/// <summary>
/// Compares two sequence ranges.
/// </summary>
/// <param name="obj">SequenceRange instance to compare.</param>
/// <returns>
/// If the Start values of the two ranges are identical then the
/// result of this comparison is the result from calling CompareTo() on
/// the two End values. If the Start values are not equal then the result
/// of this comparison is the result of calling CompareTo() on the two
/// Start values.
/// </returns>
public int CompareTo(object obj)
{
if (obj == null)
{
return(0);
}
SequenceRange sequenceRange = obj as SequenceRange;
if (obj == null)
{
return(0);
}
return(CompareTo(sequenceRange));
}
/// <summary>
/// For each group in the grouping, this method traverses through each range
/// in the group and normalizes the ranges down to the minimal spanning set
/// required to still show the same range spans.
///
/// For instance if you had in group 'Chr1' the following ranges:
///
/// -> 10 to 100
/// -> 200 to 250
/// -> 35 to 45
/// -> 90 to 150
///
/// The result of MergeOverlaps would reduce the ranges in the 'Chr1' group to:
/// For minOverlap = 0
///
/// -> 10 to 150
/// -> 200 to 250
///
/// for minOverlap = -50
///
/// -> 10 to 250
///
/// Running this method creates all new ISequenceRange objects and adds them
/// to the newly created SequenceRangeGrouping returned here.
/// </summary>
/// <param name="minOverlap">Minmum length of bases pairs should be overlapped.</param>
/// <param name="isParentSeqRangesRequired">If this flag is set to true then the sequence ranges from
/// which the new sequence range is created are added to the ParentSeqRanges property of the
/// new sequence range.</param>
/// <returns>The overlapped sequence range grouping.</returns>
public SequenceRangeGrouping MergeOverlaps(long minOverlap = 0, bool isParentSeqRangesRequired = false)
{
SequenceRangeGrouping seqRangeGroup = new SequenceRangeGrouping();
List <ISequenceRange> sortedRanges = new List <ISequenceRange>();
foreach (List <ISequenceRange> rangeList in this.groups.Values)
{
sortedRanges.AddRange(rangeList);
sortedRanges.Sort();
while (sortedRanges.Count > 0)
{
ISequenceRange seqRange = new SequenceRange(sortedRanges[0].ID,
sortedRanges[0].Start,
sortedRanges[0].End);
if (isParentSeqRangesRequired)
{
AddParent(seqRange, sortedRanges[0]);
}
sortedRanges.RemoveAt(0);
seqRangeGroup.Add(seqRange);
if (sortedRanges.Count > 0)
{
while (sortedRanges.Count > 0 && (seqRange.End - sortedRanges[0].Start) >= minOverlap)
{
seqRange.End = Math.Max(seqRange.End, sortedRanges[0].End);
if (isParentSeqRangesRequired)
{
AddParent(seqRange, sortedRanges[0]);
}
sortedRanges.RemoveAt(0);
}
}
}
sortedRanges.Clear();
}
return(seqRangeGroup);
}
/// <summary>
/// Convert given range containing any bed sequence to SequenceRange object
/// </summary>
/// <param name="userSelectedRange">Range of cells</param>
/// <param name="columnMapping">A dictionary which has a column number to BED header mapping.</param>
/// <returns>SequenceRange, Address object</returns>
public static Dictionary<ISequenceRange, string> RangeToSequenceRange(Range userSelectedRange, Dictionary<int, string> columnMapping)
{
Dictionary<ISequenceRange, string> sequenceRanges = new Dictionary<ISequenceRange, string>();
SequenceRange sequenceRange;
string rangeAddress, cellValue, columnName;
object[,] cellRange = userSelectedRange.Value2 as object[,]; // cellrange will be a base 1 array
int rangeWidth = columnMapping.Keys.Max() - columnMapping.Keys.Min() + 1;
SortedSet<int> sortedColumn = new SortedSet<int>(columnMapping.Keys);
bool idFound, startFound, endFound;
for (int row = 1; row <= cellRange.GetLength(0); row++)
{
// If hidden row, then skip
if ((userSelectedRange.Rows[row] as Range).EntireRow.Hidden)
{
continue;
}
// Reset the flags to false
idFound = false;
startFound = false;
endFound = false;
sequenceRange = new SequenceRange();
rangeAddress = string.Empty;
