/// <summary>
/// Compare two sequence ranges.
/// </summary>
/// <param name="nodeName">Xml Node name for different inputs.</param>
static void ValidateCompareTwoSequenceRanges(string nodeName)
{
// Get values from xml.
string expectedRangeID = Utility._xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStartIndex = Utility._xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEndIndex = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string expectedRangeID1 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.IDNode1);
string expectedStartIndex1 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.StartNode1);
string expectedEndIndex1 = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EndNode1);
string expectedResults = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ComparisonResult);
// Create first SequenceRange.
SequenceRange seqRange = new SequenceRange(expectedRangeID,
long.Parse(expectedStartIndex), long.Parse(expectedEndIndex));
// Create second SequenceRange.
SequenceRange secondSeqRange = new SequenceRange(expectedRangeID1,
long.Parse(expectedStartIndex1), long.Parse(expectedEndIndex1));
// Compare two SequenceRanges which are identical.
int result = seqRange.CompareTo(secondSeqRange);
// Validate result of comparison.
Assert.AreEqual(Convert.ToInt32(expectedResults), result);
Console.WriteLine("SequenceRange P1 : Successfully validated the SequenceRange comparison");
}
public void From_first_to_accepts_upper_bound_and_uses_first_as_lower()
{
var r = SequenceRange.FirstTo(Sequence.First.Add(2));
r.Lower.Should().Be(Sequence.First);
r.Upper.Should().Be(Sequence.First.Add(2));
}
public void Range_can_represent_a_sequence_of_one_item()
{
var r = SequenceRange.From(Sequence.First, Sequence.First);
r.Lower.Should().Be(Sequence.First);
r.Upper.Should().Be(Sequence.First);
}
protected object GenerateId(string sequenceName, Type idType, SqlConnection connection)
{
lock (Locker)
{
SequenceRange range;
if (!IdGenerator.TryGetValue(sequenceName, out range))
{
range = new SequenceRange {
AutoRestart = _autoRestart, RangeSize = _rangeSize
};
IdGenerator.Add(sequenceName, range);
}
if (range.Current == -1)
{
ReserveRange(sequenceName, _rangeSize, connection, range);
}
if (range.IsExhausted)
{
range.Current = 0;
ReserveRange(sequenceName, _rangeSize, connection, range);
}
range.Current += range.Increment;
return(Convert.ChangeType(range.Current, idType));
}
}
public void ValidateSequenceRangeToString()
{
var range = new SequenceRange("chr20", 0, 3);
string actualString = range.ToString();
Assert.AreEqual("ID=chr20 Start=0 End=3", actualString);
}
public void ValidateCompareTwoSequenceRanges()
{
// Get values from xml.
string expectedRangeID = utilityObj.xmlUtil.GetTextValue(
Constants.SequenceRangeNode, Constants.IDNode);
string expectedStartIndex = utilityObj.xmlUtil.GetTextValue(
Constants.SequenceRangeNode, Constants.StartNode);
string expectedEndIndex = utilityObj.xmlUtil.GetTextValue(
Constants.SequenceRangeNode, Constants.EndNode);
string expectedRangeID1 = utilityObj.xmlUtil.GetTextValue(
Constants.SequenceRangeNode, Constants.IDNode1);
string expectedStartIndex1 = utilityObj.xmlUtil.GetTextValue(
Constants.SequenceRangeNode, Constants.StartNode1);
string expectedEndIndex1 = utilityObj.xmlUtil.GetTextValue(
Constants.SequenceRangeNode, Constants.EndNode1);
// Create first SequenceRange.
SequenceRange seqRange = new SequenceRange(expectedRangeID,
long.Parse(expectedStartIndex, (IFormatProvider)null), long.Parse(expectedEndIndex, (IFormatProvider)null));
// Create second SequenceRange.
SequenceRange secondSeqRange = new SequenceRange(expectedRangeID1,
long.Parse(expectedStartIndex1, (IFormatProvider)null), long.Parse(expectedEndIndex1, (IFormatProvider)null));
// Compare two SequenceRanges which are identical.
int result = seqRange.CompareTo(secondSeqRange);
// Validate result of comparison.
Assert.AreEqual(0, result);
Console.WriteLine(
"SequenceRange BVT : Successfully validated the SequenceRange comparison");
}
/// <summary>
/// Create a SequenceRangeGrouping by passing RangeID,Start and End Index.
/// and validate created SequenceRange.
/// </summary>
/// <param name="nodeName">Xml Node name for different inputs.</param>
static void CreateSequenceRangeGrouping(string nodeName)
{
// Get values from xml.
string expectedRangeIDs = Utility._xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStartIndex = Utility._xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEndIndex = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string expectedSequenceRangeCount = Utility._xmlUtil.GetTextValue(
nodeName, Constants.SequenceRangeCountNode);
string actualRangeStarts = string.Empty;
string actualRangeEnds = string.Empty;
string actualRangeIDs = string.Empty;
string[] rangeIDs = expectedRangeIDs.Split(',');
string[] rangeStarts = expectedStartIndex.Split(',');
string[] rangeEnds = expectedEndIndex.Split(',');
SequenceRangeGrouping seqRangeGrouping = new SequenceRangeGrouping();
List <ISequenceRange> rangeList = null;
// Create a SequenceRange and add to SequenceRangeList.
for (int i = 0; i < rangeIDs.Length; i++)
{
SequenceRange seqRange = new SequenceRange(rangeIDs[i],
long.Parse(rangeStarts[i]), long.Parse(rangeEnds[i]));
seqRangeGrouping.Add(seqRange);
}
IEnumerable <string> rangeGroupIds = seqRangeGrouping.GroupIDs;
string rangeID = string.Empty;
foreach (string groupID in rangeGroupIds)
{
rangeID = groupID;
// Get SequenceRangeIds.
rangeList = seqRangeGrouping.GetGroup(rangeID);
// Validate created SequenceRanges.
