Bugs in USEARCH v4
| Bug | First | Fixed |
| Short sequences fail to match due to default minimum HSP length of 32. Work-around in versions 4.0.1 to 4.0.40 is to set small value, e.g. --minhsp 8. In v4.0.41 and later, the minimum HSP length is automatically set to half the sequence length if this is less than the --minhsp value. | 4.0.1 | 4.0.41 |
| MSVCP100. DLL or MSVCR100.DLL not found error (Windows EXE). | 4.0.1 | 4.0.41 |
| Uchime fails to find any chimeras. | 4.0.1 | 4.0.41 |
| Crash if both --cluster and --nousort specified. | 4.0.1 | 4.0.41 |
| If --maxaccepts is > 1, then multiple H records are written to the --uc output file if a query has more than one accept. Only the best hit should appear. | 4.0.1 | 4.0.41 |
| Local search with --id threshold sometimes fails. | 4.0.1 | 4.0.41 |
| Reverse-complemented seeds are included if --rev and --seedsout both specified. Should be plus strands only. | 4.0.1 | 4.0.42 |
| --iddef 2 gives incorrect identities if there are left terminal gaps. | 4.0.1 | 4.0.49 |
| The ts userfield was incorrectly calculated. Workaround is to use ts=thi-tlo+1. | 4.0.38 | 5.1 |
| Default for --maxtargets was 9, should be zero. This means that increased values of --maxaccepts and --maxrejects > 8 will not be effective. | 4.0.1 | 4.0.56 |