/// <summary>
/// Gets chromosomes in parameters.bamFile.
/// </summary>
/// <returns></returns>
private List <string> GetChromosomesInBam()
{
using (BamReader reader = new BamReader(parameters.bamFile))
{
return(reader.GetReferenceNames());
}
}
public Genome GetReferenceGenome(string genomePath)
{
var chromosomeNames = new List <string>();
var bamWorkRequests =
WorkRequests.Where(
w => w.GenomeDirectory.Equals(genomePath, StringComparison.InvariantCultureIgnoreCase)).ToList();
for (var i = 0; i < bamWorkRequests.Count(); i++)
{
var bamFilePath = bamWorkRequests[i].BamFilePath;
List <string> bamChromosomes;
using (var reader = new BamReader(bamFilePath))
{
bamChromosomes = reader.GetReferenceNames();
}
// load intervals and filter chromosomes if necessary
var bamIntervals = _bamIntervalLookup.ContainsKey(bamFilePath) ? _bamIntervalLookup[bamFilePath] : null;
chromosomeNames.AddRange(bamIntervals == null ? bamChromosomes : bamChromosomes.Where(bamIntervals.ContainsKey));
}
var genome = new Genome(genomePath, chromosomeNames.Distinct().ToList());
return(genome);
}
//wrapper should now handle all throwing and catching..
protected override void ProgramExecution()
{
var optionsUsed = _appOptionParser.ParsingResult.OptionsUsed;
var doNotPassToSubprocess = new List <string>()
{
"outFolder", "numProcesses", "exePath", "intermediateDir", "multiprocess", "chromosomes"
};
var cmdLineList = MultiProcessHelpers.GetCommandLineWithoutIgnoredArguments(optionsUsed, doNotPassToSubprocess);
var refNameMapping = new Dictionary <string, int>();
using (var bamReader = new BamReader(_options.InputBam))
{
var chroms = bamReader.GetReferenceNames();
foreach (var referenceName in chroms)
{
if (_options.Chromosomes != null && !_options.Chromosomes.ToList().Contains(referenceName))
{
continue;
}
refNameMapping.Add(referenceName, bamReader.GetReferenceIndex(referenceName));
}
}
var taskManager = new CliTaskManager(_options.NumProcesses);
var geminiProcessor = new GeminiMultiProcessor(_options, new CliTaskCreator());
var samtoolsWrapper = new SamtoolsWrapper(_options.GeminiOptions.SamtoolsPath, _options.GeminiOptions.IsWeirdSamtools);
geminiProcessor.Execute(taskManager, refNameMapping, cmdLineList, samtoolsWrapper);
}
private void Initialize()
{
var baseReader = new BamReader(_inputBam);
_chroms = baseReader.GetReferenceNames();
_header = baseReader.GetHeader();
_references = baseReader.GetReferences();
}
public Genome SetGenome(ScyllaApplicationOptions options)
{
var bamChromosomes = new List <string>()
{
};
using (var reader = new BamReader(options.BamPath))
{
bamChromosomes = reader.GetReferenceNames();
}
return(new Genome(options.GenomePath, bamChromosomes));
}
private List <GenomeMetadata.SequenceMetadata> GetReferences(string inBam)
{
List <GenomeMetadata.SequenceMetadata> bamReferences;
var refIdMapping = new Dictionary <int, string>();
using (var reader = new BamReader(inBam))
{
bamReferences = reader.GetReferences();
foreach (var referenceName in reader.GetReferenceNames())
{
refIdMapping.Add(reader.GetReferenceIndex(referenceName), referenceName);
}
}
return(bamReferences);
}
private IReadPairHandler CreatePairHandler(ReadStatusCounter readStatuses)
{
var stitcher = new BasicStitcher(_options.MinBaseCallQuality, useSoftclippedBases: _options.UseSoftClippedBases,
nifyDisagreements: _options.NifyDisagreements, debug: _options.Debug, nifyUnstitchablePairs: _options.NifyUnstitchablePairs, ignoreProbeSoftclips: !_options.StitchProbeSoftclips, maxReadLength: _options.MaxReadLength);
var refIdMapping = new Dictionary <int, string>();
using (var reader = new BamReader(_inBam))
{
foreach (var referenceName in reader.GetReferenceNames())
{
refIdMapping.Add(reader.GetReferenceIndex(referenceName), referenceName);
}
}