foreach (ISequenceRange seqRange in rangeList)
{
actualRangeIDs = string.Concat(actualRangeIDs, seqRange.ID.ToString(), ",");
actualRangeStarts = string.Concat(actualRangeStarts, seqRange.Start.ToString(), ",");
actualRangeEnds = string.Concat(actualRangeEnds, seqRange.End.ToString(), ",");
}
}
Assert.AreEqual(expectedSequenceRangeCount, rangeList.Count.ToString());
Assert.AreEqual(expectedRangeIDs,
actualRangeIDs.Substring(0, actualRangeIDs.Length - 1));
Assert.AreEqual(expectedStartIndex,
actualRangeStarts.Substring(0,
actualRangeStarts.Length - 1));
Assert.AreEqual(expectedEndIndex,
actualRangeEnds.Substring(0, actualRangeEnds.Length - 1));
Console.WriteLine(
"SequenceRange BVT : Successfully validated the SequenceStart, SequenceID and SequenceEnd.");
}
public bool EvaluateRange(SequenceRange range)
{
bool result = SequenceStates.Any(s => s.Name == range.Name &&
s.Counter >= range.MinCounter &&
s.Counter <= range.MaxCounter);
return(result);
}
public void TestSequenceRangeToString()
{
SequenceRange range = new SequenceRange("chr20", 0, 3);
string actualString = range.ToString();
string expectedString = "ID=chr20 Start=0 End=3";
Assert.AreEqual(actualString, expectedString);
}
public void Can_determine_if_sequence_is_in_range()
{
var r = SequenceRange.From(Sequence.First, Sequence.First.Add(2));
r.Includes(Sequence.First).Should().BeTrue();
r.Includes(Sequence.First.Add(1)).Should().BeTrue();
r.Includes(Sequence.First.Add(2)).Should().BeTrue();
r.Includes(Sequence.First.Add(3)).Should().BeFalse();
}
public void Range_can_represent_a_sequence_of_many_items()
{
var lower = Sequence.First;
var upper = lower.Add(10);
var r = SequenceRange.From(lower, upper);
r.Lower.Should().Be(lower);
r.Upper.Should().Be(upper);
}
// Gets ref seq index.
private int GetRefSeqID(string refSeqName)
{
SequenceRange range = _refSequences.FirstOrDefault(SR => string.Compare(SR.ID, refSeqName, StringComparison.OrdinalIgnoreCase) == 0);
if (range == null)
{
return(-1);
}
return(_refSequences.IndexOf(range));
}
public void TestSequenceRangeGroupingToString()
{
ISequenceRange range1 = new SequenceRange("chr20", 0, 3);
ISequenceRange range2 = new SequenceRange("chr21", 0, 4);
IList <ISequenceRange> ranges = new List <ISequenceRange>();
ranges.Add(range1);
ranges.Add(range2);
SequenceRangeGrouping rangegrouping = new SequenceRangeGrouping(ranges);
string actualString = rangegrouping.ToString();
string expectedString = "ID=chr20 Start=0 End=3\r\nID=chr21 Start=0 End=4\r\n".Replace("\r\n", Environment.NewLine);
Assert.AreEqual(actualString, expectedString);
}
public void ValidateSequenceRangeGroupingToString()
{
ISequenceRange range1 = new SequenceRange("chr20", 0, 3);
ISequenceRange range2 = new SequenceRange("chr21", 0, 4);
IList <ISequenceRange> ranges = new List <ISequenceRange>();
ranges.Add(range1);
ranges.Add(range2);
var rangegrouping = new SequenceRangeGrouping(ranges);
string actualString = rangegrouping.ToString();
string expectedStr = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.SequenceRangeGroupingExpectedNode);
Assert.AreEqual(expectedStr.Replace("\\r\\n", ""), actualString.Replace(System.Environment.NewLine, ""));
}
public void ValidateSequenceRange()
{
// Get values from xml.
string expectedRangeId = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.IDNode);
string expectedStartIndex = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.StartNode);
string expectedEndIndex = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.EndNode);
// Create a SequenceRange.
var seqRange = new SequenceRange(expectedRangeId,
long.Parse(expectedStartIndex, null), long.Parse(expectedEndIndex, null));
// Validate created SequenceRange.
Assert.AreEqual(expectedRangeId, seqRange.ID.ToString(null));
Assert.AreEqual(expectedStartIndex, seqRange.Start.ToString((IFormatProvider)null));
Assert.AreEqual(expectedEndIndex, seqRange.End.ToString((IFormatProvider)null));
ApplicationLog.WriteLine("SequenceRange BVT : Successfully validated the SequenceStart,SequenceID and SequenceEnd.");
}
public void ValidateFlatten()
{
// Get values from xml.
string expectedRangeIDs = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.IDNode);
string expectedStartIndex = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.StartNode);
string expectedEndIndex = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.EndNode);
string expectedSequenceRangeCount = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.SequenceRangeCountNode);
string[] rangeIDs = expectedRangeIDs.Split(',');
string[] rangeStarts = expectedStartIndex.Split(',');
string[] rangeEnds = expectedEndIndex.Split(',');
SequenceRangeGrouping seqRangeGrouping = new SequenceRangeGrouping();
List <ISequenceRange> rangeList = null;
// Create a SequenceRange and add to SequenceRangeList.
for (int i = 0; i < rangeIDs.Length; i++)
{
SequenceRange seqRange = new SequenceRange(rangeIDs[i],
long.Parse(rangeStarts[i], (IFormatProvider)null),
long.Parse(rangeEnds[i], (IFormatProvider)null));
seqRangeGrouping.Add(seqRange);
}
//Convert SequenceRangeGroup to SequenceRangeList.
rangeList = seqRangeGrouping.Flatten();
int j = 0;
// Validate created SequenceRanges.
foreach (ISequenceRange seqRange in rangeList)
{
Assert.AreEqual(rangeStarts[j], seqRange.Start.ToString((IFormatProvider)null));
Assert.AreEqual(rangeEnds[j], seqRange.End.ToString((IFormatProvider)null));
Assert.AreEqual(rangeIDs[j], seqRange.ID.ToString((IFormatProvider)null));
j++;
}
Assert.AreEqual(expectedSequenceRangeCount, rangeList.Count.ToString((IFormatProvider)null));
Console.WriteLine(
"SequenceRange BVT : Successfully validated the SequenceStart,SequenceID and SequenceEnd.");
}
public void ValidateSequenceRange()
{
// Get values from xml.
string expectedRangeId = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.IDNode);
string expectedStartIndex = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.StartNode);
string expectedEndIndex = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.EndNode);
// Create a SequenceRange.
var seqRange = new SequenceRange(expectedRangeId,
long.Parse(expectedStartIndex, null), long.Parse(expectedEndIndex, null));
// Validate created SequenceRange.
