internal static ulong GetMinOffset(ReferenceSequence refSeq, int begin)
{
int bin = BinUtilities.FirstBin(Constants.NumLevels) + (begin >> Constants.MinShift);
do
{
if (refSeq.IdToChunks.ContainsKey(bin))
{
break;
}
int firstBin = (BinUtilities.ParentBin(bin) << 3) + 1;
if (bin > firstBin)
{
bin--;
}
else
{
bin = BinUtilities.ParentBin(bin);
}
} while (bin != 0);
int bottomBin = BinUtilities.BottomBin(bin);
return(refSeq.LinearFileOffsets[bottomBin]);
}
public void GetMaxOffset_MissingAllOverlappingBins_ReturnMaxOffset()
{
const ulong expectedResults = ulong.MaxValue;
var idToChunks = new Dictionary <int, Interval[]>();
var refSeq = new ReferenceSequence(Chr2, idToChunks, null);
ulong observedResults = SearchUtilities.GetMaxOffset(refSeq, 243171329);
Assert.Equal(expectedResults, observedResults);
}
public void GetMaxOffset_MissingFirstBin()
{
const ulong expectedResults = 3724908138137;
var idToChunks = new Dictionary <int, Interval[]>
{
[860] = new[] { new Interval(3724908138137, 3724908155075) }
};
var refSeq = new ReferenceSequence(Chr2, idToChunks, null);
ulong observedResults = SearchUtilities.GetMaxOffset(refSeq, 36028417);
Assert.Equal(expectedResults, observedResults);
}
public void GetMaxOffset_Nominal()
{
const ulong expectedResults = 3591443312067;
var idToChunks = new Dictionary <int, Interval[]>
{
[6311] = new[] { new Interval(3591443312067, 3592132724129) }
};
var refSeq = new ReferenceSequence(Chr2, idToChunks, null);
ulong observedResults = SearchUtilities.GetMaxOffset(refSeq, 26699126);
Assert.Equal(expectedResults, observedResults);
}
public void GetMaxOffset_MissingBin()
{
const ulong expectedResults = 3724057593420;
var idToChunks = new Dictionary <int, Interval[]>
{
[6878] = new[] { new Interval(3724057593420, 3724057615020) }
};
var refSeq = new ReferenceSequence(Chr2, idToChunks, null);
ulong observedResults = SearchUtilities.GetMaxOffset(refSeq, 35962881);
Assert.Equal(expectedResults, observedResults);
}
public void GetMinOffset_MissingFirstBin()
{
const ulong expectedResults = 4351134646660;
var linearFileOffsets = new ulong[5353];
linearFileOffsets[5352] = expectedResults;
var idToChunks = new Dictionary <int, Interval[]>
{
[1254] = new[] { new Interval(1, 1) }
};
var refSeq = new ReferenceSequence(Chr2, idToChunks, linearFileOffsets);
ulong observedResults = SearchUtilities.GetMinOffset(refSeq, 87687168);
Assert.Equal(expectedResults, observedResults);
}
public void GetMinOffset_Nominal()
{
const ulong expectedResults = 3591443256775;
var linearFileOffsets = new ulong[1630];
linearFileOffsets[1629] = expectedResults;
var idToChunks = new Dictionary <int, Interval[]>
{
[6310] = new[] { new Interval(1, 1) }
};
var refSeq = new ReferenceSequence(Chr2, idToChunks, linearFileOffsets);
ulong observedResults = SearchUtilities.GetMinOffset(refSeq, 26699125);
Assert.Equal(expectedResults, observedResults);
}
public void GetOffset_Nominal()
{
var linearFileOffsets = new ulong[1630];
linearFileOffsets[1629] = 3591443256775;
var idToChunks = GetIdToChunks();
var refSeqs = new ReferenceSequence[2];
refSeqs[1] = new ReferenceSequence(Chr2, idToChunks, linearFileOffsets);
var index = new Index(Constants.VcfFormat, 0, 0, 0, '#', 0, refSeqs, _refNameToTabixIndex);
long observedResult = index.GetOffset("chr2", 26699126);
Assert.Equal(3591443256857, observedResult);
}
public void GetMinOffset_MissingBin()
{
const ulong expectedResults = 3723191187417;
var linearFileOffsets = new ulong[2196];
linearFileOffsets[2195] = expectedResults;
var idToChunks = new Dictionary <int, Interval[]>
{
[6876] = new[] { new Interval(1, 1) }
};
var refSeq = new ReferenceSequence(Chr2, idToChunks, linearFileOffsets);
