/// <summary>
/// Writes specified alignment object to a file.
/// The output is formatted according to the BAM specification.
/// </summary>
/// <param name="sequenceAlignmentMap">SequenceAlignmentMap object.</param>
/// <param name="bamFilename">BAM filename to write BAM data.</param>
/// <param name="indexFilename">BAM index filename to write index data.</param>
public void Format(SequenceAlignmentMap sequenceAlignmentMap, string bamFilename, string indexFilename)
{
if (sequenceAlignmentMap == null)
{
throw new ArgumentNullException("sequenceAlignmentMap");
}
if (string.IsNullOrWhiteSpace(bamFilename))
{
throw new ArgumentNullException("bamFilename");
}
if (string.IsNullOrWhiteSpace(indexFilename))
{
throw new ArgumentNullException("indexFilename");
}
if (bamFilename.Equals(indexFilename))
{
throw new ArgumentException(Resource.BAM_BAMFileNIndexFileContbeSame);
}
using (FileStream fs = new FileStream(bamFilename, FileMode.Create, FileAccess.ReadWrite))
{
using (BAMIndexFile bamIndexFile = new BAMIndexFile(indexFilename, FileMode.Create, FileAccess.Write))
{
WriteSequenceAlignment(sequenceAlignmentMap, fs, bamIndexFile);
}
}
}
internal LinearIndexArrayMaker(int refSeqLength)
{
int size;
if (refSeqLength <= 0)
{
size = BAMIndexFile.MAX_LINERINDEX_ARRAY_SIZE;
}
else
{
size = BAMIndexFile.LargestBinPossibleForSequenceLength(refSeqLength);
}
//TODO: Plus one now because weird things could happen with alignment length such that the bin is one higher
//never seen this, but not sure it can't happen.
offSetArray = new FileOffset[size + 1];
}
/// <summary>
/// Creates BAMIndex object from the specified BAM file and writes to specified BAMIndex file.
/// </summary>
/// <param name="compressedBAMStream"></param>
/// <param name="indexFile"></param>
private static void CreateIndexFile(Stream compressedBAMStream, BAMIndexFile indexFile)
{
BAMParser parser = new BAMParser();
BAMIndex bamIndex;
try
{
bamIndex = parser.GetIndexFromBAMFile(compressedBAMStream);
}
finally
{
parser.Dispose();
}
parser = null;
indexFile.Write(bamIndex);
}
/// <summary>
/// Writes specified alignment object to a stream.
/// The output is formatted according to the BAM specification.
/// </summary>
/// <param name="sequenceAlignmentMap">SequenceAlignmentMap object.</param>
/// <param name="writer">Stream to write BAM data.</param>
/// <param name="indexWriter">BAMIndexFile to write index data.</param>
public void Format(SequenceAlignmentMap sequenceAlignmentMap, Stream writer, BAMIndexFile indexWriter)
{
if (sequenceAlignmentMap == null)
{
throw new ArgumentNullException("sequenceAlignmentMap");
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
if (indexWriter == null)
{
throw new ArgumentNullException("indexWriter");
}
WriteSequenceAlignment(sequenceAlignmentMap, writer, indexWriter);
}
/// <summary>
/// Writes specified alignment object to a file. The output is formatted according to the BAM specification.
/// Also creates index file in the same location that of the specified filename.
/// If the specified filename is sample.bam then the index file name will be sample.bam.bai.