Assert.AreEqual(expectedRangeId, seqRange.ID.ToString(null));
Assert.AreEqual(expectedStartIndex, seqRange.Start.ToString((IFormatProvider) null));
Assert.AreEqual(expectedEndIndex, seqRange.End.ToString((IFormatProvider) null));
ApplicationLog.WriteLine("SequenceRange BVT : Successfully validated the SequenceStart,SequenceID and SequenceEnd.");
}
/// <summary>
/// 生成下一个序列号
/// </summary>
public long NextValue()
{
// 当前区间不存在，重新获取一个区间
if (null == _currentRange)
{
lock (_lock)
{
if (null == _currentRange)
{
_currentRange = _sequenceRangeManager.NextRange(_name);
}
}
}
// 当value值为-1时，表明区间的序列号已经分配完，需要冲洗那获取区间
long value = _currentRange.GetAndIncrement();
if (value == -1)
{
lock (_lock)
{
for (; ;)
{
if (_currentRange.Over)
{
_currentRange = _sequenceRangeManager.NextRange(_name);
}
value = _currentRange.GetAndIncrement();
if (value == -1)
{
continue;
}
break;
}
}
}
if (value < 0)
{
throw new ArgumentException($"序列值溢出。value = {value}");
}
return(value);
}
public void Supports_value_equality()
{
const int lower = 5;
const int upper = 10;
var r = SequenceRange.From(Sequence.First.Add(lower), Sequence.First.Add(upper));
var same = SequenceRange.From(Sequence.First.Add(lower), Sequence.First.Add(upper));
var toHighUpper = SequenceRange.From(Sequence.First, Sequence.First.Add(upper + 1));
var toHighLower = SequenceRange.From(Sequence.First.Add(lower + 1), Sequence.First.Add(upper));
var toLowLower = SequenceRange.From(Sequence.First.Add(lower - 1), Sequence.First.Add(upper));
var toLowUpper = SequenceRange.From(Sequence.First.Add(lower - 1), Sequence.First.Add(upper));
bool Compare(SequenceRange s) => r == s;
Compare(same).Should().BeTrue();
Compare(toHighLower).Should().BeFalse();
Compare(toHighUpper).Should().BeFalse();
Compare(toLowLower).Should().BeFalse();
Compare(toLowUpper).Should().BeFalse();
}
internal override void WriteTo(XmlWriter writer)
{
base.WriteTo(writer);
writer.WriteStartElement("Ranges");
for (int i = 0; i < this.ranges.Count; i++)
{
writer.WriteStartElement("Range");
SequenceRange range = this.ranges[i];
writer.WriteAttributeString("Lower", range.Lower.ToString(CultureInfo.InvariantCulture));
SequenceRange range2 = this.ranges[i];
writer.WriteAttributeString("Upper", range2.Upper.ToString(CultureInfo.InvariantCulture));
writer.WriteEndElement();
}
writer.WriteEndElement();
if (this.bufferRemaining != -1)
{
writer.WriteStartElement("BufferRemaining");
writer.WriteString(this.bufferRemaining.ToString(CultureInfo.InvariantCulture));
writer.WriteEndElement();
}
}
public void ValidateSequenceRange()
{
// Get values from xml.
string expectedRangeID = Utility._xmlUtil.GetTextValue(
Constants.SequenceRangeNode, Constants.IDNode);
string expectedStartIndex = Utility._xmlUtil.GetTextValue(
Constants.SequenceRangeNode, Constants.StartNode);
string expectedEndIndex = Utility._xmlUtil.GetTextValue(
Constants.SequenceRangeNode, Constants.EndNode);
// Create a SequenceRange.
SequenceRange seqRange = new SequenceRange(expectedRangeID,
long.Parse(expectedStartIndex), long.Parse(expectedEndIndex));
// Validate created SequenceRange.
Assert.AreEqual(expectedRangeID, seqRange.ID.ToString());
Assert.AreEqual(expectedStartIndex, seqRange.Start.ToString());
Assert.AreEqual(expectedEndIndex, seqRange.End.ToString());
Console.WriteLine(
"SequenceRange BVT : Successfully validated the SequenceStart,SequenceID and SequenceEnd.");
}
/// <summary>
/// Returns list of SequenceRanges objects which represents reference sequences present in this header.
/// </summary>
public IList <SequenceRange> GetReferenceSequenceRanges()
{
List <SequenceRange> ranges = new List <SequenceRange>();
List <SAMRecordField> fields = RecordFields.Where(R => String.Compare(R.Typecode, "SQ", StringComparison.OrdinalIgnoreCase) == 0).ToList();
foreach (SAMRecordField field in fields)
{
SAMRecordFieldTag tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "SN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null)
{
string refName = tag.Value;
long length;
tag = field.Tags.FirstOrDefault(F => String.Compare(F.Tag, "LN", StringComparison.OrdinalIgnoreCase) == 0);
if (tag != null && long.TryParse(tag.Value, out length))
{
SequenceRange range = new SequenceRange(refName, 0, length);
ranges.Add(range);
}
}
}
return(ranges.OrderBy(S => S.ID).ToList());
}
public void ValidateCompareTwoSequenceRanges()
{
// Get values from xml.
string expectedRangeId = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.IDNode);
string expectedStartIndex = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.StartNode);
string expectedEndIndex = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.EndNode);
string expectedRangeId1 = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.IDNode1);
string expectedStartIndex1 = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.StartNode1);
string expectedEndIndex1 = this.utilityObj.xmlUtil.GetTextValue(Constants.SequenceRangeNode, Constants.EndNode1);
// Create first SequenceRange.
var seqRange = new SequenceRange(expectedRangeId, long.Parse(expectedStartIndex, null), long.Parse(expectedEndIndex, null));
// Create second SequenceRange.
var secondSeqRange = new SequenceRange(expectedRangeId1, long.Parse(expectedStartIndex1, null), long.Parse(expectedEndIndex1, null));
// Compare two SequenceRanges which are identical.
int result = seqRange.CompareTo(secondSeqRange);
// Validate result of comparison.
Assert.AreEqual(0, result);
ApplicationLog.WriteLine("SequenceRange BVT : Successfully validated the SequenceRange comparison");
}
/// <summary>
/// Compare two sequence ranges.
