diamond 2.1.11

[BrewTestBot]

Created by brew bump

---

Created with brew bump-formula-pr.

release notes

- Improved the performance and sensitivity of the `cluster`, `deepclust` and `linclust` workflows.
- The `--faster` mode will by default use a minimizer sketch of fixed size per sequence instead of window-based minimizers.
- Added the option `--sketch-size` to enable seeding using a minimizer sketch of the given size per sequence.
- Cascaded clustering and iterated search will by default use the `--fast` mode with linearization in the second round.
- The `--round-coverage` parameter is now also applied to uni-directional coverage clustering.
- Cluster output files will correctly contain carriage returns on Windows.
- Fixed generation of the Docker container against the latest version of the NCBI toolkit.
- Fixed a bug that caused target coordinates not to be reported correctly in the tabular format in frameshift alignment mode.
- Added the options `--ungapped-evalue` and `--ungapped-evalue-short` to set e-value thresholds for the ungapped hit filter.
- Linearization of search or clustering rounds is limited to seeds of weight >= 10.
- Fixed an issue that could cause an `array size overflow` error when using very large `.dmnd` databases with taxonomic annotation.
- Fixed a bug that caused query letters to be printed as `ARND` instead of `ACGT` in the `view` workflow.
- Fixed a bug that caused using paired end input files to malfunction with an error message.
- Fixed a bug that could produce clustering errors when clustering at sequence identities >= 50% and processing the database in multiple super blocks.
- Fixed a bug that could cause a crash in global ranking mode.
- Accession parsing rules applied to database sequence accessions for the purpose of matching them to accessions in the taxonomy mapping file are now by default also applied to the accessions in the mapping file (disable using `--no-parse-seqids`).
- Fixed an issue that could cause increased memory use in the hash join stage.
- Added support for FASTA headers containing multiple sequence IDs separated by blank spaces (so far only the `\1` character was supported as a separator).
- Fixed an issue that could cause hanging or crashes in the `Computing alignments` stage.
- `--linsearch` can now be used in conjunction with `--iterate`.
- Fixed a compiler error for GCC 4.8.5.
- Fixed a compiler error on Solaris.
- Fixed compiler errors on systems that do not support the sysinfo function.
- Fixed `Bus error` occuring on Sparc systems.
- Compilation on Sparc systems can be performed without setting `-DX86=OFF`.
- Fixed two issues that could cause increased memory use in the computing alignments stage.
- Fixed a bug that caused superfluous quote characters in the JSON output format.
- Linear search modes will by default use full-matrix extension.
- Fixed an issue that could cause reduced performance in the masking sequences stage.
- Fixed a bug that could cause a crash when using mutual coverage thresholds in blastx mode.
- Fixed a bug that could cause a crash when the `--include-lineage` option was used.
- When reading protein sequences that unexpectedly only contain DNA letters, an error message is only produced if the first 10 sequences in the input file all exhibit the problem.
- Fixed a bug that caused setting `--top 100` not to function correctly.
- Fixed a bug that caused target coordinates not to be reported correctly in the output of the `realign` workflow.
- Fixed a bug that did not permit using the `--memory-limit/-M` option for the `realign` workflow.
- Fixed an issue that could cause non-deterministic output in frameshift alignment mode.
- Fixed a bug that could cause a crash when using the XML output format in the `view` workflow.
- Fixed an issue that could cause non-deterministic output for identically-scoring HSPs in the same target.
- Disabled the default use of increased coverage and identity cutoffs in earlier clustering rounds.
- Optimized the performance of the extension stage when coverage or approximate identity filters are used.
- Optimized the performance of the extension stage when not using output fields that require alignment traceback.
- Fixed an issue that could cause an incorrect order of cascaded clustering rounds.

[github-actions]

@chenrui333 has requested bottles to be published to this PR.