status CAFFile::writeDescription()
{
Track *track = getTrack();
Tag desc("desc");
int64_t chunkLength = 32;
double sampleRate = track->f.sampleRate;
Tag formatID("lpcm");
uint32_t formatFlags = 0;
if (track->f.byteOrder == AF_BYTEORDER_LITTLEENDIAN)
formatFlags |= kCAFLinearPCMFormatFlagIsLittleEndian;
if (track->f.isFloat())
formatFlags |= kCAFLinearPCMFormatFlagIsFloat;
uint32_t bytesPerPacket = track->f.bytesPerFrame(false);
uint32_t framesPerPacket = 1;
uint32_t channelsPerFrame = track->f.channelCount;
uint32_t bitsPerChannel = track->f.sampleWidth;
if (track->f.compressionType == AF_COMPRESSION_G711_ULAW)
{
formatID = "ulaw";
formatFlags = 0;
bytesPerPacket = channelsPerFrame;
bitsPerChannel = 8;
}
else if (track->f.compressionType == AF_COMPRESSION_G711_ALAW)
{
formatID = "alaw";
formatFlags = 0;
bytesPerPacket = channelsPerFrame;
bitsPerChannel = 8;
}
else if (track->f.compressionType == AF_COMPRESSION_IMA)
{
formatID = "ima4";
formatFlags = 0;
bytesPerPacket = track->f.bytesPerPacket;
framesPerPacket = track->f.framesPerPacket;
bitsPerChannel = 16;
}
if (!writeTag(&desc) ||
!writeS64(&chunkLength) ||
!writeDouble(&sampleRate) ||
!writeTag(&formatID) ||
!writeU32(&formatFlags) ||
!writeU32(&bytesPerPacket) ||
!writeU32(&framesPerPacket) ||
!writeU32(&channelsPerFrame) ||
!writeU32(&bitsPerChannel))
return AF_FAIL;
return AF_SUCCEED;
}
void summarizeLibraryTypeCounts(boost::filesystem::path& opath){
LibraryFormat fmt1(ReadType::SINGLE_END, ReadOrientation::NONE, ReadStrandedness::U);
LibraryFormat fmt2(ReadType::SINGLE_END, ReadOrientation::NONE, ReadStrandedness::U);
std::ofstream ofile(opath.string());
fmt::MemoryWriter errstr;
auto log = spdlog::get("jointLog");
uint64_t numFmt1{0};
uint64_t numFmt2{0};
uint64_t numAgree{0};
uint64_t numDisagree{0};
for (auto& rl : readLibraries_) {
auto fmt = rl.format();
auto& counts = rl.libTypeCounts();
// If the format is un-stranded, check that
// we have a similar number of mappings in both
// directions and then aggregate the forward and
// reverse counts.
if (fmt.strandedness == ReadStrandedness::U) {
std::vector<ReadStrandedness> strands;
switch (fmt.orientation) {
case ReadOrientation::SAME:
case ReadOrientation::NONE:
strands.push_back(ReadStrandedness::S);
strands.push_back(ReadStrandedness::A);
break;
case ReadOrientation::AWAY:
case ReadOrientation::TOWARD:
strands.push_back(ReadStrandedness::AS);
strands.push_back(ReadStrandedness::SA);
break;
}
fmt1.type = fmt.type; fmt1.orientation = fmt.orientation;
fmt1.strandedness = strands[0];
fmt2.type = fmt.type; fmt2.orientation = fmt.orientation;
fmt2.strandedness = strands[1];
numFmt1 = 0;
numFmt2 = 0;
numAgree = 0;
numDisagree = 0;
for (size_t i = 0; i < counts.size(); ++i) {
if (i == fmt1.formatID()) {
numFmt1 = counts[i];
} else if (i == fmt2.formatID()) {
numFmt2 = counts[i];
} else {
numDisagree += counts[i];
}
}
numAgree = numFmt1 + numFmt2;
double ratio = static_cast<double>(numFmt1) / (numFmt1 + numFmt2);
if ( std::abs(ratio - 0.5) > 0.01) {
errstr << "NOTE: Read Lib [" << rl.readFilesAsString() << "] :\n";
errstr << "\nDetected a strand bias > 1\% in an unstranded protocol "
<< "check the file: " << opath.string() << " for details\n";
log->warn() << errstr.str();
errstr.clear();
}
ofile << "========\n"
<< "Read library consisting of files: "
<< rl.readFilesAsString()
<< "\n\n"
<< "Expected format: " << rl.format()
<< "\n\n"
<< "# of consistent alignments: " << numAgree << "\n"
<< "# of inconsistent alignments: " << numDisagree << "\n"
<< "strand bias = " << ratio << " (0.5 is unbiased)\n"
<< "# alignments with format " << fmt1 << ": " << numFmt1 << "\n"
<< "# alignments with format " << fmt2 << ": " << numFmt2 << "\n"
<< "\n========\n";
} else {
numAgree = 0;
numDisagree = 0;
for (size_t i = 0; i < counts.size(); ++i) {
if (i == fmt.formatID()) {
numAgree = counts[i];
} else {
numDisagree += counts[i];
}
} // end for
ofile << "========\n"
<< "Read library consisting of files: "
<< rl.readFilesAsString()
<< "\n\n"
<< "Expected format: " << rl.format()
<< "\n\n"
<< "# of consistent alignments: " << numAgree << "\n"
<< "# of inconsistent alignments: " << numDisagree << "\n"
<< "\n========\n";
} //end else
double disagreeRatio = static_cast<double>(numDisagree) / (numAgree + numDisagree);
if (disagreeRatio > 0.05) {
errstr << "NOTE: Read Lib [" << rl.readFilesAsString() << "] :\n";
errstr << "\nGreater than 5\% of the alignments (but not, necessarily reads) "
<< "disagreed with the provided library type; "
<< "check the file: " << opath.string() << " for details\n";
log->warn() << errstr.str();
errstr.clear();
}
ofile << "---- counts for each format type ---\n";
for (size_t i = 0; i < counts.size(); ++i) {
ofile << LibraryFormat::formatFromID(i) << " : " << counts[i] << "\n";
}
ofile << "------------------------------------\n\n";
}
ofile.close();
}