virtual void main()
{
//init
StatisticsReads stats;
FastqEntry entry;
QStringList infiles;
QStringList in1 = getInfileList("in1");
QStringList in2 = getInfileList("in2");
if (in2.count()!=0 && in1.count()!=in2.count())
{
THROW(CommandLineParsingException, "Input file lists 'in1' and 'in2' differ in counts!");
}
//process
for (int i=0; i<in1.count(); ++i)
{
//forward
FastqFileStream stream(in1[i]);
while(!stream.atEnd())
{
stream.readEntry(entry);
stats.update(entry, StatisticsReads::FORWARD);
}
infiles << in1[i];
//reverse (optional)
if (i<in2.count())
{
FastqFileStream stream2(in2[i]);
while(!stream2.atEnd())
{
stream2.readEntry(entry);
stats.update(entry, StatisticsReads::REVERSE);
}
//check read counts matches
if (stream.index()!=stream2.index())
{
THROW(ArgumentException, "Differing number of reads in file '" + in1[i] + "' and '" + in2[i] + "'!");
}
infiles << in2[i];
}
}
//store output
QCCollection metrics = stats.getResult();
if (getFlag("txt"))
{
QStringList output;
metrics.appendToStringList(output);
Helper::storeTextFile(Helper::openFileForWriting(getOutfile("out"), true), output);
}
else
{
metrics.storeToQCML(getOutfile("out"), infiles, "");
}
}
virtual void main()
{
//init
StatisticsReads stats;
FastqEntry entry;
QStringList infiles;
//process forward read file
QString in1 = getInfile("in1");
FastqFileStream stream(in1);
while(!stream.atEnd())
{
stream.readEntry(entry);
stats.update(entry, StatisticsReads::FORWARD);
}
infiles << in1;
//process reverse read file
QString in2 = getInfile("in2");
if (in2!="")
{
FastqFileStream stream2(in2);
while(!stream2.atEnd())
{
stream2.readEntry(entry);
stats.update(entry, StatisticsReads::REVERSE);
}
//check read counts matches
if (stream.index()!=stream2.index())
{
THROW(ArgumentException, "Differing number of reads in file '" + in1 + "' and '" + in2 + "'!");
}
infiles << in2;
}
//store output
QCCollection metrics = stats.getResult();
if (getFlag("txt"))
{
QStringList output;
metrics.appendToStringList(output);
Helper::storeTextFile(Helper::openFileForWriting(getOutfile("out"), true), output);
}
else
{
metrics.storeToQCML(getOutfile("out"), infiles, "");
}
}
void QCCollection::insert(const QCCollection& collection)
{
for (int i=0; i<collection.count(); ++i)
{
insert(collection[i]);
}
}
QCCollection NGSD::getQCData(const QString& filename)
{
QString ps_id = processedSampleId(filename, false);
//get QC data
SqlQuery q = getQuery();
q.exec("SELECT n.name, nm.value, n.description, n.qcml_id FROM processed_sample_qc as nm, qc_terms as n WHERE nm.processed_sample_id='" + ps_id + "' AND nm.qc_terms_id=n.id");
QCCollection output;
while(q.next())
{
output.insert(QCValue(q.value(0).toString(), q.value(1).toString(), q.value(2).toString(), q.value(3).toString()));
}
//get KASP data
SqlQuery q2 = getQuery();
q2.exec("SELECT random_error_prob FROM kasp_status WHERE processed_sample_id='" + ps_id + "'");
QString value = "n/a";
if (q2.size()>0)
{
q2.next();
float numeric_value = 100.0 * q2.value(0).toFloat();
if (numeric_value>100.0) //special case: random_error_prob>100%
{
value = "<font color=orange>KASP not performed (see NGSD)</font>";
}
else if (numeric_value>1.0) //random_error_prob>1% => warn
{
value = "<font color=red>"+QString::number(numeric_value)+"%</font>";
}
else
{
value = QString::number(numeric_value)+"%";
}
}
output.insert(QCValue("kasp", value));
return output;
}
virtual void main()
{
//init
QString roi_file = getInfile("roi");
bool wgs = getFlag("wgs");
QString in = getInfile("in");
int min_maqp = getInt("min_mapq");
//check that either ROI or WGS is given
if (roi_file=="" && !wgs)
{
THROW(CommandLineParsingException, "You have to provide the parameter 'roi' or 'wgs'!");
}
QStringList parameters;
QCCollection metrics;
if (wgs)
{
metrics = Statistics::mapping(in, min_maqp);
//parameters
parameters << "-wgs";
}
else
{
//load ROI
BedFile roi;
roi.load(roi_file);
roi.merge();
//calculate metrics
metrics = Statistics::mapping(roi, in, min_maqp);
//parameters
parameters << "-roi" << QFileInfo(roi_file).fileName();
}
//special QC for 3 exons
QMap<QString, int> precision_overwrite;
precision_overwrite.insert("error estimation N percentage", 4);
precision_overwrite.insert("error estimation SNV percentage", 4);
precision_overwrite.insert("error estimation indel percentage", 4);
QCCollection metrics_3exons;
if (getFlag("3exons"))
{
metrics_3exons = Statistics::mapping3Exons(in);
//parameters
parameters << "-3exons";
}
//store output
QString out = getOutfile("out");
if (getFlag("txt"))
{
QStringList output;
metrics.appendToStringList(output);
output << "";
metrics_3exons.appendToStringList(output, precision_overwrite);
Helper::storeTextFile(Helper::openFileForWriting(out, true), output);
}
else
{
metrics.insert(metrics_3exons);
metrics.storeToQCML(out, QStringList() << in, parameters.join(" "), precision_overwrite);
}
}