ulong observedResults = SearchUtilities.GetMinOffset(refSeq, 35979265);
Assert.Equal(expectedResults, observedResults);
}
public void GetTabixReferenceSequence_NullChromosome_ReturnNull()
{
var linearFileOffsets = new ulong[1630];
linearFileOffsets[1629] = 3591443256775;
var idToChunks = GetIdToChunks();
var refSeqs = new ReferenceSequence[2];
refSeqs[1] = new ReferenceSequence(Chr2, idToChunks, linearFileOffsets);
var index = new Index(Constants.VcfFormat, 0, 0, 0, '#', 0, refSeqs, _refNameToTabixIndex);
var refSeq = index.GetTabixReferenceSequence(null);
Assert.Null(refSeq);
}
public void GetTabixReferenceSequence_Nominal()
{
var linearFileOffsets = new ulong[1630];
linearFileOffsets[1629] = 3591443256775;
var idToChunks = GetIdToChunks();
var refSeqs = new ReferenceSequence[2];
refSeqs[1] = new ReferenceSequence(Chr2, idToChunks, linearFileOffsets);
var index = new Index(Constants.VcfFormat, 0, 0, 0, '#', 0, refSeqs, _refNameToTabixIndex);
var refSeq = index.GetTabixReferenceSequence("chr2");
Assert.Equal("chr2", refSeq.Chromosome.UcscName);
}
public void GetOffset_NoOverlappingBins_UseLinearIndex_WithTruncatedIndex_ReturnMinusOne()
{
var chr1 = new Chromosome("chr1", "1", 0);
var linearFileOffsets = new ulong[1];
linearFileOffsets[0] = 11418;
var idToChunks = new Dictionary <int, Interval[]>();
var refSeqs = new ReferenceSequence[2];
refSeqs[0] = new ReferenceSequence(chr1, idToChunks, linearFileOffsets);
var index = new Index(Constants.VcfFormat, 0, 0, 0, '#', 0, refSeqs, _refNameToTabixIndex);
long observedResult = index.GetOffset("chr1", 100_000);
Assert.Equal(-1, observedResult);
}
public void GetOffset_HandleDiff_TabixIndex_And_RefIndex()
{
var linearFileOffsets = new ulong[1630];
linearFileOffsets[1629] = 3591443256775;
var idToChunks = GetIdToChunks();
// tabix index 10 = chr2 = ref index 1
var refSeqs = new ReferenceSequence[11];
refSeqs[10] = new ReferenceSequence(Chr2, idToChunks, linearFileOffsets);
var refNameToTabixIndex = new Dictionary <string, ushort> {
["chr2"] = 10
};
var index = new Index(Constants.VcfFormat, 0, 0, 0, '#', 0, refSeqs, refNameToTabixIndex);
long observedResult = index.GetOffset("chr2", 26699126);
Assert.Equal(3591443256857, observedResult);
}
public void GetOffset_FixNegativeBeginCoordinate()
{
var linearFileOffsets = new ulong[1];
linearFileOffsets[0] = 3213608733669;
var idToChunks = new Dictionary <int, Interval[]>
{
[585] = new[] { new Interval(3213608740412, 3213608740487) },
[4681] = new[] { new Interval(3213608733669, 3213608740412) },
[4682] = new[] { new Interval(3213608740487, 3214303562687) }
};
var refSeqs = new ReferenceSequence[2];
refSeqs[1] = new ReferenceSequence(Chr2, idToChunks, linearFileOffsets);
var index = new Index(Constants.VcfFormat, 0, 0, 0, '#', 0, refSeqs, _refNameToTabixIndex);
long observedResult = index.GetOffset("chr2", 0);
Assert.Equal(3213608733669, observedResult);
}
public ReferenceSequence GetReferenceSequence()
{
string input = _reader.ReadLine();
if (input == null)
{
return(null);
}
if (!input.StartsWith(">"))
{
throw new UserErrorException($"Encountered a FASTA header that did not start with '>': {input}");
}
var match = _nameRegex.Match(input);
var referenceSequence = new ReferenceSequence
{
Name = match.Groups[1].Value
};
_sb.Clear();
for (int index = _reader.Peek(); index != -1 && index != 62; index = _reader.Peek())
{
string str = _reader.ReadLine();
if (str != null)
{
_sb.Append(str);
}
else
{
break;
}
}
referenceSequence.Bases = _sb.ToString();
return(referenceSequence);
}
internal static ulong GetMaxOffset(ReferenceSequence refSeq, int end)
{
