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, "");
}
}