/// <summary>
/// Parses specified BAM file using index file.
/// Index file is assumed to be in the same location as that of the specified bam file with the name "filename".bai
/// For example, if the specified bam file name is D:\BAMdata\sample.bam then index file name will be taken as D:\BAMdata\sample.bam.bai
/// If index file is not available then this method throw an exception.
/// </summary>
/// <param name="parser">BAM parser</param>
/// <param name="fileName">BAM file name.</param>
/// <param name="refSeqName">Name of reference sequence.</param>
/// <returns>SequenceAlignmentMap object which contains alignments for specified reference sequence.</returns>
public static SequenceAlignmentMap ParseRange(this BAMParser parser, string fileName, string refSeqName)
{
if (parser == null)
{
throw new ArgumentNullException("parser");
}
if (string.IsNullOrWhiteSpace(fileName))
{
throw new ArgumentNullException("fileName");
}
if (refSeqName == null)
{
throw new ArgumentNullException("refSeqName");
}
using (var bamStream = File.OpenRead(fileName))
{
string bamIndexFileName = GetBAMIndexFileName(fileName);
using (FileStream bamIndexFile = File.OpenRead(bamIndexFileName))
using (var bamIndexStorage = new BAMIndexStorage(bamIndexFile))
{
return(parser.GetAlignment(bamStream, bamIndexStorage, refSeqName));
}
}
}
/// <summary>
/// Parses specified BAM file using index file.
/// </summary>
/// <param name="parser">BAM parser</param>
/// <param name="fileName">BAM file name.</param>
/// <param name="range">SequenceRange object which contains reference sequence name and start and end co-ordinates.</param>
/// <returns>SequenceAlignmentMap object which contains alignments for specified reference sequence and for specified range.</returns>
public static SequenceAlignmentMap ParseRange(this BAMParser parser, string fileName, SequenceRange range)
{
if (parser == null)
{
throw new ArgumentNullException("parser");
}
if (string.IsNullOrWhiteSpace(fileName))
{
throw new ArgumentNullException("fileName");
}
if (range == null)
{
throw new ArgumentNullException("range");
}
if (string.IsNullOrEmpty(range.ID))
{
throw new ArgumentException("Reference sequence name (range.ID) can't empty or null.");
}
int start = range.Start >= int.MaxValue ? int.MaxValue : (int)range.Start;
int end = range.End >= int.MaxValue ? int.MaxValue : (int)range.End;
using (FileStream bamStream = File.OpenRead(fileName))
{
string bamIndexFileName = GetBAMIndexFileName(fileName);
using (FileStream bamIndexFile = File.OpenRead(bamIndexFileName))
using (BAMIndexStorage bamIndexStorage = new BAMIndexStorage(bamIndexFile))
{
if (start == 0 && end == int.MaxValue)
{
return(parser.GetAlignment(bamStream, bamIndexStorage, range.ID));
}
return(parser.GetAlignment(bamStream, bamIndexStorage, range.ID, start, end));
}
}
}