/// </summary>
/// <param name="nodeName">Xml Node name for different inputs.</param>
private void ValidateCompareTwoSequenceRanges(string nodeName)
{
// Get values from xml.
string expectedRangeId = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.IDNode);
string expectedStartIndex = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.StartNode);
string expectedEndIndex = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.EndNode);
string expectedRangeId1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.IDNode1);
string expectedStartIndex1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.StartNode1);
string expectedEndIndex1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.EndNode1);
string expectedResults = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ComparisonResult);
// Create first SequenceRange.
var seqRange = new SequenceRange(expectedRangeId, long.Parse(expectedStartIndex, null), long.Parse(expectedEndIndex, null));
// Create second SequenceRange.
var secondSeqRange = new SequenceRange(expectedRangeId1, long.Parse(expectedStartIndex1, null), long.Parse(expectedEndIndex1, null));
// Compare two SequenceRanges which are identical.
int result = seqRange.CompareTo(secondSeqRange);
// Validate result of comparison.
Assert.AreEqual(Convert.ToInt32(expectedResults, null), result);
ApplicationLog.WriteLine("SequenceRange P1 : Successfully validated the SequenceRange comparison");
}
/// <summary>
/// Formats the Range/RangeGroup for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
private void FormatterGeneralTestCases(string nodeName,
AdditionalParameters addParam)
{
IList <ISequenceRange> rangeList = new List <ISequenceRange>();
var rangeGroup = new SequenceRangeGrouping();
// Gets the file name.
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode).TestDir();
// Condition to check if Parse() happens before Format()
switch (addParam)
{
case AdditionalParameters.ParseRangeGroup:
var initialParserGroupObj = new BedParser();
rangeGroup =
initialParserGroupObj.ParseRangeGrouping(filePath);
break;
case AdditionalParameters.ParseRange:
var initialParserObj = new BedParser();
rangeList = initialParserObj.ParseRange(filePath);
break;
default:
// Gets all the expected values from xml.
string expectedID = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEnd = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string[] expectedIDs = expectedID.Split(',');
string[] expectedStarts = expectedStart.Split(',');
string[] expectedEnds = expectedEnd.Split(',');
// Gets the Range Group or Range based on the additional parameter
switch (addParam)
{
case AdditionalParameters.RangeGroupTextWriter:
case AdditionalParameters.RangeGroupFileName:
for (int i = 0; i < expectedIDs.Length; i++)
{
var rangeObj1 = new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], null),
long.Parse(expectedEnds[i], null));
rangeGroup.Add(rangeObj1);
}
break;
default:
for (int i = 0; i < expectedIDs.Length; i++)
{
var rangeObj2 = new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], null),
long.Parse(expectedEnds[i], null));
rangeList.Add(rangeObj2);
}
break;
}
break;
}
var formatterObj = new BedFormatter();
// Gets the Range list/Range Group based on the parameters.
switch (addParam)
{
case AdditionalParameters.RangeFileName:
case AdditionalParameters.ParseRange:
formatterObj.Format(rangeList, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeTextWriter:
using (var txtWriter =
File.Create(Constants.BedTempFileName))
{
formatterObj.Format(txtWriter, rangeList);
}
break;
case AdditionalParameters.RangeGroupFileName:
case AdditionalParameters.ParseRangeGroup:
formatterObj.Format(rangeGroup, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeGroupTextWriter:
using (var txtWriter =
File.Create(Constants.BedTempFileName))
{
formatterObj.Format(txtWriter, rangeGroup);
}
break;
default:
break;
}
// Reparse to validate the results
var parserObj = new BedParser();
IList <ISequenceRange> newRangeList =
parserObj.ParseRange(Constants.BedTempFileName);
// Validation of all the properties.
for (int i = 0; i < rangeList.Count; i++)
{
Assert.AreEqual(rangeList[i].ID, newRangeList[i].ID);
Assert.AreEqual(rangeList[i].Start, newRangeList[i].Start);
Assert.AreEqual(rangeList[i].End, newRangeList[i].End);
// Validation of all metadata information.
if (rangeList[i].Metadata.Count > 0)
{
if (rangeList[i].Metadata.ContainsKey("Name"))
{
Assert.AreEqual(rangeList[i].Metadata["Name"],
newRangeList[i].Metadata["Name"]);
}
if (rangeList[i].Metadata.ContainsKey("Score"))
{
Assert.AreEqual(rangeList[i].Metadata["Score"],
newRangeList[i].Metadata["Score"]);
}
if (rangeList[i].Metadata.ContainsKey("Strand"))
{
Assert.AreEqual(rangeList[i].Metadata["Strand"],
newRangeList[i].Metadata["Strand"]);
}
if (rangeList[i].Metadata.ContainsKey("ThickStart"))
{
Assert.AreEqual(rangeList[i].Metadata["ThickStart"],
newRangeList[i].Metadata["ThickStart"]);
}
if (rangeList[i].Metadata.ContainsKey("ThickEnd"))
{
Assert.AreEqual(rangeList[i].Metadata["ThickEnd"],
newRangeList[i].Metadata["ThickEnd"]);
}
if (rangeList[i].Metadata.ContainsKey("ItemRGB"))
{
Assert.AreEqual(rangeList[i].Metadata["ItemRGB"],
newRangeList[i].Metadata["ItemRGB"]);
}
if (rangeList[i].Metadata.ContainsKey("BlockCount"))
{
Assert.AreEqual(rangeList[i].Metadata["BlockCount"],
newRangeList[i].Metadata["BlockCount"]);
}
if (rangeList[i].Metadata.ContainsKey("BlockSizes"))
{
Assert.AreEqual(rangeList[i].Metadata["BlockSizes"],
newRangeList[i].Metadata["BlockSizes"]);
}
if (rangeList[i].Metadata.ContainsKey("BlockStarts"))
{
Assert.AreEqual(rangeList[i].Metadata["BlockStarts"],
newRangeList[i].Metadata["BlockStarts"]);
}
ApplicationLog.WriteLine(
"Bed Formatter BVT: Successfully validated all the metadata information");
}
}
ApplicationLog.WriteLine(
"Bed Formatter BVT: Successfully validated the ID, Start and End Ranges");
// Cleanup the file.
if (File.Exists(Constants.BedTempFileName))
{
File.Delete(Constants.BedTempFileName);
}
}
public void ValidateFlatten()
{
// Get values from xml.