/// </summary>
/// <param name="sequenceAlignmentMap">SequenceAlignmentMap object.</param>
/// <param name="filename">BAM file name to write BAM data.</param>
public void Format(SequenceAlignmentMap sequenceAlignmentMap, string filename)
{
if (sequenceAlignmentMap == null)
{
throw new ArgumentNullException("sequenceAlignmentMap");
}
if (string.IsNullOrWhiteSpace(filename))
{
throw new ArgumentNullException("filename");
}
using (FileStream fs = new FileStream(filename, FileMode.Create, FileAccess.ReadWrite))
{
using (BAMIndexFile bamIndexFile = new BAMIndexFile(filename + Resource.BAM_INDEXFILEEXTENSION, FileMode.Create, FileAccess.Write))
{
WriteSequenceAlignment(sequenceAlignmentMap, fs, bamIndexFile);
}
}
}
public SAMAlignmentHeader GetFileHeader()
{
SAMAlignmentHeader header;
using (FileStream bamStream = new FileStream(_fileName, FileMode.Open, FileAccess.Read, FileShare.Read))
{
string bamIndexFileName = getBAMIndexFileName(_fileName);
using (BAMIndexFile bamIndexFile = new BAMIndexFile(bamIndexFileName, FileMode.Open, FileAccess.Read))
{
readStream = bamStream;
if (readStream == null || readStream.Length == 0)
{
throw new FileFormatException(Properties.Resource.BAM_InvalidBAMFile);
}
ValidateReader();
header = GetHeader();
}
}
return(header);
}
public IEnumerable <CompactSAMSequence> ParseRangeAsEnumerableSequences(string fileName, string refSeqName, int start = 0, int end = Int32.MaxValue)
{
if (refSeqName == null)
{
throw new ArgumentNullException("refSeqName");
}
using (FileStream bamStream = new FileStream(fileName, FileMode.Open, FileAccess.Read, FileShare.Read))
{
string bamIndexFileName = getBAMIndexFileName(fileName);
using (BAMIndexFile bamIndexFile = new BAMIndexFile(bamIndexFileName, FileMode.Open, FileAccess.Read))
{
readStream = bamStream;
if (readStream == null || readStream.Length == 0)
{
throw new FileFormatException(Properties.Resource.BAM_InvalidBAMFile);
}
ValidateReader();
SAMAlignmentHeader header = GetHeader();
// verify whether there is any reads related to chromosome.
int refSeqIndex = refSeqNames.IndexOf(refSeqName);
if (refSeqIndex < 0)
{
string message = string.Format(CultureInfo.InvariantCulture, Properties.Resource.BAM_RefSeqNotFound, refSeqName);
throw new ArgumentException(message, "refSeqName");
}
BAMIndex bamIndexInfo = bamIndexFile.Read();
BAMReferenceIndexes refIndex = bamIndexInfo.RefIndexes[refSeqIndex];
IList <Chunk> chunks = GetChunks(refIndex, start, end);
foreach (var s in EnumerateAlignedSequences(chunks))
{
if (s != null && (s.RName == "*" || (s.Pos >= (start - 1) && s.RefEndPos < end)))
{
yield return(s);
}
}
readStream = null;
}
}
}
/// <summary>
/// Writes sequence alignment to specified stream.
/// </summary>
/// <param name="sequenceAlignment">Sequence alignment object</param>
/// <param name="writer">Stream to write.</param>
/// <param name="indexFile">BAMIndex file.</param>
private void WriteSequenceAlignment(ISequenceAlignment sequenceAlignment, Stream writer, BAMIndexFile indexFile)
{
// validate sequenceAlignment.
SequenceAlignmentMap sequenceAlignmentMap = ValidateAlignment(sequenceAlignment);
string tempFilename = Path.GetTempFileName();
// write bam struct to temp file.
using (FileStream fstemp = new FileStream(tempFilename, FileMode.Create, FileAccess.ReadWrite))
{
WriteUncompressed(sequenceAlignmentMap, fstemp);
fstemp.Seek(0, SeekOrigin.Begin);
// Compress and write to the specified stream.
CompressBAMFile(fstemp, writer);
// if index file need to be created.
if (indexFile != null)
{
writer.Seek(0, SeekOrigin.Begin);
CreateIndexFile(writer, indexFile);
}
}
// delete the temp file.
File.Delete(tempFilename);
}
