplicates = _options.GeminiOptions.SkipAndRemoveDups;
var dataSourceFactory = new GeminiDataSourceFactory(_options.StitcherOptions, _options.GeminiOptions.GenomePath,
_options.GeminiOptions.SkipAndRemoveDups, _options.GeminiSampleOptions.RefId, Path.Combine(_options.OutputDirectory, "Regions.txt"), debug: _options.GeminiOptions.Debug);
var dataOutputFactory = new GeminiDataOutputFactory(_options.StitcherOptions.NumThreads);
var samtoolsWrapper = new SamtoolsWrapper(_options.GeminiOptions.SamtoolsPath, _options.GeminiOptions.IsWeirdSamtools);
var geminiWorkflow = new GeminiWorkflow(dataSourceFactory, dataOutputFactory, _options.GeminiOptions,
_options.GeminiSampleOptions, _options.RealignmentOptions, _options.StitcherOptions, _options.OutputDirectory, _options.RealignmentAssessmentOptions, _options.IndelFilteringOptions, samtoolsWrapper);
geminiWorkflow.Execute();
}