int bin = BinUtilities.FirstBin(Constants.NumLevels) + ((end - 1) >> Constants.MinShift) + 1;
while (true)
{
while (bin % 8 == 1)
{
bin = BinUtilities.ParentBin(bin);
}
if (bin == 0)
{
return(ulong.MaxValue);
}
if (refSeq.IdToChunks.TryGetValue(bin, out var chunks) && chunks.Length > 0)
{
return(chunks[0].Begin);
}
bin++;
}
}
/// <summary>
/// Convert the delta alignment object to its sequence representation
/// </summary>
/// <returns>Reference sequence alignment at 0th index and
/// Query sequence alignment at 1st index</returns>
internal PairwiseAlignedSequence ConvertDeltaToSequences()
{
PairwiseAlignedSequence alignedSequence = new PairwiseAlignedSequence();
Sequence referenceSequence = null;
Sequence querySequence = null;
int gap = 0;
int length = 0;
List <int> startOffsets = new List <int>(2);
List <int> endOffsets = new List <int>(2);
List <int> insertions = new List <int>(2);
startOffsets.Add(FirstSequenceStart);
startOffsets.Add(SecondSequenceStart);
endOffsets.Add(FirstSequenceEnd);
endOffsets.Add(SecondSequenceEnd);
insertions.Add(0);
insertions.Add(0);
// Create the new sequence object with given start and end indices
referenceSequence = new Sequence(ReferenceSequence.Alphabet);
referenceSequence.IsReadOnly = false;
length = FirstSequenceEnd - FirstSequenceStart + 1;
referenceSequence.InsertRange(
0,
ReferenceSequence.Range(FirstSequenceStart, length).ToString());
querySequence = new Sequence(QuerySequence.Alphabet);
querySequence.IsReadOnly = false;
length = SecondSequenceEnd - SecondSequenceStart + 1;
querySequence.InsertRange(
0,
QuerySequence.Range(SecondSequenceStart, length).ToString());
// Insert the Alignment character at delta position
// +ve delta: Insertion in reference sequence
// -ve delta: Insertion in query sequence (deletion in reference sequence)
foreach (int delta in Deltas)
{
gap += Math.Abs(delta);
if (delta < 0)
{
referenceSequence.Insert(gap - 1, DnaAlphabet.Instance.Gap.Symbol);
insertions[0]++;
}
else
{
querySequence.Insert(gap - 1, DnaAlphabet.Instance.Gap.Symbol);
insertions[1]++;
}
}
alignedSequence.FirstSequence = referenceSequence;
alignedSequence.SecondSequence = querySequence;
alignedSequence.Metadata["StartOffsets"] = startOffsets;
alignedSequence.Metadata["EndOffsets"] = endOffsets;
alignedSequence.Metadata["Insertions"] = insertions;
return(alignedSequence);
}
public override void WriteOpenXml(OpenXmlWriter writer)
{
X14.ConditionalFormatting cf = new X14.ConditionalFormatting();
cf.AddNamespaceDeclaration("xm", "http://schemas.microsoft.com/office/excel/2006/main");
ReferenceSequence referenceSequence = new ReferenceSequence();
referenceSequence.Text = $"{SpreadsheetHelper.ExcelColumnFromNumber(RangeStart.ColumnIndex)}{RangeStart.RowIndex}:{SpreadsheetHelper.ExcelColumnFromNumber(RangeEnd.ColumnIndex)}{RangeEnd.RowIndex}";
X14.ConditionalFormattingRule conditionalFormattingRule = new X14.ConditionalFormattingRule()
{
Type = ConditionalFormatValues.IconSet, Priority = 1, Id = Guid.NewGuid().ToString("B").ToUpper()
};
X14.IconSet iconSet1 = new X14.IconSet()
{
IconSetTypes = new EnumValue <IconSetTypeValues>(IconSetTypeValues.FourTrafficLights), ShowValue = false, Custom = true
};
//ConditionalFormattingIcon
var conditionalFormattingIcon1 = new X14.ConditionalFormattingIcon()
{
IconSet = X14.IconSetTypeValues.NoIcons, IconId = (UInt32Value)0U
};
var conditionalFormattingIcon2 = new X14.ConditionalFormattingIcon()
{
IconSet = X14.IconSetTypeValues.ThreeSymbols2, IconId = (UInt32Value)2U
};
var conditionalFormattingIcon3 = new X14.ConditionalFormattingIcon()
{
IconSet = X14.IconSetTypeValues.ThreeSymbols, IconId = (UInt32Value)1U
};
var conditionalFormattingIcon4 = new X14.ConditionalFormattingIcon()
