void
GzipWriterFilterSupplier::onClosing(
DataWriterSupplier* supplier)
{
if (bamFormat) {
closing = true;
DataWriter* writer = supplier->getWriter();
// write empty block as BAM end of file marker
static _uint8 eof[] = {
0x1f, 0x8b, 0x08, 0x04, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0x06, 0x00, 0x42, 0x43,
0x02, 0x00, 0x1b, 0x00, 0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00
};
char* buffer;
size_t bytes;
if (! (writer->getBuffer(&buffer, &bytes) && bytes >= sizeof(eof))) {
WriteErrorMessage("no space to write eof marker\n");
soft_exit(1);
}
memcpy(buffer, eof, sizeof(eof));
writer->advance(sizeof(eof));
// add final translation for last empty block
writer->nextBatch();
char* ignore;
pair<_uint64,_uint64> last;
size_t used;
writer->getBatch(-1, &ignore, NULL, &used, (size_t*) &last.second, NULL, (size_t*) &last.first);
last.second += used;
translation.push_back(last);
writer->close();
delete writer;
}
// sort translations
std::sort(translation.begin(), translation.end(), translationComparator);
}
