void CDFData::SetUInt32ToGenericHdr(const std::wstring& name, u_int32_t value)
{
ParameterNameValueType paramType;
paramType.SetName(name);
paramType.SetValueUInt32(value);
GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
hdr->AddNameValParam(paramType);
}
/**
* No more probesets will be processed, this is a chance to finish outputting
* results and clean up.
* @param qMethod - Quantification method that was used.
* @return true if success, false otherwise.
*/
bool QuantMethodExprCCCHPReport::finish(QuantMethod &qMethod)
{
// Sanity to check we saw all the probe sets we were expecting.
if (m_CurrentProbeSetCount != m_Info.m_NumProbeSets) {
Err::errAbort("QuantMethodExprCCCHPReport::finish() - Expecting: " + ToStr(m_Info.m_NumProbeSets) +
" but got: " + ToStr(m_CurrentProbeSetCount) + ". Command Console CHP file will be corrupt.");
}
// Flush remaining signal entries in the buffer.
m_ExpressionQuantificationBufferWriter.FlushBuffer();
// Rewrite CHP files to get chip summary entires
Verbose::out(1,"Creating final files for CHP output");
Verbose::progressBegin(1, ToStr("Finalizing Expression CHP Files"),
m_CHPFileNames.size(), 1, m_CHPFileNames.size());
try {
for (unsigned int chip = 0; chip < m_CHPFileNames.size(); chip++) {
// open up tmp chp file to pull results from
GenericData data;
GenericFileReader reader;
std::string filename = m_CHPFileNames[chip]+".tmp";
reader.SetFilename(filename);
reader.ReadHeader(data);
GenericDataHeader* hdr = data.Header().GetGenericDataHdr();
GenericDataHeader updateHdr;
for (int source = 0; source < m_ChipSummaries.size(); source++) {
ChipSummary::metricDefVec_t metricDefs = m_ChipSummaries[source]->getMetricDefs();
for (int i = 0; i < metricDefs.size(); i++) {
ChipSummary::Metric metric;
if (!m_ChipSummaries[source]->getMetric(chip, metricDefs[i].m_name, metric)) {
Err::errAbort("QuantMethodExprCCCHPReport: metric '" + metricDefs[i].m_name +
"' was not found");
}
std::wstring mName(CHIP_SUMMARY_PARAMETER_NAME_PREFIX);
mName += StringUtils::ConvertMBSToWCS(metric.m_Name);
ParameterNameValueType param;
if (hdr->FindNameValParam(mName, param) == false) {
Err::errAbort("QuantMethodExprCCCHPReport: metric name '" + StringUtils::ConvertWCSToMBS(mName) +
"' could not be found in the header of " + filename);
}
switch (param.GetParameterType()) {
case ParameterNameValueType::Int8Type:
param.SetValueInt8((int8_t)metric.m_Integer);
break;
case ParameterNameValueType::UInt8Type:
param.SetValueUInt8((u_int8_t)metric.m_Integer);
break;
case ParameterNameValueType::Int16Type:
param.SetValueInt16((int16_t)metric.m_Integer);
break;
case ParameterNameValueType::UInt16Type:
param.SetValueUInt16((u_int16_t)metric.m_Integer);
break;
case ParameterNameValueType::Int32Type:
param.SetValueInt32((int32_t)metric.m_Integer);
break;
case ParameterNameValueType::UInt32Type:
param.SetValueUInt32((u_int32_t)metric.m_Integer);
break;
case ParameterNameValueType::FloatType:
param.SetValueFloat((float)metric.m_Double);
break;
case ParameterNameValueType::TextType:
param.SetValueText(StringUtils::ConvertMBSToWCS(metric.m_String), (int) metric.m_String.length());
break;
case ParameterNameValueType::AsciiType:
if (metric.m_String.size() > 256) {
Err::errAbort("QuantMethodExprCCCHPReport: string header parameter too long, name = '" +
metric.m_Name + "', value = '" + metric.m_String + "'");
}
param.SetValueAscii(metric.m_String, (int) metric.m_String.length());
break;
default:
Err::errAbort("QuantMethodExprCCCHPReport: unknown header parameter type found in file " +
filename);
}
updateHdr.AddNameValParam(param);
}
}
std::ofstream os;
Fs::aptOpen(os, filename, std::ios::out|std::ios::binary|std::ios::in);
if (!os) {
Err::errAbort("QuantMethodExprCCCHPReport: file " + filename +
" could not be opened for writing");
}
GenericDataHeaderUpdater updater;
updater.Update(os, updateHdr, *hdr);
os.close();
Verbose::progressStep(1);
}
} catch (...) {
removeAllChps();
Err::errAbort("Error in creating final CHP output.");
}
Verbose::progressEnd(1, ToStr("Done."));
// Remove .tmp extension
for (unsigned int i = 0; i < m_CHPFileNames.size(); i++) {