for (int col = 1; col <= cellRange.GetLength(1); col++)
{
if (cellRange[row, col] != null)
{
cellValue = cellRange[row, col].ToString();
if (columnMapping.TryGetValue((userSelectedRange[1, col] as Range).Column, out columnName))
{
switch (columnName) // mapped header for current column
{
case CHROM_ID:
sequenceRange.ID = cellValue;
idFound = true;
break;
case CHROM_START:
sequenceRange.Start = long.Parse(cellValue, CultureInfo.InvariantCulture);
startFound = true;
break;
case CHROM_END:
sequenceRange.End = long.Parse(cellValue, CultureInfo.InvariantCulture);
endFound = true;
break;
default:
// any other item goes into the metadata dictionary
sequenceRange.Metadata.Add(columnMapping[(userSelectedRange[1, col] as Range).Column], cellValue);
break;
}
}
}
}
if (idFound & startFound & endFound)
{
rangeAddress = GetRangeAddress(userSelectedRange, sortedColumn, rangeWidth, row);
sequenceRanges.Add(sequenceRange, rangeAddress);
}
}
return sequenceRanges;
}
/// <summary>
/// Subtracts the query SequenceRangeGrouping from this SequenceRangeGrouping.
///
/// For example,
///
/// Ranges in this instance Ranges in the query
/// 1 to 4 2 to 6
/// 4 to 8 3 to 6
/// 8 to 12 9 to 14
/// 25 to 35
///
/// Result for minOverlap set to 1
/// 1. If outputType is IntervalsWithNoOverlap
/// 25 to 35
///
/// 2. If outputType is NonOverlappingPiecesOfIntervals
/// 1 to 2
/// 6 to 8
/// 8 to 9
/// 25 to 35
///
/// Running this method creates all new ISequenceRange objects and adds them
/// to the newly created SequenceRangeGrouping returned here.
/// </summary>
/// <param name="query">Query grouping.</param>
/// <param name="minOverlap">Minmum length of overlap. By default this will be set to 1</param>
/// <param name="outputType">
/// Type of output required, IntervalsWithNoOverlap or NonOverlappingPiecesOfIntervals.
/// By default this will be set to NonOverlappingPiecesOfIntervals that is non overlapping
/// pieces of intervels along with non overlapping ranges from this instance
/// will be returned.
/// </param>
/// <param name="isParentSeqRangesRequired">If this flag is set to true then the sequence ranges from
/// which the new sequence range is created are added to the ParentSeqRanges property of the
/// new sequence range.</param>
/// <returns>The resultant Sequence range grouping.</returns>
public SequenceRangeGrouping Subtract(SequenceRangeGrouping query,
long minOverlap = 1,
SubtractOutputType outputType = SubtractOutputType.NonOverlappingPiecesOfIntervals,
bool isParentSeqRangesRequired = false)
{
if (query == null)
{
throw new ArgumentNullException("query");
}
SequenceRangeGrouping result = new SequenceRangeGrouping();
List<ISequenceRange> refSeqRanges = new List<ISequenceRange>();
List<ISequenceRange> querySeqRanges = new List<ISequenceRange>();
List<ISequenceRange> previousSeqRanges = new List<ISequenceRange>();
SequenceRange range = null;
// merge the query sequence ranges.
IList<ISequenceRange> queryList = null;
if (isParentSeqRangesRequired)
{
queryList = query.Flatten();
}
query = query.MergeOverlaps(0, isParentSeqRangesRequired);
foreach (string id in groups.Keys)
{
refSeqRanges.Clear();
querySeqRanges.Clear();
refSeqRanges.AddRange(groups[id]);
if (query.groups.ContainsKey(id))
{
querySeqRanges.AddRange(query.groups[id]);
querySeqRanges.Sort();
}
if (querySeqRanges.Count > 0)
{
foreach (ISequenceRange refRange in refSeqRanges)
{
previousSeqRanges.Clear();
IList<ISequenceRange> overlappingQueryRanges = GetOverlappingRenges(refRange,
querySeqRanges,
minOverlap);
if (overlappingQueryRanges == null || overlappingQueryRanges.Count == 0)
{
if (minOverlap > 0 || outputType == SubtractOutputType.NonOverlappingPiecesOfIntervals)
{
range = new SequenceRange(refRange.ID, refRange.Start, refRange.End);
CopyOfMetadata(range, refRange);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
result.Add(range);
}
continue;
}
// no need to proceed if only non overlapping intervels needed.