return(new PairHandler(refIdMapping, stitcher, _options.FilterUnstitchablePairs, readStatuses));
}
public Genome GetReferenceGenome(string genomePath)
{
var chromosomeNames = new List <string>();
var bamWorkRequests =
WorkRequests.Where(
w => w.GenomeDirectory.Equals(genomePath, StringComparison.CurrentCultureIgnoreCase)).ToList();
for (var i = 0; i < bamWorkRequests.Count(); i++)
{
var bamFilePath = bamWorkRequests[i].BamFilePath;
List <string> bamChromosomes;
using (var reader = new BamReader(bamFilePath))
{
bamChromosomes = reader.GetReferenceNames();
}
var filteredChromosomes = FilterBamChromosomes(bamChromosomes, bamFilePath);
if (!string.IsNullOrEmpty(_baseOptions.ChromosomeFilter))
{
filteredChromosomes.RemoveAll(c => c != _baseOptions.ChromosomeFilter);
}
chromosomeNames.AddRange(filteredChromosomes);
}
var genome = new Genome(genomePath, chromosomeNames.Distinct().ToList());
if (genome.ChromosomesToProcess.Count() < chromosomeNames.Distinct().Count())
{
Logger.WriteToLog("Warning: Not all requested sequences were found in {0} to process.", genome.GetGenomeBuild());
Logger.WriteToLog("Check BAM file matches reference genome.");
if (string.IsNullOrEmpty(_baseOptions.ChromosomeFilter))
{
Logger.WriteToLog("Requested sequences: {0}", (string.Join(",", chromosomeNames.Distinct().ToList())));
}
else
{
Logger.WriteToLog("Requested sequences: {0}", _baseOptions.ChromosomeFilter);
}
}
return(genome);
}
private IBamWriter CreateBamWriter()
{
string bamHeader;
List <GenomeMetadata.SequenceMetadata> bamReferences;
var refIdMapping = new Dictionary <int, string>();
using (var reader = new BamReader(_inBam))
{
bamReferences = reader.GetReferences();
var oldBamHeader = reader.GetHeader();
bamHeader = UpdateBamHeader(oldBamHeader);
foreach (var referenceName in reader.GetReferenceNames())
{
refIdMapping.Add(reader.GetReferenceIndex(referenceName), referenceName);
}
}
return(new BamWriterWrapper(new BamWriter(_outBam, bamHeader, bamReferences)));
}
private IBamWriterMultithreaded CreateBamWriter()
{
string bamHeader;
List <GenomeMetadata.SequenceMetadata> bamReferences;
var refIdMapping = new Dictionary <int, string>();
using (var reader = new BamReader(_inBam))
{
bamReferences = reader.GetReferences();
var oldBamHeader = reader.GetHeader();
bamHeader = UpdateBamHeader(oldBamHeader);
foreach (var referenceName in reader.GetReferenceNames())
{
refIdMapping.Add(reader.GetReferenceIndex(referenceName), referenceName);
}
}
if (_options.SortMemoryGB <= 0)
{
return(new BamWriterMultithreaded(_outBam, bamHeader, bamReferences, _options.NumThreads, 1));
}
return(new BamWriterInMem(_outBam, bamHeader, bamReferences, _options.SortMemoryGB, _options.NumThreads, 1));
}
private List <IReadPairHandler> CreatePairHandlers(ReadStatusCounter readStatuses, int numThreads)
{
var handlers = new List <IReadPairHandler>(numThreads);
var refIdMapping = new Dictionary <int, string>();
using (var reader = new BamReader(_inBam))
{
foreach (var referenceName in reader.GetReferenceNames())
{
refIdMapping.Add(reader.GetReferenceIndex(referenceName), referenceName);
}
}
for (int i = 0; i < numThreads; ++i)
{
var stitcher = new BasicStitcher(_options.MinBaseCallQuality, useSoftclippedBases: _options.UseSoftClippedBases,
nifyDisagreements: _options.NifyDisagreements, debug: _options.Debug, nifyUnstitchablePairs: _options.NifyUnstitchablePairs, ignoreProbeSoftclips: !_options.StitchProbeSoftclips, maxReadLength: _options.MaxReadLength, ignoreReadsAboveMaxLength: _options.IgnoreReadsAboveMaxLength, minMapQuality: _options.FilterMinMapQuality, dontStitchHomopolymerBridge: _options.DontStitchHomopolymerBridge);
handlers.Add(new PairHandler(refIdMapping, stitcher, readStatuses, _options.FilterUnstitchablePairs, true));
}
return(handlers);
}