string expectedRangeIDs = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.IDNode);
string expectedStartIndex = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.StartNode);
string expectedEndIndex = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.EndNode);
string expectedSequenceRangeCount = this.utilityObj.xmlUtil.GetTextValue(
Constants.SmallSizeBedNodeName, Constants.SequenceRangeCountNode);
string[] rangeIDs = expectedRangeIDs.Split(',');
string[] rangeStarts = expectedStartIndex.Split(',');
string[] rangeEnds = expectedEndIndex.Split(',');
var seqRangeGrouping = new SequenceRangeGrouping();
List<ISequenceRange> rangeList = null;
// Create a SequenceRange and add to SequenceRangeList.
for (int i = 0; i < rangeIDs.Length; i++)
{
var seqRange = new SequenceRange(rangeIDs[i],
long.Parse(rangeStarts[i], null),
long.Parse(rangeEnds[i], null));
seqRangeGrouping.Add(seqRange);
}
//Convert SequenceRangeGroup to SequenceRangeList.
rangeList = seqRangeGrouping.Flatten();
int j = 0;
// Validate created SequenceRanges.
foreach (ISequenceRange seqRange in rangeList)
{
Assert.AreEqual(rangeStarts[j], seqRange.Start.ToString((IFormatProvider) null));
Assert.AreEqual(rangeEnds[j], seqRange.End.ToString((IFormatProvider) null));
Assert.AreEqual(rangeIDs[j], seqRange.ID.ToString(null));
j++;
}
Assert.AreEqual(expectedSequenceRangeCount, rangeList.Count.ToString((IFormatProvider) null));
ApplicationLog.WriteLine("SequenceRange BVT : Successfully validated the SequenceStart,SequenceID and SequenceEnd.");
}
/// <summary>
/// Parse a set of ISequenceRange objects from a stream.
/// </summary>
/// <param name="stream">The stream from which the sequence range is to be parsed.</param>
/// <returns>The list of sequence ranges.</returns>
public IList<ISequenceRange> ParseRange(Stream stream)
{
if (stream == null)
{
throw new ArgumentNullException("stream");
}
var result = new List<ISequenceRange>();
char[] splitters = { '\t' };
using (StreamReader reader = stream.OpenRead())
{
string line;
while ((line = reader.ReadLine()) != null)
{
// TODO: Handle Track definitions
if (line.StartsWith("track", StringComparison.Ordinal))
{
continue;
}
string[] split = line.Split(splitters, StringSplitOptions.RemoveEmptyEntries);
if (split.Length < 3)
{
continue;
}
var range = new SequenceRange
{
ID = split[0],
Start = long.Parse(split[1], CultureInfo.InvariantCulture),
End = long.Parse(split[2], CultureInfo.InvariantCulture)
};
// Optional parameters
// TODO: When implementing track definitions update this section for 'use{feature}' declarations
if (split.Length >= 4)
{
range.Metadata["Name"] = split[3];
}
if (split.Length >= 5)
{
range.Metadata["Score"] = int.Parse(split[4], CultureInfo.InvariantCulture);
}
if (split.Length >= 6)
{
range.Metadata["Strand"] = split[5][0];
}
if (split.Length >= 7)
{
range.Metadata["ThickStart"] = int.Parse(split[6], CultureInfo.InvariantCulture);
}
if (split.Length >= 8)
{
range.Metadata["ThickEnd"] = int.Parse(split[7], CultureInfo.InvariantCulture);
}
if (split.Length >= 9)
{
range.Metadata["ItemRGB"] = split[8];
}
if (split.Length >= 10)
{
range.Metadata["BlockCount"] = int.Parse(split[9], CultureInfo.InvariantCulture);
}
if (split.Length >= 11)
{
range.Metadata["BlockSizes"] = split[10];
}
if (split.Length >= 12)
{
range.Metadata["BlockStarts"] = split[11];
}
result.Add(range);
}
}
return result;
}
/// <summary>
/// Create a SequenceRangeGrouping by passing RangeID,Start and End Index.
/// and validate created SequenceRange.
/// </summary>
/// <param name="nodeName">Xml Node name for different inputs.</param>
private void CreateSequenceRangeGrouping(string nodeName)
{
// Get values from xml.
string expectedRangeIDs = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStartIndex = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEndIndex = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string expectedSequenceRangeCount = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SequenceRangeCountNode);
string[] rangeIDs = expectedRangeIDs.Split(',');
string[] rangeStarts = expectedStartIndex.Split(',');
string[] rangeEnds = expectedEndIndex.Split(',');
var seqRangeGrouping = new SequenceRangeGrouping();
List<ISequenceRange> rangeList = null;
// Create a SequenceRange and add to SequenceRangeList.
for (int i = 0; i < rangeIDs.Length; i++)
{
var seqRange = new SequenceRange(rangeIDs[i],
long.Parse(rangeStarts[i], null), long.Parse(rangeEnds[i], null));
seqRangeGrouping.Add(seqRange);
}
IEnumerable<string> rangeGroupIds = seqRangeGrouping.GroupIDs;
string rangeID = string.Empty;
int j = 0;
foreach (string groupID in rangeGroupIds)
{
rangeID = groupID;
// Get SequenceRangeIds.
rangeList = seqRangeGrouping.GetGroup(rangeID);
// Validate created SequenceRanges.
foreach (ISequenceRange seqRange in rangeList)
{
Assert.AreEqual(rangeStarts[j], seqRange.Start.ToString((IFormatProvider) null));
Assert.AreEqual(rangeEnds[j], seqRange.End.ToString((IFormatProvider) null));
Assert.AreEqual(rangeIDs[j], seqRange.ID.ToString(null));
j++;
}
}
Assert.AreEqual(expectedSequenceRangeCount,
rangeList.Count.ToString((IFormatProvider) null));
ApplicationLog.WriteLine(
"SequenceRange BVT : Successfully validated the SequenceStart, SequenceID and SequenceEnd.");
}
private static IQueryable <RillCommitEntity> Matching(this IQueryable <RillCommitEntity> commits, SequenceRange range)
{
var seekedLower = (long)range.Lower;
var seekedUpper = (long)range.Upper;
//a) the commits lower bound is between seeked range
//b) the commits upper bound is between seeked range
//c) the commits range spans over the seeked range
return(commits
.Where(c => (c.SequenceLowerBound >= seekedLower && c.SequenceLowerBound <= seekedUpper) ||
(c.SequenceUpperBound >= seekedLower && c.SequenceUpperBound <= seekedUpper) ||
(c.SequenceLowerBound <= seekedLower && c.SequenceUpperBound >= seekedUpper)));
}
/// <summary>
/// Formats the Range/RangeGroup for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
private void FormatterGeneralTestCases(string nodeName,
AdditionalParameters addParam)
{
IList<ISequenceRange> rangeList = new List<ISequenceRange>();
var rangeGroup = new SequenceRangeGrouping();
// Gets the file name.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
// Condition to check if Parse() happens before Format()
switch (addParam)
{
case AdditionalParameters.ParseRangeGroup:
case AdditionalParameters.ParseRangeGroupTextWriter:
var initialParserGroupObj = new BedParser();
rangeGroup =
initialParserGroupObj.ParseRangeGrouping(filePath);
break;
case AdditionalParameters.ParseRange:
case AdditionalParameters.ParseRangeTextWriter:
var initialParserObj = new BedParser();
rangeList = initialParserObj.ParseRange(filePath);
break;
default:
// Gets all the expected values from xml.