if (outputType == SubtractOutputType.IntervalsWithNoOverlap)
{
continue;
}
ISequenceRange previousOverlappingRange = null;
foreach (ISequenceRange queryRange in overlappingQueryRanges)
{
// in case of non overlapping pieces of intervals get the non overlapping
// ranges from reference sequence range.
if (refRange.Start < queryRange.Start)
{
if (previousSeqRanges.Count > 0 && previousSeqRanges[0].Start < queryRange.Start)
{
// if the previous overlapping range's start and end are equal then no need to change the metadataSeqRanges.
if (previousOverlappingRange == null || previousOverlappingRange.Start != queryRange.Start && previousOverlappingRange.End != queryRange.End)
{
for (int i = previousSeqRanges.Count - 1; i >= 0; i--)
{
if (previousSeqRanges[i].End > queryRange.Start)
{
previousSeqRanges[i].End = queryRange.Start;
}
else if (previousSeqRanges[i].End < queryRange.Start)
{
previousSeqRanges.RemoveAt(i);
}
}
}
if (isParentSeqRangesRequired)
{
if (queryList.Contains(queryRange))
{
AddParent(previousSeqRanges[0], queryRange);
}
else
{
if (queryRange.ParentSeqRanges.Count > 0)
{
AddParent(previousSeqRanges[0], queryRange.ParentSeqRanges);
}
}
}
}
else
{
if (previousOverlappingRange == null || previousOverlappingRange.Start != queryRange.Start && previousOverlappingRange.End != queryRange.End)
{
range = new SequenceRange(refRange.ID, refRange.Start, queryRange.Start);
result.Add(range);
CopyOfMetadata(range, refRange);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
}
if (isParentSeqRangesRequired)
{
if (queryList.Contains(queryRange))
{
AddParent(range, queryRange);
}
else
{
if (queryRange.ParentSeqRanges.Count > 0)
{
AddParent(range, queryRange.ParentSeqRanges);
}
}
}
}
}
if (queryRange.End < refRange.End)
{
if (previousOverlappingRange == null || previousOverlappingRange.Start != queryRange.Start && previousOverlappingRange.End != queryRange.End)
{
range = new SequenceRange(refRange.ID, queryRange.End, refRange.End);
CopyOfMetadata(range, refRange);
result.Add(range);
previousSeqRanges.Add(range);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
}
if (isParentSeqRangesRequired)
{
if (queryList.Contains(queryRange))
{
AddParent(range, queryRange);
}
else
{
if (queryRange.ParentSeqRanges.Count > 0)
{
AddParent(range, queryRange.ParentSeqRanges);
}
}
}
}
previousOverlappingRange = queryRange;
}
}
}
else
{
foreach (SequenceRange refRange in refSeqRanges)
{
range = new SequenceRange(refRange.ID, refRange.Start, refRange.End);
CopyOfMetadata(range, refRange);
result.Add(range);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
}
}
}
return result;
}
/// <summary>
/// Returns overlapping sequence ranges from this and specified SequenceRangeGroup for each group in this grouping.
///
/// For instance if you had in group 'Chr1' the following ranges:
///
/// Ranges in this instance Ranges in the query
/// 0 to 10 20 to 40
/// 30 to 50 70 to 100
/// 60 to 80 400 to 800
/// 300 to 500 850 to 900
/// 600 to 700 900 to 1200
/// 800 to 1000
///
/// Result for minOverlap set to 1
/// 1. If outputType is OverlappingPiecesOfIntervals.
/// 30 to 40
/// 70 to 80
/// 400 to 500
/// 600 o 700
/// 850 to 900
/// 900 to 1000
/// 2. If outputType is OverlappingIntervals
/// 30 to 50
/// 60 to 80
/// 300 to 500
/// 600 to 700
/// 800 to 1000
///
/// Running this method creates all new ISequenceRange objects and adds them
/// to the newly created SequenceRangeGrouping returned here.
