public AlignedPositionMapBuilder(AlignedPositionMapBuilderOptions options, string fileName)
{
this._options = options;
_format = options.GetSAMFormat();
_file = SAMFactory.GetReader(fileName, true);
_list = new AlignedPositionMapList();
_done = new List<AlignedPositionMap>();
}
public AlignedPositionMapBuilder(AlignedPositionMapBuilderOptions options, string fileName)
{
this._options = options;
_format = options.GetSAMFormat();
_file = SAMFactory.GetReader(fileName, true);
_list = new AlignedPositionMapList();
_done = new List <AlignedPositionMap>();
}
public static void SortByNameAndScore <T>(this List <T> list, ISAMFormat format) where T : ISAMItem
{
list.Sort((m1, m2) =>
{
var result = m1.Qname.CompareTo(m2.Qname);
if (result == 0)
{
result = format.CompareScore(m1.AlignmentScore, m2.AlignmentScore);
}
return(result);
});
}
/// <summary>
/// The default constructor which chooses the default encoding based on the alphabet.
/// </summary>
public SAMAlignedItemBAMParser(ISAMFormat samformat, string bamFileName, string refSeqName)
: base(bamFileName, refSeqName)
{
Format = samformat;
}