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 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 string GetHeader(string inBam)
{
using (var reader = new BamReader(inBam))
{
var oldBamHeader = reader.GetHeader();
return(UpdateBamHeader(oldBamHeader));
}
}
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));
}
}
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)));
}
public void HappyPath()
{
//var bamFilePath = Path.Combine(TestPaths.SharedBamDirectory, "Chr17Chr19.bam");
//Assert.True(File.Exists(bamFilePath));
// TODO figure out how to access the shared bams
var tempPath = $"TemporaryBamFile_{Guid.NewGuid()}.bam";
if (File.Exists(tempPath))
{
File.Delete(tempPath);
}
using (var bamWriter = new BamWriter(tempPath, "header", new List <GenomeMetadata.SequenceMetadata>()))
{
bamWriter.WriteAlignment(TestHelpers.CreateBamAlignment("ATCG", 1, 10, 30, true));
}
var bamWriterFactory = new BamWriterFactory(1, tempPath);
var tempPath2 = $"TemporaryBamFile_{Guid.NewGuid()}.bam";
if (File.Exists(tempPath2))
{
File.Delete(tempPath2);
}
var bamWriterHandle = bamWriterFactory.CreateSingleBamWriter(tempPath2);
bamWriterHandle.WriteAlignment(TestHelpers.CreateBamAlignment("ATCAG", 1, 10, 30, true));
bamWriterHandle.WriteAlignment(null);
using (var reader = new BamReader(tempPath2))
{
// TODO more specific?
var header = reader.GetHeader();
Assert.Contains("ID:Gemini", header);
Assert.Contains("PN:Gemini", header);
}
File.Delete(tempPath);
File.Delete(tempPath2);
}
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));
}
/// <summary>
/// Reads in a bam file and marks within the BitArrays which genomic mers are present.
/// </summary>
/// <param name="bamFile">bam file read alignments from.</param>
/// <param name="observedAlignments">Dictioanry of BitArrays, one for each chromosome, to store the alignments in.</param>
static void LoadObservedAlignmentsBAM(string bamFile, bool isPairedEnd, string chromosome, CanvasCoverageMode coverageMode, HitArray observed, Int16[] fragmentLengths)
{
// Sanity check: The .bai file must exist, in order for us to seek to our target chromosome!
string indexPath = bamFile + ".bai";
if (!File.Exists(indexPath))
{
throw new Exception(string.Format("Fatal error: Bam index not found at {0}", indexPath));
}
using (BamReader reader = new BamReader(bamFile))
{
int desiredRefIndex = -1;
desiredRefIndex = reader.GetReferenceIndex(chromosome);
if (desiredRefIndex == -1)
{
throw new ApplicationException(
string.Format("Unable to retrieve the reference sequence index for {0} in {1}.", chromosome,
bamFile));
}
bool result = reader.Jump(desiredRefIndex, 0);
if (!result)
{
// Note: This is not necessarily an error, it just means that there *are* no reads for this chromosome in this
// .bam file. That is not uncommon e.g. for truseq amplicon.
return;
}
int readCount = 0;
int keptReadCount = 0;
string header = reader.GetHeader();
BamAlignment alignment = new BamAlignment();
while (reader.GetNextAlignment(ref alignment, true))
{
readCount++;
// Flag check - Require reads to be aligned, passing filter, non-duplicate:
if (!alignment.IsMapped())
{
continue;
}
if (alignment.IsFailedQC())
{
continue;
}
if (alignment.IsDuplicate())
{
continue;
}
if (alignment.IsReverseStrand())
{
continue;
}
if (!alignment.IsMainAlignment())
{
continue;
}
// Require the alignment to start with 35 bases of non-indel:
if (alignment.CigarData[0].Type != 'M' || alignment.CigarData[0].Length < 35)
{
continue;
}
if (isPairedEnd && !alignment.IsProperPair())
{
continue;
}
int refID = alignment.RefID;
// quit if the current reference index is different from the desired reference index
if (refID != desiredRefIndex)
{
break;
}
if (refID == -1)
{
continue;
}
keptReadCount++;
if (coverageMode == CanvasCoverageMode.Binary)
{
observed.Data[alignment.Position] = 1;
}
else
{
observed.Set(alignment.Position);
}
// store fragment size, make sure it's within Int16 range and is positive (simplification for now)
if (coverageMode == CanvasCoverageMode.GCContentWeighted)
{
fragmentLengths[alignment.Position] = Convert.ToInt16(Math.Max(Math.Min(Int16.MaxValue, alignment.FragmentLength), 0));
}
}
Console.WriteLine("Kept {0} of {1} total reads", keptReadCount, readCount);
}
}