/// </summary>
/// <param name="query">Query grouping.</param>
/// <param name="minOverlap">Minmum length of bases pairs should be overlapped.
/// By default this will be set to 1.</param>
/// <param name="outputType">
/// Type of output required, OverlappingPiecesOfIntervals or OverlappingIntervals.
/// By default this will be set to OverlappingPiecesOfIntervals that is only the base pairs that overlaps with
/// query ranges will be returned.</param>
/// <param name="isParentSeqRangesRequired">If this flag is set to true then the sequence ranges from
/// which the new sequence range is created are added to the ParentSeqRanges property of the
/// new sequence ranges.</param>
/// <returns>The intersected result.</returns>
public SequenceRangeGrouping Intersect(SequenceRangeGrouping query, long minOverlap = 1, IntersectOutputType outputType = IntersectOutputType.OverlappingPiecesOfIntervals, bool isParentSeqRangesRequired = false)
{
if (query == null)
{
throw new ArgumentNullException("query");
}
SequenceRangeGrouping result = new SequenceRangeGrouping();
List<ISequenceRange> refSeqRanges = new List<ISequenceRange>();
List<ISequenceRange> querySeqRanges = new List<ISequenceRange>();
SequenceRange range = null;
// merge the query sequence ranges.
IList<ISequenceRange> queryList = null;
if (isParentSeqRangesRequired)
{
queryList = query.Flatten();
}
query = query.MergeOverlaps(0, isParentSeqRangesRequired);
foreach (string id in groups.Keys)
{
refSeqRanges.Clear();
querySeqRanges.Clear();
refSeqRanges.AddRange(groups[id]);
if (query.groups.ContainsKey(id))
{
querySeqRanges.AddRange(query.groups[id]);
querySeqRanges.Sort();
}
if (querySeqRanges.Count > 0)
{
foreach (ISequenceRange refRange in refSeqRanges)
{
IList<ISequenceRange> overlappingQueryRanges = GetOverlappingRenges(refRange, querySeqRanges, minOverlap);
if (overlappingQueryRanges == null || overlappingQueryRanges.Count == 0)
{
// If the minOverlap is lessthan or equal to zero and overlapping intervals are required.
// then add the ref seq to result.
if (minOverlap <= 0 && outputType == IntersectOutputType.OverlappingIntervals)
{
range = new SequenceRange(refRange.ID, refRange.Start, refRange.End);
CopyOfMetadata(range, refRange);
result.Add(range);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
}
continue;
}
ISequenceRange previousOverlappingRange = null;
foreach (ISequenceRange queryRange in overlappingQueryRanges)
{
if (outputType == IntersectOutputType.OverlappingPiecesOfIntervals)
{
// Add ref sequence only once for query ranges having same start and end.
if (previousOverlappingRange == null || (previousOverlappingRange.Start != queryRange.Start && previousOverlappingRange.End != queryRange.End))
{
range = new SequenceRange(
refRange.ID,
Math.Max(queryRange.Start, refRange.Start),
Math.Min(queryRange.End, refRange.End));
result.Add(range);
CopyOfMetadata(range, refRange);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
}
if (isParentSeqRangesRequired)
{
if (queryList.Contains(queryRange))
{
AddParent(range, queryRange);
}
else
{
if (queryRange.ParentSeqRanges.Count > 0)
{
AddParent(range, queryRange.ParentSeqRanges);
}
}
}
}
else
{
// Add ref sequence only once.
if (previousOverlappingRange == null)
{
range = new SequenceRange(refRange.ID, refRange.Start, refRange.End);
CopyOfMetadata(range, refRange);
result.Add(range);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
else
{
break;
}
}
if (isParentSeqRangesRequired)
{
if (queryList.Contains(queryRange))
{
AddParent(range, queryRange);
}
else
{
if (queryRange.ParentSeqRanges.Count > 0)
{
AddParent(range, queryRange.ParentSeqRanges);
}
}
}
}
previousOverlappingRange = queryRange;
}
}
}
}
return result;
}
/// <summary>
/// For each group in the grouping, this method traverses through each range
/// in the group and normalizes the ranges down to the minimal spanning set
/// required to still show the same range spans.