string expectedID = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEnd = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string[] expectedIDs = expectedID.Split(',');
string[] expectedStarts = expectedStart.Split(',');
string[] expectedEnds = expectedEnd.Split(',');
// Gets the Range Group or Range based on the additional parameter
switch (addParam)
{
case AdditionalParameters.RangeGroupTextWriter:
case AdditionalParameters.RangeGroupFileName:
for (int i = 0; i < expectedIDs.Length; i++)
{
var rangeObj1 =
new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], null),
long.Parse(expectedEnds[i], null));
rangeGroup.Add(rangeObj1);
}
break;
default:
for (int i = 0; i < expectedIDs.Length; i++)
{
var rangeObj2 =
new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], null),
long.Parse(expectedEnds[i], null));
rangeList.Add(rangeObj2);
}
break;
}
break;
}
var formatterObj = new BedFormatter();
// Gets the Range list/Range Group based on the parameters.
switch (addParam)
{
case AdditionalParameters.RangeFileName:
case AdditionalParameters.ParseRange:
formatterObj.Format(rangeList, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeTextWriter:
case AdditionalParameters.ParseRangeTextWriter:
using (var txtWriter = File.Create(Constants.BedTempFileName))
{
formatterObj.Format(txtWriter, rangeList);
}
break;
case AdditionalParameters.RangeGroupFileName:
case AdditionalParameters.ParseRangeGroup:
formatterObj.Format(rangeGroup, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeGroupTextWriter:
case AdditionalParameters.ParseRangeGroupTextWriter:
using (var txtWriter = File.Create(Constants.BedTempFileName))
{
formatterObj.Format(txtWriter, rangeGroup);
}
break;
default:
break;
}
// Reparse to validate the results
var parserObj = new BedParser();
IList<ISequenceRange> newRangeList =
parserObj.ParseRange(Constants.BedTempFileName);
// Validation of all the properties.
for (int i = 0; i < rangeList.Count; i++)
{
Assert.AreEqual(rangeList[0].ID, newRangeList[0].ID);
Assert.AreEqual(rangeList[0].Start, newRangeList[0].Start);
Assert.AreEqual(rangeList[0].End, newRangeList[0].End);
}
ApplicationLog.WriteLine(
"Bed Formatter P1: Successfully validated the ID, Start and End Ranges");
// Cleanup the file.
if (File.Exists(Constants.BedTempFileName))
File.Delete(Constants.BedTempFileName);
}
public void Requires_logic_order_of_range()
{
Action failing = () => SequenceRange.From(Sequence.Max, Sequence.First);
failing.Should().ThrowExactly <ArgumentException>().WithMessage("Range must be from low to high.");
}
/// <summary>
/// Parse a set of ISequenceRange objects from a reader.
/// </summary>
/// <param name="reader">The reader from which the sequence range is to be parsed.</param>
/// <returns>The list of sequence ranges.</returns>
public IList <ISequenceRange> ParseRange(TextReader reader)
{
if (reader == null)
{
throw new ArgumentNullException("reader");
}
List <ISequenceRange> result = new List <ISequenceRange>();
char[] splitters = { '\t' };
string line = null;
while ((line = reader.ReadLine()) != null)
{
// TODO: Handle Track definitions
if (line.StartsWith("track", StringComparison.Ordinal))
{
continue;
}
string[] split = line.Split(splitters, StringSplitOptions.RemoveEmptyEntries);
if (split.Length < 3)
{
continue;
}
SequenceRange range = new SequenceRange();
range.ID = split[0];
range.Start = long.Parse(split[1], CultureInfo.InvariantCulture);
range.End = long.Parse(split[2], CultureInfo.InvariantCulture);
// Optional parameters
// TODO: When implementing track definitions update this section for 'use{feature}' declarations
if (split.Length >= 4)
{
range.Metadata["Name"] = split[3];
}
if (split.Length >= 5)
{
range.Metadata["Score"] = int.Parse(split[4], CultureInfo.InvariantCulture);
}
if (split.Length >= 6)
{
range.Metadata["Strand"] = split[5][0];
}
if (split.Length >= 7)
{
range.Metadata["ThickStart"] = int.Parse(split[6], CultureInfo.InvariantCulture);
}
if (split.Length >= 8)
{
range.Metadata["ThickEnd"] = int.Parse(split[7], CultureInfo.InvariantCulture);
}
if (split.Length >= 9)
{
range.Metadata["ItemRGB"] = split[8];
}
if (split.Length >= 10)
{
range.Metadata["BlockCount"] = int.Parse(split[9], CultureInfo.InvariantCulture);
}
if (split.Length >= 11)
{
range.Metadata["BlockSizes"] = split[10];
}
if (split.Length >= 12)
{
range.Metadata["BlockStarts"] = split[11];
}
result.Add(range);
}
reader.Close();
return(result);
}
private static void ReserveRange(string sequenceName, int rangeSize, SqlConnection connection, SequenceRange entry)
{
using (var sqlCmd = new SqlCommand((entry.IsSequenceExhausted && entry.AutoRestart ? string.Format(SequenceRestartSql, sequenceName) : "") + SequenceGetRangeSql, connection))
{
sqlCmd.CommandType = CommandType.StoredProcedure;
var firstValueParam = new SqlParameter("@range_first_value", SqlDbType.Variant)
{
Direction = ParameterDirection.Output
};
var lastValueParam = new SqlParameter("@range_last_value", SqlDbType.Variant)
{
Direction = ParameterDirection.Output
};
var incrementValueParam = new SqlParameter("@sequence_increment", SqlDbType.Variant)
{
Direction = ParameterDirection.Output
};
var maxValueParam = new SqlParameter("@sequence_max_value", SqlDbType.Variant)
{
Direction = ParameterDirection.Output
};
sqlCmd.Parameters.AddWithValue("@sequence_name", sequenceName);
sqlCmd.Parameters.AddWithValue("@range_size", rangeSize);
sqlCmd.Parameters.Add(firstValueParam);
sqlCmd.Parameters.Add(lastValueParam);
sqlCmd.Parameters.Add(incrementValueParam);
sqlCmd.Parameters.Add(maxValueParam);
sqlCmd.ExecuteNonQuery();
entry.Current = entry.First = Convert.ToInt64(firstValueParam.Value);
entry.Last = Convert.ToInt64(lastValueParam.Value);
entry.Increment = Convert.ToInt32(incrementValueParam.Value);
entry.MaxValue = Convert.ToInt64(maxValueParam.Value);
if (!entry.IsValid)
{
entry.Increment = 1;
}
}
}
public void ValidateSequenceRangeGroupingToString()
{
ISequenceRange range1 = new SequenceRange("chr20", 0, 3);
ISequenceRange range2 = new SequenceRange("chr21", 0, 4);
IList<ISequenceRange> ranges = new List<ISequenceRange>();
ranges.Add(range1);
ranges.Add(range2);
var rangegrouping = new SequenceRangeGrouping(ranges);
string actualString = rangegrouping.ToString();
string expectedStr = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.SequenceRangeGroupingExpectedNode);
Assert.AreEqual(expectedStr.Replace("\\r\\n", ""), actualString.Replace(System.Environment.NewLine, ""));
}
/// <summary>
/// Parses specified BAM file using index file.
