/// <summary>
/// Validate BED Operations(Merge,Intersect)..
/// </summary>
/// <param name="nodeName">Xml Node name for different inputs.</param>
/// <param name="operationPam">Different Bed operations.</param>
/// <param name="overlappingBasePair">overlapping base pair</param>
/// <param name="IsParentSeqRangeRequired">Is Parent Sequence Range required?</param>
void ValidateBedOperations(string nodeName,
BedOperationsParameters operationPam,
bool overlappingBasePair, bool IsParentSeqRangeRequired)
{
// Get values from xml.
string expectedRangeIDs = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStartIndex = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEndIndex = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string referenceFilePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string queryFilePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QueryFilePath);
string minimalOverlap = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.OverlapValue);
string rangeID = string.Empty;
bool result = false;
List <ISequenceRange> rangeList = null;
SequenceRangeGrouping operationResult = null;
// Parse a BED file.
BedParser parserObj = new BedParser();
SequenceRangeGrouping referenceGroup = parserObj.ParseRangeGrouping(referenceFilePath);
SequenceRangeGrouping queryGroup = parserObj.ParseRangeGrouping(queryFilePath);
IntersectOutputType intersectOutputType = IntersectOutputType.OverlappingIntervals;
if (overlappingBasePair)
{
intersectOutputType = IntersectOutputType.OverlappingPiecesOfIntervals;
}
SubtractOutputType subtractOutputType = SubtractOutputType.NonOverlappingPiecesOfIntervals;
if (overlappingBasePair)
{
subtractOutputType = SubtractOutputType.IntervalsWithNoOverlap;
}
switch (operationPam)
{
case BedOperationsParameters.Merge:
operationResult = referenceGroup.MergeOverlaps();
break;
case BedOperationsParameters.MergeWithPam:
operationResult = referenceGroup.MergeOverlaps(queryGroup,
0, IsParentSeqRangeRequired);
break;
case BedOperationsParameters.Intersect:
operationResult = referenceGroup.Intersect(queryGroup,
long.Parse(minimalOverlap, (IFormatProvider)null), intersectOutputType, IsParentSeqRangeRequired);
break;
case BedOperationsParameters.MergeQueryWithReference:
operationResult = queryGroup.MergeOverlaps(referenceGroup,
0, IsParentSeqRangeRequired);
break;
case BedOperationsParameters.Subtract:
operationResult = referenceGroup.Subtract(queryGroup,
long.Parse(minimalOverlap, (IFormatProvider)null), subtractOutputType, IsParentSeqRangeRequired);
break;
default:
break;
}
// Get a result SequenceGroup Id.
IEnumerable <string> groupId = operationResult.GroupIDs;
string[] expectedRangeIdsArray = expectedRangeIDs.Split(',');
string[] expectedStartIndexArray = expectedStartIndex.Split(',');
string[] expectedEndIndexArray = expectedEndIndex.Split(',');
int i = 0;
foreach (string grpID in groupId)
{
rangeID = grpID;
rangeList = operationResult.GetGroup(rangeID);
// Validate result sequence range.
foreach (ISequenceRange range in rangeList)
{
Assert.AreEqual(expectedRangeIdsArray[i], range.ID);
Assert.AreEqual(expectedStartIndexArray[i], range.Start.ToString((IFormatProvider)null));
Assert.AreEqual(expectedEndIndexArray[i], range.End.ToString((IFormatProvider)null));
i++;
}
}
// Validate ParentSeqRange.
result = ValidateParentSeqRange(operationResult, referenceGroup,
queryGroup, IsParentSeqRangeRequired);
Assert.IsTrue(result);
ApplicationLog.WriteLine(
"Bed Operations BVT: Successfully validated the BED SequenceID, Start and End Ranges");
}
/// <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>
/// 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>
public SequenceRangeGrouping Subtract(SequenceRangeGrouping query,
long minOverlap = 1,
SubtractOutputType outputType = SubtractOutputType.NonOverlappingPiecesOfIntervals,
bool isParentSeqRangesRequired = false)
{
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>
/// Validate Subtract SequenceRangeGrouping.
/// </summary>
/// <param name="nodeName">Xml Node name for different inputs.</param>
/// <param name="overlappingBasePair">Value of overlappingBasePair</param>
/// <param name="IsParentSeqRangesRequired">Is Parent Sequence Range required?</param>
void SubtractSequenceRange(string nodeName,
bool overlappingBasePair, bool IsParentSeqRangeRequired)
{
// Get values from xml.
string[] expectedRangeIDs = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.IDNode).Split(',');
string[] expectedStartIndex = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.StartNode).Split(',');
string[] expectedEndIndex = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.EndNode).Split(',');
string referenceFilePath = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string queryFilePath = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.QueryFilePath);
string minimalOverlap = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.OverlapValue);
string rangeID = string.Empty;
bool result = false;
List <ISequenceRange> rangeList = null;
// Parse a BED file.
BedParser parserObj = new BedParser();
SequenceRangeGrouping referenceGroup = parserObj.ParseRangeGrouping(referenceFilePath);
SequenceRangeGrouping queryGroup = parserObj.ParseRangeGrouping(queryFilePath);
SubtractOutputType subtractOutputType = SubtractOutputType.NonOverlappingPiecesOfIntervals;
if (overlappingBasePair)
{
subtractOutputType = SubtractOutputType.IntervalsWithNoOverlap;
}
// Subtract a SequenceRangeGroup.
SequenceRangeGrouping subtractGroup = referenceGroup.Subtract(queryGroup,
long.Parse(minimalOverlap, (IFormatProvider)null), subtractOutputType, IsParentSeqRangeRequired);
// Get a intersect SequenceGroup Id.
IEnumerable <string> groupIds = subtractGroup.GroupIDs;
int j = 0;
foreach (string grpID in groupIds)
{
rangeID = grpID;
rangeList = subtractGroup.GetGroup(rangeID);
// Validate intersect sequence range.
foreach (ISequenceRange range in rangeList)
{
Assert.AreEqual(expectedStartIndex[j], range.Start.ToString((IFormatProvider)null));
Assert.AreEqual(expectedEndIndex[j], range.End.ToString((IFormatProvider)null));
Assert.AreEqual(expectedRangeIDs[j], range.ID.ToString((IFormatProvider)null));
j++;
}
}
// Validate ParentSeqRanges.
result = ValidateParentSeqRange(
subtractGroup, referenceGroup, queryGroup, IsParentSeqRangeRequired);
Assert.IsTrue(result);
ApplicationLog.WriteLine(
"Bed Parser BVT: Successfully validated the subtract SequeID, Start and End Ranges");
Console.WriteLine(string.Format((IFormatProvider)null,
"Bed Parser BVT: Successfully validated the subtracted SequeID, Start and End Ranges"));
}
