// Gets new header with sorted SQ Fields.
// If SQ fields are already sorted then returns the same header.
private SAMAlignmentHeader GetHeaderWithSortedSQFields(SAMAlignmentHeader header, bool canChangeOtherTagPos)
{
if (IsSortedByChromosomeNames(GetSQHeaders(header.RecordFields)))
{
return(header);
}
SAMAlignmentHeader newHeader = new SAMAlignmentHeader();
int i = 0;
if (canChangeOtherTagPos)
{
List <SAMRecordField> sqHeaders = new List <SAMRecordField>();
for (; i < header.RecordFields.Count; i++)
{
SAMRecordField field = header.RecordFields[i];
if (field.Typecode.Equals("SQ"))
{
sqHeaders.Add(field);
}
else
{
newHeader.RecordFields.Add(field);
}
sqHeaders.Sort(CompareByChromosomeName);
foreach (SAMRecordField sqfield in sqHeaders)
{
newHeader.RecordFields.Add(sqfield);
}
foreach (string str in header.Comments)
{
newHeader.Comments.Add(str);
}
}
}
else
{
Bio.Util.SortedList <SAMRecordField, int> map = new Bio.Util.SortedList <SAMRecordField, int>(new ComparisonWrapper <SAMRecordField>(CompareByChromosomeName));
for (; i < header.RecordFields.Count; i++)
{
SAMRecordField field = header.RecordFields[i];
if (field.Typecode.Equals("SQ"))
{
map.Add(field, i);
}
newHeader.RecordFields.Add(field);
}
i = 0;
foreach (int index in map.Values.OrderBy(I => I))
{
newHeader.RecordFields[index] = map.Keys[i++];
}
foreach (string str in header.Comments)
{
newHeader.Comments.Add(str);
}
}
return(newHeader);
}
// Gets new header with sorted SQ Fields.
// If SQ fields are already sorted then returns the same header.
private SAMAlignmentHeader GetHeaderWithSortedSQFields(SAMAlignmentHeader header, bool canChangeOtherTagPos)
{
if (IsSortedByChromosomeNames(GetSQHeaders(header.RecordFields)))
return header;
SAMAlignmentHeader newHeader = new SAMAlignmentHeader();
int i = 0;
if (canChangeOtherTagPos)
{
List<SAMRecordField> sqHeaders = new List<SAMRecordField>();
for (; i < header.RecordFields.Count; i++)
{
SAMRecordField field = header.RecordFields[i];
if (field.Typecode.Equals("SQ"))
{
sqHeaders.Add(field);
}
else
{
newHeader.RecordFields.Add(field);
}
sqHeaders.Sort(CompareByChromosomeName);
foreach (SAMRecordField sqfield in sqHeaders)
{
newHeader.RecordFields.Add(sqfield);
}
foreach (string str in header.Comments)
{
newHeader.Comments.Add(str);
}
}
}
else
{
Bio.Util.SortedList<SAMRecordField, int> map = new Bio.Util.SortedList<SAMRecordField, int>(new ComparisonWrapper<SAMRecordField>(CompareByChromosomeName));
for (; i < header.RecordFields.Count; i++)
{
SAMRecordField field = header.RecordFields[i];
if (field.Typecode.Equals("SQ"))
{
map.Add(field, i);
}
newHeader.RecordFields.Add(field);
}
i = 0;
foreach (int index in map.Values.OrderBy(I => I))
{
newHeader.RecordFields[index] = map.Keys[i++];
}
foreach (string str in header.Comments)
{
newHeader.Comments.Add(str);
}
}
return newHeader;
}