/// </summary>
/// <param name="parser">BAM parser</param>
/// <param name="fileName">BAM file name.</param>
/// <param name="range">SequenceRange object which contains reference sequence name and start and end co-ordinates.</param>
/// <returns>SequenceAlignmentMap object which contains alignments for specified reference sequence and for specified range.</returns>
public static SequenceAlignmentMap ParseRange(this BAMParser parser, string fileName, SequenceRange range)
{
if (parser == null)
{
throw new ArgumentNullException("parser");
}
if (string.IsNullOrWhiteSpace(fileName))
{
throw new ArgumentNullException("fileName");
}
if (range == null)
{
throw new ArgumentNullException("range");
}
if (string.IsNullOrEmpty(range.ID))
{
throw new ArgumentException("Reference sequence name (range.ID) can't empty or null.");
}
int start = range.Start >= int.MaxValue ? int.MaxValue : (int)range.Start;
int end = range.End >= int.MaxValue ? int.MaxValue : (int)range.End;
using (FileStream bamStream = File.OpenRead(fileName))
{
string bamIndexFileName = GetBAMIndexFileName(fileName);
using (FileStream bamIndexFile = File.OpenRead(bamIndexFileName))
using (BAMIndexStorage bamIndexStorage = new BAMIndexStorage(bamIndexFile))
{
if (start == 0 && end == int.MaxValue)
return parser.GetAlignment(bamStream, bamIndexStorage, range.ID);
return parser.GetAlignment(bamStream, bamIndexStorage, range.ID, start, end);
}
}
}
public void TestSequenceRangeGroupingToString()
{
ISequenceRange range1 = new SequenceRange("chr20", 0, 3);
ISequenceRange range2 = new SequenceRange("chr21", 0, 4);
IList<ISequenceRange> ranges = new List<ISequenceRange>();
ranges.Add(range1);
ranges.Add(range2);
SequenceRangeGrouping rangegrouping = new SequenceRangeGrouping(ranges);
string actualString = rangegrouping.ToString();
string expectedString = "ID=chr20 Start=0 End=3\r\nID=chr21 Start=0 End=4\r\n".Replace("\r\n", Environment.NewLine);
Assert.AreEqual(actualString, expectedString);
}
/// <summary>
/// Formats the Range/RangeGroup for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
void FormatterGeneralTestCases(string nodeName,
AdditionalParameters addParam)
{
IList <ISequenceRange> rangeList = new List <ISequenceRange>();
SequenceRangeGrouping rangeGroup = new SequenceRangeGrouping();
// Gets the file name.
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
// Condition to check if Parse() happens before Format()
switch (addParam)
{
case AdditionalParameters.ParseRangeGroup:
case AdditionalParameters.ParseRangeGroupTextWriter:
BedParser initialParserGroupObj = new BedParser();
rangeGroup =
initialParserGroupObj.ParseRangeGrouping(filePath);
break;
case AdditionalParameters.ParseRange:
case AdditionalParameters.ParseRangeTextWriter:
BedParser initialParserObj = new BedParser();
rangeList = initialParserObj.ParseRange(filePath);
break;
default:
// Gets all the expected values from xml.
string expectedID = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.IDNode);
string expectedStart = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartNode);
string expectedEnd = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndNode);
string[] expectedIDs = expectedID.Split(',');
string[] expectedStarts = expectedStart.Split(',');
string[] expectedEnds = expectedEnd.Split(',');
// Gets the Range Group or Range based on the additional parameter
switch (addParam)
{
case AdditionalParameters.RangeGroupTextWriter:
case AdditionalParameters.RangeGroupFileName:
for (int i = 0; i < expectedIDs.Length; i++)
{
SequenceRange rangeObj1 =
new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], (IFormatProvider)null),
long.Parse(expectedEnds[i], (IFormatProvider)null));
rangeGroup.Add(rangeObj1);
}
break;
default:
for (int i = 0; i < expectedIDs.Length; i++)
{
SequenceRange rangeObj2 =
new SequenceRange(expectedIDs[i],
long.Parse(expectedStarts[i], (IFormatProvider)null),
long.Parse(expectedEnds[i], (IFormatProvider)null));
rangeList.Add(rangeObj2);
}
break;
}
break;
}
BedFormatter formatterObj = new BedFormatter();
// Gets the Range list/Range Group based on the parameters.