///
/// For instance if you had in group 'Chr1' the following ranges:
///
/// -> 10 to 100
/// -> 200 to 250
/// -> 35 to 45
/// -> 90 to 150
///
/// The result of MergeOverlaps would reduce the ranges in the 'Chr1' group to:
/// For minOverlap = 0
///
/// -> 10 to 150
/// -> 200 to 250
///
/// for minOverlap = -50
///
/// -> 10 to 250
///
/// Running this method creates all new ISequenceRange objects and adds them
/// to the newly created SequenceRangeGrouping returned here.
/// </summary>
/// <param name="minOverlap">Minmum length of bases pairs should be overlapped.</param>
/// <param name="isParentSeqRangesRequired">If this flag is set to true then the sequence ranges from
/// which the new sequence range is created are added to the ParentSeqRanges property of the
/// new sequence range.</param>
/// <returns>The overlapped sequence range grouping.</returns>
public SequenceRangeGrouping MergeOverlaps(long minOverlap = 0, bool isParentSeqRangesRequired = false)
{
SequenceRangeGrouping seqRangeGroup = new SequenceRangeGrouping();
List<ISequenceRange> sortedRanges = new List<ISequenceRange>();
foreach (List<ISequenceRange> rangeList in this.groups.Values)
{
sortedRanges.AddRange(rangeList);
sortedRanges.Sort();
while (sortedRanges.Count > 0)
{
ISequenceRange seqRange = new SequenceRange(sortedRanges[0].ID,
sortedRanges[0].Start,
sortedRanges[0].End);
if (isParentSeqRangesRequired)
{
AddParent(seqRange, sortedRanges[0]);
}
sortedRanges.RemoveAt(0);
seqRangeGroup.Add(seqRange);
if (sortedRanges.Count > 0)
{
while (sortedRanges.Count > 0 && (seqRange.End - sortedRanges[0].Start) >= minOverlap)
{
seqRange.End = Math.Max(seqRange.End, sortedRanges[0].End);
if (isParentSeqRangesRequired)
{
AddParent(seqRange, sortedRanges[0]);
}
sortedRanges.RemoveAt(0);
}
}
}
sortedRanges.Clear();
}
return seqRangeGroup;
}
/// <summary>
/// Subtracts the query SequenceRangeGrouping from this SequenceRangeGrouping.
///
/// For example,
///
/// Ranges in this instance Ranges in the query
/// 1 to 4 2 to 6
/// 4 to 8 3 to 6
/// 8 to 12 9 to 14
/// 25 to 35
///
/// Result for minOverlap set to 1
/// 1. If outputType is IntervalsWithNoOverlap
/// 25 to 35
///
/// 2. If outputType is NonOverlappingPiecesOfIntervals
/// 1 to 2
/// 6 to 8
/// 8 to 9
/// 25 to 35
///
/// Running this method creates all new ISequenceRange objects and adds them
/// to the newly created SequenceRangeGrouping returned here.
/// </summary>
/// <param name="query">Query grouping.</param>
/// <param name="minOverlap">Minmum length of overlap. By default this will be set to 1</param>
/// <param name="outputType">
/// Type of output required, IntervalsWithNoOverlap or NonOverlappingPiecesOfIntervals.
/// By default this will be set to NonOverlappingPiecesOfIntervals that is non overlapping
/// pieces of intervels along with non overlapping ranges from this instance
/// will be returned.
/// </param>
/// <param name="isParentSeqRangesRequired">If this flag is set to true then the sequence ranges from
/// which the new sequence range is created are added to the ParentSeqRanges property of the
/// new sequence range.</param>
/// <returns>The resultant Sequence range grouping.</returns>
public SequenceRangeGrouping Subtract(SequenceRangeGrouping query,
long minOverlap = 1,
SubtractOutputType outputType = SubtractOutputType.NonOverlappingPiecesOfIntervals,
bool isParentSeqRangesRequired = false)
{
if (query == null)
{
throw new ArgumentNullException("query");
}
SequenceRangeGrouping result = new SequenceRangeGrouping();
List <ISequenceRange> refSeqRanges = new List <ISequenceRange>();
List <ISequenceRange> querySeqRanges = new List <ISequenceRange>();
List <ISequenceRange> previousSeqRanges = new List <ISequenceRange>();
SequenceRange range = null;
// merge the query sequence ranges.
