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root/gclib/tophat_cpp/reads.cpp
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# Line 596 | Line 596
596  
597   bool ReadStream::next_read(Read& r, ReadFormat read_format) {
598    FLineReader fr(fstream.file);
599 <  while (read_pq.size()<100000 && !r_eof) {
599 >  while (read_pq.size()<500000 && !r_eof) {
600      //keep the queue topped off
601      Read rf;
602      if (!next_fastx_read(fr, rf, read_format)) {
# Line 621 | Line 621
621                           Read& read,
622                           ReadFormat read_format,
623                           bool strip_slash,
624                         FILE* um_out, //unmapped reads output
625                         bool um_write_found,
624                           uint64_t begin_id,
625 <                         uint64_t end_id) {
625 >                         uint64_t end_id,
626 >                         FILE* um_out, //unmapped reads output
627 >                         bool um_write_found //write the found ones
628 >                         ) {
629    if (!fstream.file)
630         err_die("Error: calling ReadStream::getRead() with no file handle!");
631    if (r_id<last_id)
# Line 655 | Line 656
656        }
657      else if (id > r_id)
658        {
659 <        read_pq.push(make_pair(id, read));
660 <        break;
659 >      // this can't be right, read_pq should be maintained by next_read()
660 >      //read_pq.push(make_pair(id, read));
661 >      fprintf(stderr, "WARNING: unexpected ID order encountered!(%lul > %lu)\n",
662 >           id, r_id);
663 >      break;
664        }
665  
666      if (um_out && (um_write_found || !found)) {

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