/// <summary>
/// Return the position of the last base in the read. Note that this is equivalent to the result before the update to Isas BamAlignment at c348f98 in PICS-847.
/// </summary>
/// <param name="alignment"></param>
/// <returns></returns>
public static int GetLastBasePosition(this BamAlignment alignment)
{
return(alignment.GetEndPosition());
}
/// <summary>
/// Returns the "one-based end position", which is the end position of the alignment + 1 (Isas BamAlignment is zero-based). Note that this will return a different value (-1) than before the update to Isas BamAlignment.
/// </summary>
/// <param name="alignment"></param>
/// <returns></returns>
public static int OneBasedEndPosition(this BamAlignment alignment)
{
// NOTE this will return a different value (-1) than before the update to Isas BamAlignment. Nothing internal to Pisces is using it.
return(alignment.GetEndPosition() + 1);
}
public static int OneBasedEndPosition(this BamAlignment alignment)
{
return(alignment.GetEndPosition() + 1);
}