{
IconSet = X14.IconSetTypeValues.ThreeSymbols, IconId = (UInt32Value)0U
};
X14.ConditionalFormattingValueObject conditionalFormattingValueObject1 = new X14.ConditionalFormattingValueObject()
{
Type = X14.ConditionalFormattingValueObjectTypeValues.Numeric
};
Formula formula1 = new Formula();
formula1.Text = "0";
conditionalFormattingValueObject1.Append(formula1);
X14.ConditionalFormattingValueObject conditionalFormattingValueObject2 = new X14.ConditionalFormattingValueObject()
{
Type = X14.ConditionalFormattingValueObjectTypeValues.Numeric
};
Formula formula2 = new Formula();
formula2.Text = "1";
conditionalFormattingValueObject2.Append(formula2);
X14.ConditionalFormattingValueObject conditionalFormattingValueObject3 = new X14.ConditionalFormattingValueObject()
{
Type = X14.ConditionalFormattingValueObjectTypeValues.Numeric
};
Formula formula3 = new Formula();
formula3.Text = "2";
conditionalFormattingValueObject3.Append(formula3);
X14.ConditionalFormattingValueObject conditionalFormattingValueObject4 = new X14.ConditionalFormattingValueObject()
{
Type = X14.ConditionalFormattingValueObjectTypeValues.Numeric
};
Formula formula4 = new Formula();
formula4.Text = "3";
conditionalFormattingValueObject4.Append(formula4);
iconSet1.Append(
conditionalFormattingValueObject1
, conditionalFormattingValueObject2
, conditionalFormattingValueObject3
, conditionalFormattingValueObject4
, conditionalFormattingIcon1
, conditionalFormattingIcon2
, conditionalFormattingIcon3
, conditionalFormattingIcon4
);
conditionalFormattingRule.Append(iconSet1);
cf.Append(conditionalFormattingRule);
cf.Append(referenceSequence);
writer.WriteElement(cf);
}
private void CreateResourcesWorksheet(Dictionary <string, object[]> fieldDictionary, DataTable dataTable,
WorkbookPart workbookPart, Dictionary <string, int> sharedStringIndices)
{
var worksheetPart = workbookPart.AddNewPart <WorksheetPart>("rId1");
var worksheet = new Worksheet(new SheetProperties {
CodeName = "Sheet1"
},
new SheetDimension
{
Reference =
string.Format("A1:{0}{1}",
GetColId(fieldDictionary.Count - 1),
dataTable.Rows.Count + 2)
}, new SheetViews(
new SheetView(
new Pane
{
VerticalSplit = 1D,
TopLeftCell = "A3",
ActivePane = PaneValues.BottomLeft,
State = PaneStateValues.Frozen
},
new Selection
{
ActiveCell = "A2",
SequenceOfReferences =
new ListValue <StringValue> {
InnerText = "A2"
}
},
new Selection {
Pane = PaneValues.BottomLeft
})
{
TabSelected = true,
TopLeftCell = "A2",
WorkbookViewId = (UInt32Value)0U
}))
{
MCAttributes = new MarkupCompatibilityAttributes {
Ignorable = "x14ac"
}
};
worksheet.AddNamespaceDeclaration("r", R_SCHEMA);
worksheet.AddNamespaceDeclaration("mc", MC_SCHEMA);
worksheet.AddNamespaceDeclaration("x14ac", X14_AC_SCHEMA);
var columns = new Columns();
UInt32Value colIndex = 1U;
foreach (var pair in fieldDictionary)
{
var column = new Column
{
Min = colIndex,
Max = colIndex,
Width = 9.140625D,
Style = 1U,
BestFit = true,
CustomWidth = true
};
if (pair.Key.Equals("ID") || pair.Key.Equals("Title"))
{
column.Style = 5U;
}
if (pair.Key.Equals("SharePointAccount") && new Act(_spWeb).IsOnline)
{
column.Hidden = true;
}
columns.AppendChild(column);
colIndex++;
}
columns.AppendChild(new Column {
Min = colIndex, Max = 16384U, Width = 9.140625D, Style = 1U
});
var sheetData = new SheetData();
for (UInt32Value i = 1; i <= dataTable.Rows.Count + 2; i++)
{
var row = new Row {
RowIndex = i
};
if (i == 1)
{
row.Hidden = true;
}
else if (i == 2)
{
row.StyleIndex = 4U;
row.CustomFormat = true;
}
var rowId = (int)(i - 1);
for (int j = 0; j < fieldDictionary.Count; j++)
{
var cellValue = new CellValue();
