/// <summary>
/// Looks for a key in the array of key/values of the parameter string. If not found, return the specified default value
/// </summary>
/// <param name="items">The list to look in</param>
/// <param name="key">The key to find</param>
/// <param name="defValue">The default value to return if the key is not found</param>
/// <returns>The value corresponding to the specified key, or the default value if not found.</returns>
static internal string FindKey(System.Collections.Generic.SortedList <string, string> items, string key, string defValue)
{
string ret;
if (items.TryGetValue(key, out ret))
{
return(ret);
}
return(defValue);
}
/// <summary>
/// Sort the index of SequenceAlignmentMap by QName.
/// Fill the index (sorted by QName) into a list, when the list size reaches
/// the maximum limit, write the list to file and clear the list.
/// </summary>
private IList <string> SortByReadNames()
{
IList <string> files = new List <string>();
var sortedList = new System.Collections.Generic.SortedList <object, string>();
for (int index = 0; index < sequenceAlignMap.QuerySequences.Count; index++)
{
SAMAlignedSequence alignedSeq = sequenceAlignMap.QuerySequences[index];
string indices = string.Empty;
if (!sortedList.TryGetValue(alignedSeq.QName, out indices))
{
sortedList.Add(alignedSeq.QName, index.ToString(CultureInfo.InvariantCulture));
}
else
{
indices = string.Format(CultureInfo.InvariantCulture, "{0},{1}", indices, index.ToString(CultureInfo.InvariantCulture));
sortedList[alignedSeq.QName] = indices;
}
if (sortedList.Count >= SortedListMaxCount)
{
if (files == null)
{
files = new List <string>();
}
files.Add(WriteToFile(sortedList));
sortedList.Clear();
}
}
if (sortedList.Count > 0)
{
files.Add(WriteToFile(sortedList));
sortedList.Clear();
}
return(files);
}
/// <summary>
/// Sort the index of SequenceAlignmentMap by QName.
/// Fill the index (sorted by QName) into a list, when the list size reaches
/// the maximum limit, write the list to file and clear the list.
/// </summary>
private IList<string> SortByReadNames()
{
IList<string> files = new List<string>();
var sortedList = new System.Collections.Generic.SortedList<object,string>();
for (int index = 0; index < sequenceAlignMap.QuerySequences.Count; index++)
{
SAMAlignedSequence alignedSeq = sequenceAlignMap.QuerySequences[index];
string indices = string.Empty;
if (!sortedList.TryGetValue(alignedSeq.QName, out indices))
{
sortedList.Add(alignedSeq.QName, index.ToString(CultureInfo.InvariantCulture));
}
else
{
indices = string.Format(CultureInfo.InvariantCulture, "{0},{1}", indices, index.ToString(CultureInfo.InvariantCulture));
sortedList[alignedSeq.QName] = indices;
}
if (sortedList.Count >= SortedListMaxCount)
{
if (files == null)
{
files = new List<string>();
}
files.Add(WriteToFile(sortedList));
sortedList.Clear();
}
}
if (sortedList.Count > 0)
{
files.Add(WriteToFile(sortedList));
sortedList.Clear();
}
return files;
}