switch (addParam)
{
case AdditionalParameters.RangeFileName:
case AdditionalParameters.ParseRange:
formatterObj.Format(rangeList, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeTextWriter:
case AdditionalParameters.ParseRangeTextWriter:
using (TextWriter txtWriter =
new StreamWriter(Constants.BedTempFileName))
{
formatterObj.Format(rangeList, txtWriter);
}
break;
case AdditionalParameters.RangeGroupFileName:
case AdditionalParameters.ParseRangeGroup:
formatterObj.Format(rangeGroup, Constants.BedTempFileName);
break;
case AdditionalParameters.RangeGroupTextWriter:
case AdditionalParameters.ParseRangeGroupTextWriter:
using (TextWriter txtWriter =
new StreamWriter(Constants.BedTempFileName))
{
formatterObj.Format(rangeGroup, txtWriter);
}
break;
default:
break;
}
// Reparse to validate the results
BedParser parserObj = new BedParser();
IList <ISequenceRange> newRangeList =
parserObj.ParseRange(Constants.BedTempFileName);
// Validation of all the properties.
for (int i = 0; i < rangeList.Count; i++)
{
Assert.AreEqual(rangeList[0].ID, newRangeList[0].ID);
Assert.AreEqual(rangeList[0].Start, newRangeList[0].Start);
Assert.AreEqual(rangeList[0].End, newRangeList[0].End);
}
ApplicationLog.WriteLine(
"Bed Formatter P1: Successfully validated the ID, Start and End Ranges");
Console.WriteLine(
"Bed Formatter P1: Successfully validated the ID, Start and End Ranges");
// Cleanup the file.
if (File.Exists(Constants.BedTempFileName))
{
File.Delete(Constants.BedTempFileName);
}
}
public void MapBlob(string blob)
{
var parsed = JSON.Parse(blob);
var threads = parsed["TextThreads"].AsArray;
TextThreads = new List<TextThread>();
foreach(var thread in threads.Childs)
{
TextThread newThread = new TextThread();
newThread.IsDefaultThread = thread["IsDefaultThread"].AsBool;
newThread.Name = thread["Name"];
var sequenceState = thread["SequenceState"].AsObject;
SequenceRange newState = new SequenceRange();
newState.Name = sequenceState["Name"];
newState.MinCounter = sequenceState["MinCounter"].AsInt;
newState.MaxCounter = sequenceState["MaxCounter"].AsInt;
newThread.SequenceRange = newState;
newThread.TextContent = new List<TextContent>();
var content = thread["TextContent"].AsArray;
foreach(var contentItem in content.Childs)
{
TextContent newTextContent = new TextContent();
newTextContent.Speaker = contentItem["Speaker"];
newTextContent.Dialogue = contentItem["Dialogue"];
newTextContent.DialogueEvents = new List<DialogueEvent>();
// Map Dialogue Options...
newTextContent.Options = new List<DialogueOption>();
var dialogueOptions = contentItem["Options"];
foreach(var dialogueOption in dialogueOptions.Childs)
{
DialogueOption newOption = new DialogueOption();
newOption.Text = dialogueOption["Text"];
newOption.TargetID = dialogueOption["TargetID"].AsInt;
newTextContent.Options.Add(newOption);
}
// Map Dialogue Events...
var dialogueEvents = contentItem["DialogueEvents"].AsArray;
foreach(var dialogueEvent in dialogueEvents.Childs)
{
DialogueEvent newDialogueEvent = new DialogueEvent();
newDialogueEvent.MessageName = dialogueEvent["MessageName"];
newDialogueEvent.Args = new List<string>();
var eventArgs = dialogueEvent["Args"].AsArray;
foreach(var eventArg in eventArgs.Childs)
{
newDialogueEvent.Args.Add(eventArg);
}
newTextContent.DialogueEvents.Add(newDialogueEvent);
}
newThread.TextContent.Add(newTextContent);
}
TextThreads.Add(newThread);
}
}
public void ValidateSequenceRangeToString()
{
var range = new SequenceRange("chr20", 0, 3);
string actualString = range.ToString();
Assert.AreEqual("ID=chr20 Start=0 End=3", actualString);
}
/// <summary>
/// Parses specified BAM file using index file.
/// </summary>
/// <param name="fileName">BAM file name.</param>
/// <param name="range">SequenceRange object which contains reference sequence name and start and end co-ordinates.</param>
/// <returns>SequenceAlignmentMap object which contains alignments for specified reference sequence and for specified range.</returns>
public SequenceAlignmentMap ParseRange(string fileName, SequenceRange range)
{
if (string.IsNullOrWhiteSpace(fileName))
{
throw new ArgumentNullException("fileName");
}
if (range == null)
{
throw new ArgumentNullException("range");
}
if (string.IsNullOrEmpty(range.ID))
{
throw new ArgumentException("Reference sequence name (range.ID) can't empty or null.");
}
int start = range.Start >= int.MaxValue ? int.MaxValue : (int)range.Start;
int end = range.End >= int.MaxValue ? int.MaxValue : (int)range.End;
if (start == 0 && end == int.MaxValue)
{
using (FileStream bamStream = new FileStream(fileName, FileMode.Open, FileAccess.Read, FileShare.Read))
{
string bamIndexFileName = getBAMIndexFileName(fileName);
using (BAMIndexFile bamIndexFile = new BAMIndexFile(bamIndexFileName, FileMode.Open, FileAccess.Read))
{
return GetAlignment(bamStream, bamIndexFile, range.ID);
}
}
}
else
{
using (FileStream bamStream = new FileStream(fileName, FileMode.Open, FileAccess.Read, FileShare.Read))
{
string bamIndexFileName = getBAMIndexFileName(fileName);
using (BAMIndexFile bamIndexFile = new BAMIndexFile(bamIndexFileName, FileMode.Open, FileAccess.Read))
{
return GetAlignment(bamStream, bamIndexFile, range.ID, start, end);
}
}
}
}
internal static RillEntity New(RillReference reference, SequenceRange sequenceRange, Timestamp createdAt) => From(reference, sequenceRange, createdAt, createdAt);
public void TestSequenceRangeToString()
{
SequenceRange range = new SequenceRange("chr20", 0, 3);
string actualString = range.ToString();
string expectedString = "ID=chr20 Start=0 End=3";
Assert.AreEqual(actualString, expectedString);
}
internal static IQueryable <RillCommitEntity> Matching(this IQueryable <RillCommitEntity> commits, RillReference reference, SequenceRange range)
=> range == SequenceRange.Any
? commits.Matching(reference)
: commits.Matching(reference).Matching(range);