IList <ISequenceRange> queryList = null;
if (isParentSeqRangesRequired)
{
queryList = query.Flatten();
}
query = query.MergeOverlaps(0, isParentSeqRangesRequired);
foreach (string id in groups.Keys)
{
refSeqRanges.Clear();
querySeqRanges.Clear();
refSeqRanges.AddRange(groups[id]);
if (query.groups.ContainsKey(id))
{
querySeqRanges.AddRange(query.groups[id]);
querySeqRanges.Sort();
}
if (querySeqRanges.Count > 0)
{
foreach (ISequenceRange refRange in refSeqRanges)
{
previousSeqRanges.Clear();
IList <ISequenceRange> overlappingQueryRanges = GetOverlappingRenges(refRange,
querySeqRanges,
minOverlap);
if (overlappingQueryRanges == null || overlappingQueryRanges.Count == 0)
{
if (minOverlap > 0 || outputType == SubtractOutputType.NonOverlappingPiecesOfIntervals)
{
range = new SequenceRange(refRange.ID, refRange.Start, refRange.End);
CopyOfMetadata(range, refRange);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
result.Add(range);
}
continue;
}
// no need to proceed if only non overlapping intervels needed.
if (outputType == SubtractOutputType.IntervalsWithNoOverlap)
{
continue;
}
ISequenceRange previousOverlappingRange = null;
foreach (ISequenceRange queryRange in overlappingQueryRanges)
{
// in case of non overlapping pieces of intervals get the non overlapping
// ranges from reference sequence range.
if (refRange.Start < queryRange.Start)
{
if (previousSeqRanges.Count > 0 && previousSeqRanges[0].Start < queryRange.Start)
{
// if the previous overlapping range's start and end are equal then no need to change the metadataSeqRanges.
if (previousOverlappingRange == null || previousOverlappingRange.Start != queryRange.Start && previousOverlappingRange.End != queryRange.End)
{
for (int i = previousSeqRanges.Count - 1; i >= 0; i--)
{
if (previousSeqRanges[i].End > queryRange.Start)
{
previousSeqRanges[i].End = queryRange.Start;
}
else if (previousSeqRanges[i].End < queryRange.Start)
{
previousSeqRanges.RemoveAt(i);
}
}
}
if (isParentSeqRangesRequired)
{
if (queryList.Contains(queryRange))
{
AddParent(previousSeqRanges[0], queryRange);
}
else
{
if (queryRange.ParentSeqRanges.Count > 0)
{
AddParent(previousSeqRanges[0], queryRange.ParentSeqRanges);
}
}
}
}
else
{
if (previousOverlappingRange == null || previousOverlappingRange.Start != queryRange.Start && previousOverlappingRange.End != queryRange.End)
{
range = new SequenceRange(refRange.ID, refRange.Start, queryRange.Start);
result.Add(range);
CopyOfMetadata(range, refRange);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
}
if (isParentSeqRangesRequired)
{
if (queryList.Contains(queryRange))
{
AddParent(range, queryRange);
}
else
{
if (queryRange.ParentSeqRanges.Count > 0)
{
AddParent(range, queryRange.ParentSeqRanges);
}
}
}
}
}
if (queryRange.End < refRange.End)
{
if (previousOverlappingRange == null || previousOverlappingRange.Start != queryRange.Start && previousOverlappingRange.End != queryRange.End)
{
range = new SequenceRange(refRange.ID, queryRange.End, refRange.End);
CopyOfMetadata(range, refRange);
result.Add(range);
previousSeqRanges.Add(range);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
}
if (isParentSeqRangesRequired)
{
if (queryList.Contains(queryRange))
{
AddParent(range, queryRange);
}
else
{
if (queryRange.ParentSeqRanges.Count > 0)
{
AddParent(range, queryRange.ParentSeqRanges);
}
}
}
}
previousOverlappingRange = queryRange;
}
}
}
else
{
foreach (SequenceRange refRange in refSeqRanges)
{
range = new SequenceRange(refRange.ID, refRange.Start, refRange.End);
CopyOfMetadata(range, refRange);
result.Add(range);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
}
}
}
return(result);
}
/// <summary>
/// Returns overlapping sequence ranges from this and specified SequenceRangeGroup for each group in this grouping.
