/// <summary>
/// calls the Sort() method in BAMSort and checks if a BAMSortedIndex is returned.
/// </summary>
/// <param name="seqAlignment">SequenceAlignmentMap to be sorted</param>
/// <param name="sortType">The sort type to be used when sorting using BAMSort</param>
private void ValidateSort(SequenceAlignmentMap seqAlignment, BAMSortByFields sortType)
{
var sorter = new BAMSort(seqAlignment, sortType);
IList<BAMSortedIndex> sortedIndex = sorter.Sort();
Assert.IsNotNull(sortedIndex);
Assert.IsTrue(this.IsSortedIndex(sortedIndex, sortType));
}
/// <summary>
/// Sort Sequence Alignments.
/// </summary>
/// <param name="map">SAM object to be sorted.</param>
/// <param name="bAMSortType">Sort based on genomic coordinates or read name.</param>
/// <returns></returns>
private IList<BAMSortedIndex> Sort(SequenceAlignmentMap map, BAMSortByFields bAMSortType)
{
BAMSort sort = new BAMSort(map, bAMSortType);
return sort.Sort();
}