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  • Fixed a bug (present since v2.0.12) that caused the diamond view workflow to report a zero bit score for all alignments.
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  • Fixed a compiler error on Linux systems that do not define _SC_LEVEL3_CACHE_SIZE.
  • Fixed an error when using --unal 1 with the cigar output field.
  • Fixed an illegal instruction error on systems that did not support AVX2.
  • Fixed a bug (present since v2.0.12) that could cause an error or suboptimal alignments when HSP filter settings were used.
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  • Fixed a bug that caused invalid bit scores in frameshift alignment mode.
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  • Fixed an error when using HSP filter settings together with a BLAST database.
  • Optimized the performance of alignment traceback.
  • A non-default setting of --max-hsps will now recompute a full-matrix Smith Waterman alignment with the ranges of the known HSPs masked in the target.
  • A non-default setting for --max-hsps can now be used together with --ext full.
  • The sensitivity levels used for iterated searches can now be manually set by using a space-separated list after the --iterate option.
  • Seeds are masked based on complexity instead of frequency by default.
  • Added the option --seed-cut to set a complexity cutoff for indexed seeds.
  • Added the option --freq-masking to enable masking seeds based on frequency.
  • The fast, default, mid-sensitive and sensitive modes will by default softmask a fixed set of highly abundant sequence motifs.
  • Added the option --motif-masking (0,1) to enable or disable motif masking.
  • Added the option --masking seg to enable SEG masking of target sequences (BLAST default) instead of tantan masking.
  • Fixed a bug that caused the full_sseq output field to contain invalid information or to produce an error when using a BLAST database.
  • Changed composition based statistics to use BLOSUM62 background frequencies.
  • Fixed the zstd dependency in the Dockerfile.
  • Added support for gap letters in BLAST databases.
  • Fixed a bug that caused the --custom-matrix option not to function correctly.
  • Changed the overlap for merging adjoining bands to >0.0.
  • Use more moderate filtering of HSPs in the chaining stage.
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  • Fixed a bug that could cause invalid output when using --masking 0 combined with the global ranking mode.
  • Enabled lazy repeat masking in the query-indexed and contiguous seed modes when using global ranking.
  • Added detection of cache size to auto-enable query-indexed mode.
1126b71
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  • Using BLAST databases now requires a preprocessing step using the command prepdb. The command line is: diamond prepdb -d /path/to/database. This call runs quickly and will write some small auxiliary files into the database directory.
  • Improved performance of searching small query files.
  • Added the "iterative" search mode (option --iterate) to search the query dataset with increasing sensitivity, only searching queries at the target sensitivity that do not produce a significant alignment at a lower sensitivity search. For example, using --sensitive --iterate will first search the query file at default sensitivity, and search all query sequences again in --sensitive mode that fail to align in the first round.
  • Added the "global ranking" mode (option -g) to set a limit on the number of Smith Waterman extensions per query, with the target sequences ranked by their ungapped extension scores.
  • Added the --fast sensitivity mode that is faster and less sensitive than the default mode.
  • Reduced the time for loading target sequences from BLAST databases.
  • Added the contiguous-seed mode (option --algo ctg) to improve performance for small query files.
  • Added support for using --comp-based-stats (3,4) in combination with --ext full.
  • Fixed a bug that could cause a Traceback error when using --comp-based-stats (3,4) in rare cases.
  • Changed the full_sseq output field to always contain unmasked sequences.
  • Fixed an issue that could cause target output order to be nondeterministic in case of identically scoring hits.
  • Added support for reading zstd-compressed input files (auto-detected) and writing zstd-compressed output files (option --compress zstd) (requires compilation using cmake -DWITH_ZSTD=ON).
  • Compilation with BLAST database support requires the zstd library.
  • Added error message when reading protein sequences from FASTA files that only contain DNA letters (can be disabled using --ignore-warnings).
cd16d51
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  • Reduced the memory use of database building with taxonomy mapping.
  • Removed the limitation of sequence accession length.
  • Fixed a bug that could cause using a BLAST database not to function correctly.
  • Added support for using BLAST alias databases (created by blastdb_aliastool).
  • Reduced the memory use of the seed hit sorting stage.
  • Improved the consistency of results when running in query-indexed mode (--algo 1).
  • Added the option --skip-missing-seqids to ignore cases of missing sequences
    in the database when using the --seqidlist option.
  • The --min-orf parameter now defaults to 1 in frameshift alignment mode.
  • Added support for using BLAST databases to the Docker container.
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  • Added support for directly using BLAST database files instead of the Diamond-formatted .dmnd database files. This feature is not yet available through all release channels. It can currently be accessed by downloading the GitHub release version or by compiling from source. Taxonomy features are not yet supported for BLAST databases.
  • Added the option --seqidlist to filter the database by sequence accession (only supported for BLAST databases).
  • Fixed a bug that caused the --dbsize option not to function correctly.
  • Added the command makeidx and the option --target-indexed that provide an optimisation specialized for small databases (<10 Mb). (see: https://github.com/bbuchfink/diamond/wiki/5.-Advanced-topics#small-database-optimization)
  • Added the option --mp-recover to recover aborted runs in multiprocessing mode.
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  • Added support for computing full-matrix instead of banded Smith Waterman extensions (command line option --ext full).
  • Added support for the new prot.accession2taxid.FULL.gz taxonomy mapping file from NCBI.
  • Added the option --gapped-filter-evalue to set the e-value threshold of the gapped filter heuristic.
  • Added setting the scores of the mask letter according to BLAST rules when a compositionally adjusted matrix is used.
  • Changed formatting of e-values to print two decimals instead of one.
  • Added the output field qseq_translated to print the translation of the aligned part of the query sequence.
  • Added support for providing two input files to --query/-q when running alignment in blastx mode.
  • Added the output field full_qseq_mate to print the sequence of the query's mate (enabled when using two query files in blastx mode).
  • Fixed a bug that could cause a crash in blastx mode for very long queries.
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  • Changed the computation of expected values to use the method described in Park, Y., Sheetlin, S., Ma, N. et al. New finite-size correction for local alignment score distributions. BMC Res Notes 5, 286 (2012).
  • Enabled the use of a custom scoring matrix without having to specify the statistical parameters (option --custom-matrix).
  • Added support for compositional matrix adjust as described in Yi-Kuo Yu, Stephen F. Altschul, The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions, Bioinformatics, Volume 21, Issue 7, 1 April 2005, Pages 902–911. Three additional modes have been added that can be enabled by setting --comp-based-stats (2,3,4) (the feature is not enabled by default and does not support translated searches at the moment).
  • Fixed a bug that could cause incorrect alignment coordinates, gaps counts and sequence identities being reported by diamond view.
  • Targets are sorted by bit score instead of e-value in the alignment output when the --top parameter is used.
  • Disabled support of custom scoring matrices for the DAA format.
  • Fixed a bug that caused the use of a custom scoring matrix not to function correctly.
  • Fixed an issue that caused the portable binary not to function on systems that did not support AVX.
  • Added the option --no-unlink to prevent unlinking of temporary files.