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#include <pbdata/amos/AfgBasWriter.hpp>
unsigned char AfgBasWriter::pacbioQVtoPhredQV(unsigned char pacbio)
{
return (unsigned char)floor(10.0 * log10(1.0 + pow(10.0, pacbio / 100.0)) + 0.5);
}
AfgBasWriter::AfgBasWriter()
{
firstRecord = true;
recordCount = 1;
defaultQuality = 5;
}
AfgBasWriter::~AfgBasWriter()
{
firstRecord = true;
recordCount = 1;
defaultQuality = 5;
}
void AfgBasWriter::Initialize(std::string _afgFileName)
{
afgFileName = _afgFileName;
CrucialOpen(afgFileName, afgOut);
}
void AfgBasWriter::Close() { afgOut.close(); }
void AfgBasWriter::SetDefaultQuality(int _defaultQuality) { defaultQuality = _defaultQuality; }
int AfgBasWriter::Write(SMRTSequence &seq)
{
if (firstRecord) {
WriteHeader();
firstRecord = false;
}
WriteOpen();
WriteIdentifier(seq);
WriteBases(seq);
WriteQualities(seq);
WriteClose();
return 1;
}
void AfgBasWriter::WriteHeader()
{
afgOut << "{UNV" << std::endl;
afgOut << "iid:1" << std::endl;
afgOut << "com:" << std::endl;
afgOut << "generated by AfgBasWriter" << std::endl;
afgOut << "Mon Jun 28 14:43:52 2010" << std::endl; // TODO put in real date
afgOut << "." << std::endl << "}" << std::endl;
afgOut << "{LIB" << std::endl << "iid:1" << std::endl;
afgOut << "{DST" << std::endl
<< "mea:0" << std::endl
<< "std:0" << std::endl
<< "}" << std::endl
<< "}" << std::endl;
}
void AfgBasWriter::WriteOpen(void)
{
afgOut << "{RED" << std::endl;
afgOut << "frg:" << recordCount + 1 << std::endl;
afgOut << "iid:" << recordCount << std::endl;
}
void AfgBasWriter::WriteIdentifier(SMRTSequence &seq)
{
afgOut << "clr:0," << seq.length << std::endl;
afgOut << "eid:";
std::string fastaTitle;
seq.GetFASTATitle(fastaTitle);
afgOut << fastaTitle << std::endl;
}
void AfgBasWriter::WriteClose()
{
recordCount++;
afgOut << "}" << std::endl;
afgOut << "{FRG" << std::endl;
afgOut << "iid:" << recordCount << std::endl;
afgOut << "lib:1" << std::endl << "typ:I" << std::endl << "}" << std::endl;
recordCount++;
}
void AfgBasWriter::WriteBases(SMRTSequence &seq)
{
afgOut << "seq:" << std::endl;
(static_cast<DNASequence *>(&seq))->PrintSeq(afgOut, lineLength);
afgOut << "." << std::endl;
}
void AfgBasWriter::WriteQualities(SMRTSequence &seq)
{
afgOut << "qlt:" << std::endl;
DNALength i;
for (i = 0; i < seq.length; i++) {
unsigned char quality = seq.qual.data ? seq.qual[i] : defaultQuality;
quality = quality + charToQuality;
quality = quality > maxAfgQuality ? maxAfgQuality : quality;
quality = quality < minAfgQuality ? minAfgQuality : quality;
afgOut << quality;
if (i > 0 and (i + 1) % lineLength == 0) afgOut << std::endl;
}
if (i == 0 or i % lineLength != 0) {
afgOut << std::endl;
}
afgOut << "." << std::endl;
}
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