KeyValuePair <string, object[]> pair = fieldDictionary.ElementAt(j);
object oValue = null;
string value = string.Empty;
if (rowId > 1)
{
oValue = dataTable.Rows[rowId - 2][pair.Key];
if (pair.Key.Equals("ResourceLevel"))
{
foreach (var l in ((IList <string>)pair.Value[2])
.Select(level => level.Split('|'))
.Where(l => l[0].Equals(oValue.ToString())))
{
oValue = l[1];
break;
}
}
value = oValue.ToString();
}
switch (rowId)
{
case 0:
cellValue.Text = sharedStringIndices[pair.Key].ToString(CultureInfo.InvariantCulture);
break;
case 1:
cellValue.Text =
sharedStringIndices[pair.Value[0].ToString()].ToString(CultureInfo.InvariantCulture);
break;
default:
cellValue.Text = sharedStringIndices[value].ToString(CultureInfo.InvariantCulture);
break;
}
var cell = new Cell {
CellReference = GetColId(j) + i, StyleIndex = 1U
};
if (rowId > 1)
{
switch ((SPFieldType)pair.Value[1])
{
case SPFieldType.Counter:
case SPFieldType.Integer:
case SPFieldType.Number:
cellValue.Text = value;
break;
case SPFieldType.DateTime:
cell.StyleIndex = 3U;
cellValue.Text = oValue != null && oValue != DBNull.Value
? ((DateTime)oValue).ToOADate()
.ToString(CultureInfo.InvariantCulture)
: null;
break;
case SPFieldType.Currency:
cell.StyleIndex = 2U;
cellValue.Text = value;
break;
case SPFieldType.Boolean:
cell.DataType = CellValues.Boolean;
cellValue.Text = value;
break;
default:
cell.DataType = CellValues.SharedString;
break;
}
switch (pair.Key)
{
case "ID":
case "Title":
case "Generic":
case "SharePointAccount":
case "Email":
cell.StyleIndex = 5U;
break;
}
}
else
{
cell.DataType = CellValues.SharedString;
}
if (i == 2)
{
cell.StyleIndex = 4U;
}
cell.AppendChild(cellValue);
row.AppendChild(cell);
}
sheetData.AppendChild(row);
}
var worksheetExtensionList = new WorksheetExtensionList();
var worksheetExtension = new WorksheetExtension {
Uri = "{CCE6A557-97BC-4b89-ADB6-D9C93CAAB3DF}"
};
worksheetExtension.AddNamespaceDeclaration("x14", X14_SCHEMA);
var dataValidations = new X14.DataValidations {
Count = 0U
};
dataValidations.AddNamespaceDeclaration("xm", XM_SCHEMA);
for (int i = 0; i < fieldDictionary.Count; i++)
{
string colId = GetColId(i);
KeyValuePair <string, object[]> pair = fieldDictionary.ElementAt(i);
var spFieldType = (SPFieldType)pair.Value[1];
if (spFieldType != SPFieldType.Boolean && spFieldType != SPFieldType.Lookup &&
spFieldType != SPFieldType.User && spFieldType != SPFieldType.Choice)
{
continue;
}
if (pair.Key.Equals("SharePointAccount"))
{
continue;
}
if ((bool)pair.Value[3])
{
continue;
}
dataValidations.Count++;
var dataValidation = new X14.DataValidation
{
Type = DataValidationValues.List,
AllowBlank = true,
ShowInputMessage = true,
ShowErrorMessage = true
};
string formulaValue = string.Empty;
switch (spFieldType)
{
case SPFieldType.Boolean:
formulaValue = "BValues!$A$1:$A$2";
break;
case SPFieldType.Lookup:
case SPFieldType.Choice:
int count = ((List <string>)pair.Value[2]).Count();
formulaValue = pair.Key.Replace("_x0020_", "__") + "Values!$A$1" +
(count > 1 ? ":$A$" + count : string.Empty);
break;
case SPFieldType.User:
formulaValue = "DNValues!$D:$D";
break;
}
var dataValidationForumla = new X14.DataValidationForumla1();
var formula = new Formula {
Text = formulaValue
};
dataValidationForumla.AppendChild(formula);
var refSeq = new ReferenceSequence {
Text = string.Format("{0}3:{0}1048576", colId)
};
dataValidation.Append(dataValidationForumla, refSeq);
dataValidations.AppendChild(dataValidation);
}
worksheetExtension.AppendChild(dataValidations);
worksheetExtensionList.AppendChild(worksheetExtension);
worksheet.Append(columns, sheetData, worksheetExtensionList);
worksheetPart.Worksheet = worksheet;
}
