private void InitializeReader(string chromosomeFilter = null)
{
_bamReader = new BamReader(_bamFilePath);
_references = _bamReader.GetReferences().OrderBy(r => r.Index).ToList();
_bamIsStitched = CheckIfBamHasBeenStitched(_bamReader.GetHeader());
if (!string.IsNullOrEmpty(chromosomeFilter))
{
var chrReference = _references.FirstOrDefault(r => r.Name == chromosomeFilter);
if (chrReference == null)
{
throw new Exception(string.Format("Cannot set chr filter to '{0}'. This chr is not in the bam.", chromosomeFilter));
}
_bamIndexFilter = chrReference.Index;
}
var chrToStart = !string.IsNullOrEmpty(chromosomeFilter)
? chromosomeFilter
: _references.First().Name;
var position = 0;
if (_remainingIntervals != null && _remainingIntervals.ContainsKey(chrToStart))
{
position = _remainingIntervals[chrToStart][0].StartPosition - 1;
}
Jump(chrToStart, position);
}
private void InitializeReader(string chromosomeFilter = null)
{
_bamReader = new BamReader(_bamFilePath);
_references = _bamReader.GetReferences().OrderBy(r => r.Index).ToList();
if (!_bamIsStitched)
{
_bamIsStitched = CheckBamHeaderIfBamHasBeenStitched(_bamReader.GetHeader());
}
SourceIsCollapsed = CheckIfBamHasBeenCollapsed(_bamReader.GetHeader());
if (!string.IsNullOrEmpty(chromosomeFilter))
{
var chrReference = _references.FirstOrDefault(r => r.Name == chromosomeFilter);
if (chrReference == null)
{
throw new InvalidDataException(string.Format("Cannot set chr filter to '{0}'. This chr is not in the bam.", chromosomeFilter));
}
_bamIndexFilter = chrReference.Index;
}
var chrToStart = !string.IsNullOrEmpty(chromosomeFilter)
? chromosomeFilter
: _references.First().Name;
Jump(chrToStart);
}
private void Initialize()
{
var baseReader = new BamReader(_inputBam);
_chroms = baseReader.GetReferenceNames();
_header = baseReader.GetHeader();
_references = baseReader.GetReferences();
}
private BamWriter GetWriter(string outputFile)
{
using (var reader = new BamReader(_inputFile))
{
var genome = reader.GetReferences();
string originalSamHeader = reader.GetHeader();
var updatedHeader = UpdateBamHeader(originalSamHeader);
return(new BamWriter(outputFile, updatedHeader, genome));
}
}
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);
}
public void Initialize()
{
var outputDirectory = Path.GetDirectoryName(_outputFile);
if (!Directory.Exists(outputDirectory))
{
Directory.CreateDirectory(outputDirectory);
}
using (var reader = new BamReader(_inputFile))
{
var genome = reader.GetReferences();
_bamWriter = new BamWriter(_temp1File, reader.GetHeader(), 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));
}