std::string from = m_CHPFileNames[i] + ".tmp";
std::string to = m_CHPFileNames[i];
if (!Fs::fileRename(from.c_str(),to.c_str())) {
removeAllChps();
Err::errAbort("Unable to rename '" + from + "' to '" + to + "'");
}
}
removeTmpChps();
return true;
}
void CalvinCHPMultiDataFileUpdaterTest::CreateReferenceFile2()
{
CHPMultiDataData data(TEST2_FILE);
vector<ColumnInfo> cols;
ParameterNameValueType nv;
ByteColumn bcol(L"byte");
cols.push_back(bcol);
UByteColumn ubcol(L"ubyte");
cols.push_back(ubcol);
ShortColumn scol(L"short");
cols.push_back(scol);
UShortColumn uscol(L"ushort");
cols.push_back(uscol);
IntColumn icol(L"int");
cols.push_back(icol);
UIntColumn uicol(L"uint");
cols.push_back(uicol);
FloatColumn fcol(L"float");
cols.push_back(fcol);
ASCIIColumn acol(L"ascii", 7);
cols.push_back(acol);
UnicodeColumn tcol(L"text", 10);
cols.push_back(tcol);
ProbeSetMultiDataGenotypeData e;
data.SetEntryCount(GenotypeMultiDataType, 4, 10, cols);
CHPMultiDataFileWriter *writer = new CHPMultiDataFileWriter(data);
nv.SetName(L"byte");
nv.SetValueInt8(8);
e.metrics.push_back(nv);
nv.SetName(L"ubyte");
nv.SetValueUInt8(8);
e.metrics.push_back(nv);
nv.SetName(L"short");
nv.SetValueInt16(16);
e.metrics.push_back(nv);
nv.SetName(L"ushort");
nv.SetValueUInt16(16);
e.metrics.push_back(nv);
nv.SetName(L"int");
nv.SetValueInt32(32);
e.metrics.push_back(nv);
nv.SetName(L"uint");
nv.SetValueUInt32(32);
e.metrics.push_back(nv);
nv.SetName(L"float");
nv.SetValueFloat(44.0f);
e.metrics.push_back(nv);
nv.SetName(L"ascii");
nv.SetValueAscii("ascii");
e.metrics.push_back(nv);
nv.SetName(L"text");
nv.SetValueText(L"text");
e.metrics.push_back(nv);
writer->SeekToDataSet(GenotypeMultiDataType);
e.name = "1";
e.call = 1;
e.confidence = 10.0f;
writer->WriteEntry(e);
e.name = "2";
e.call = 2;
e.confidence = 20.0f;
writer->WriteEntry(e);
e.name = "3";
e.call = 3;
e.confidence = 30.0f;
writer->WriteEntry(e);
e.name = "4";
e.call = 4;
e.confidence = 40.0f;
writer->WriteEntry(e);
delete writer;
}
void CalvinCHPMultiDataFileUpdaterTest::CreateReferenceFile3()
{
CHPMultiDataData data(TEST3_FILE);
vector<ColumnInfo> cols;
ParameterNameValueType nv;
ByteColumn bcol(L"byte");
cols.push_back(bcol);
UByteColumn ubcol(L"ubyte");
cols.push_back(ubcol);
ShortColumn scol(L"short");
cols.push_back(scol);
UShortColumn uscol(L"ushort");
cols.push_back(uscol);
IntColumn icol(L"int");
cols.push_back(icol);
UIntColumn uicol(L"uint");
cols.push_back(uicol);
FloatColumn fcol(L"float");
cols.push_back(fcol);
ASCIIColumn acol(L"ascii", 7);
cols.push_back(acol);
UnicodeColumn tcol(L"text", 10);
cols.push_back(tcol);
ProbeSetMultiDataCopyNumberData e;
ProbeSetMultiDataCytoRegionData c;
data.SetEntryCount(CopyNumberMultiDataType, 4, 10, cols);
data.SetEntryCount(CytoMultiDataType, 2, 10);
CHPMultiDataFileWriter *writer = new CHPMultiDataFileWriter(data);
nv.SetName(L"byte");
nv.SetValueInt8(8);
e.metrics.push_back(nv);
nv.SetName(L"ubyte");
nv.SetValueUInt8(8);
e.metrics.push_back(nv);
nv.SetName(L"short");
nv.SetValueInt16(16);
e.metrics.push_back(nv);
nv.SetName(L"ushort");
nv.SetValueUInt16(16);
e.metrics.push_back(nv);
nv.SetName(L"int");
nv.SetValueInt32(32);
e.metrics.push_back(nv);
nv.SetName(L"uint");
nv.SetValueUInt32(32);
e.metrics.push_back(nv);
nv.SetName(L"float");
nv.SetValueFloat(44.0f);
e.metrics.push_back(nv);
nv.SetName(L"ascii");
nv.SetValueAscii("ascii");
e.metrics.push_back(nv);
nv.SetName(L"text");
nv.SetValueText(L"text");
e.metrics.push_back(nv);
writer->SeekToDataSet(CopyNumberMultiDataType);
e.name = "1";
e.chr = 1;
e.position = 10;
writer->WriteEntry(e);
e.name = "2";
e.chr = 2;
e.position = 20;
writer->WriteEntry(e);
e.name = "3";
e.chr = 3;
e.position = 30;
writer->WriteEntry(e);
e.name = "4";
e.chr = 4;
e.position = 40;
writer->WriteEntry(e);
writer->SeekToDataSet(CytoMultiDataType);
c.name = "1";
c.chr= 1;
c.startPosition = 1;
c.stopPosition = 2;
c.call = 1;
c.confidenceScore = 10.0f;
writer->WriteEntry(c);
c.name = "2";
c.chr= 2;
c.startPosition = 2;
c.stopPosition = 3;
c.call = 2;
c.confidenceScore = 20.0f;
writer->WriteEntry(c);
delete writer;
}