///
/// For instance if you had in group 'Chr1' the following ranges:
///
/// Ranges in this instance Ranges in the query
/// 0 to 10 20 to 40
/// 30 to 50 70 to 100
/// 60 to 80 400 to 800
/// 300 to 500 850 to 900
/// 600 to 700 900 to 1200
/// 800 to 1000
///
/// Result for minOverlap set to 1
/// 1. If outputType is OverlappingPiecesOfIntervals.
/// 30 to 40
/// 70 to 80
/// 400 to 500
/// 600 o 700
/// 850 to 900
/// 900 to 1000
/// 2. If outputType is OverlappingIntervals
/// 30 to 50
/// 60 to 80
/// 300 to 500
/// 600 to 700
/// 800 to 1000
///
/// Running this method creates all new ISequenceRange objects and adds them
/// to the newly created SequenceRangeGrouping returned here.
/// </summary>
/// <param name="query">Query grouping.</param>
/// <param name="minOverlap">Minmum length of bases pairs should be overlapped.
/// By default this will be set to 1.</param>
/// <param name="outputType">
/// Type of output required, OverlappingPiecesOfIntervals or OverlappingIntervals.
/// By default this will be set to OverlappingPiecesOfIntervals that is only the base pairs that overlaps with
/// query ranges will be returned.</param>
/// <param name="isParentSeqRangesRequired">If this flag is set to true then the sequence ranges from
/// which the new sequence range is created are added to the ParentSeqRanges property of the
/// new sequence ranges.</param>
/// <returns>The intersected result.</returns>
public SequenceRangeGrouping Intersect(SequenceRangeGrouping query, long minOverlap = 1, IntersectOutputType outputType = IntersectOutputType.OverlappingPiecesOfIntervals, bool isParentSeqRangesRequired = false)
{
if (query == null)
{
throw new ArgumentNullException("query");
}
SequenceRangeGrouping result = new SequenceRangeGrouping();
List <ISequenceRange> refSeqRanges = new List <ISequenceRange>();
List <ISequenceRange> querySeqRanges = new List <ISequenceRange>();
SequenceRange range = null;
// merge the query sequence ranges.
IList <ISequenceRange> queryList = null;
if (isParentSeqRangesRequired)
{
queryList = query.Flatten();
}
query = query.MergeOverlaps(0, isParentSeqRangesRequired);
foreach (string id in groups.Keys)
{
refSeqRanges.Clear();
querySeqRanges.Clear();
refSeqRanges.AddRange(groups[id]);
if (query.groups.ContainsKey(id))
{
querySeqRanges.AddRange(query.groups[id]);
querySeqRanges.Sort();
}
if (querySeqRanges.Count > 0)
{
foreach (ISequenceRange refRange in refSeqRanges)
{
IList <ISequenceRange> overlappingQueryRanges = GetOverlappingRenges(refRange, querySeqRanges, minOverlap);
if (overlappingQueryRanges == null || overlappingQueryRanges.Count == 0)
{
// If the minOverlap is lessthan or equal to zero and overlapping intervals are required.
// then add the ref seq to result.
if (minOverlap <= 0 && outputType == IntersectOutputType.OverlappingIntervals)
{
range = new SequenceRange(refRange.ID, refRange.Start, refRange.End);
CopyOfMetadata(range, refRange);
result.Add(range);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
}
continue;
}
ISequenceRange previousOverlappingRange = null;
foreach (ISequenceRange queryRange in overlappingQueryRanges)
{
if (outputType == IntersectOutputType.OverlappingPiecesOfIntervals)
{
// Add ref sequence only once for query ranges having same start and end.
if (previousOverlappingRange == null || (previousOverlappingRange.Start != queryRange.Start && previousOverlappingRange.End != queryRange.End))
{
range = new SequenceRange(
refRange.ID,
Math.Max(queryRange.Start, refRange.Start),
Math.Min(queryRange.End, refRange.End));
result.Add(range);
CopyOfMetadata(range, refRange);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
}
if (isParentSeqRangesRequired)
{
if (queryList.Contains(queryRange))
{
AddParent(range, queryRange);
}
else
{
if (queryRange.ParentSeqRanges.Count > 0)
{
AddParent(range, queryRange.ParentSeqRanges);
}
}
}
}
else
{
// Add ref sequence only once.
