Пример #1
0
    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);
}
Пример #2
0
    void
SimpleReadWriter::close()
{
    writer->close();
}