if (previousOverlappingRange == null)
{
range = new SequenceRange(refRange.ID, refRange.Start, refRange.End);
CopyOfMetadata(range, refRange);
result.Add(range);
if (isParentSeqRangesRequired)
{
AddParent(range, refRange);
}
else
{
break;
}
}
if (isParentSeqRangesRequired)
{
if (queryList.Contains(queryRange))
{
AddParent(range, queryRange);
}
else
{
if (queryRange.ParentSeqRanges.Count > 0)
{
AddParent(range, queryRange.ParentSeqRanges);
}
}
}
}
previousOverlappingRange = queryRange;
}
}
}
}
return(result);
}
/// <summary>
/// Indentify hot spot chromosomes for length anamoly regions.
/// </summary>
/// <param name="inputFile"> Input file</param>
/// <param name="mean">Mean value</param>
/// <param name="standardDeviation">Standard deviation</param>
private void IdentifyLentghAnamolies(string filename,
float mean = -1, float deviation = -1)
{
bool calculateMeanNdeviation = false;
if (mean == -1 || deviation == -1)
{
calculateMeanNdeviation = true;
}
SequenceAlignmentMap alignmentMapobj = null;
if (!SAMInput)
{
BAMParser bamParser = new BAMParser();
alignmentMapobj = bamParser.ParseOne<SequenceAlignmentMap>(filename);
}
else
{
SAMParser samParser = new SAMParser();
alignmentMapobj = samParser.ParseOne<SequenceAlignmentMap>(filename);
}
// get reads from sequence alignment map object.
IList<PairedRead> pairedReads = null;
if (calculateMeanNdeviation)
{
pairedReads = alignmentMapobj.GetPairedReads();
}
else
{
pairedReads = alignmentMapobj.GetPairedReads(mean, deviation);
}
// Get the orphan regions.
var orphans = pairedReads.Where(PR => PR.PairedType == PairedReadType.Orphan);
if (orphans.Count() == 0)
{
Console.WriteLine("No Orphans to display");
}
List<ISequenceRange> orphanRegions = new List<ISequenceRange>(orphans.Count());
foreach (PairedRead orphanRead in orphans)
{
orphanRegions.Add(GetRegion(orphanRead.Read1));
}
// Get sequence range grouping for Orphan regions.
SequenceRangeGrouping orphanRangegroup = new SequenceRangeGrouping(orphanRegions);
// Get the Length anomalies regions.
var lengthAnomalies = pairedReads.Where(PE => PE.PairedType == PairedReadType.LengthAnomaly);
if (lengthAnomalies.Count() == 0)
{
Console.WriteLine("No Anomalies to display");
}
List<ISequenceRange> lengthAnomalyRegions = new List<ISequenceRange>(lengthAnomalies.Count());
foreach (PairedRead laRead in lengthAnomalies)
{
SequenceRange range = new SequenceRange();
range.ID = laRead.Read1.RName;
range.Start = laRead.Read1.Pos;
range.End = laRead.Read1.Pos + laRead.InsertLength;
lengthAnomalyRegions.Add(range);
}
// Get sequence range grouping for length anomaly regions.
SequenceRangeGrouping lengthAnomalyRangegroup =
new SequenceRangeGrouping(lengthAnomalyRegions);
if (lengthAnomalyRangegroup.GroupIDs.Count() == 0)
{
Console.Write("\r\nNo Length anomalies reads to display");
}
else
{
Console.Write("Region of length anomaly:");
DisplaySequenceRange(lengthAnomalyRangegroup);
}
if (orphanRangegroup.GroupIDs.Count() == 0)
{
Console.Write("\r\nNo Orphan reads to display");
}
else
{
Console.Write("\r\nRegion of Orphan reads:");
DisplaySequenceRange(orphanRangegroup);
}
SequenceRangeGrouping intersectedRegions =
lengthAnomalyRangegroup.Intersect(orphanRangegroup);
if (intersectedRegions.GroupIDs.Count() == 0)
{
Console.Write("\r\nNo Hot spots found");
}
else
{
Console.Write("\r\nChromosomal Hot spot of length anomaly and Orphan region:");
DisplaySequenceRange(intersectedRegions);
}
}
