diamond

• Fixed an issue that could cause high memory use in frameshift alignment mode.

• Fixed a bug that could cause the --max-target-seqs/-k, --ext-chunk-size and --file-buffer-size options not to function correctly on macOS.

• Added a new sensitivity mode that is between the default mode and the sensitive mode in sensitivity (option --mid-sensitive).
• Added counters for total number of reference blocks, shapes and index chunks to the status messages.
• Fixed a bug (persisting since v2.0.2) that could cause secondary HSPs within one target not to be reported if the --max-hsps option was used with a non-default setting.
• Fixed a bug that could cause an invalid error message with regard to the database format in certain cases.
• The --no-self-hits option is no longer supported in blastx mode.
• Changed the semantics of the --no-self-hits option to check for equality of both sequence and sequence id, independent of the computed alignment.
• The selection of the top hit when using --top will respect the identity, coverage and no-self-hits filter settings (does not apply when frameshift alignment is enabled).
• The inclusion criterion for --top is applied to the bit score instead of the raw score and is no longer affected by integer rounding (does not apply when frameshift alignment is enabled).
• Improved the accuracy of the ranking heuristic.
• Added the options --ext-chunk-size and --no-ranking to control the ranking heuristic.

• Fixed a bug (persisting since v2.0.0) that could cause incomplete results in blastx mode.
• Reduced the use of temporary disk space.
• Fixed an issue that could cause long runtimes when using the --taxon-list option.

• Added feature for using the tool in a distributed computing environment. (See here for details: http://www.diamondsearch.org/index.php?pages/distributed_computing/)
• Fixed an issue that could cause increased memory usage and runtimes in certain cases.
• Fixed a bug that could cause a crash when using --comp-based-stats 0.
• Fixed a bug that could cause a crash for small input files in certain cases.
• Fixed a bug that could cause filtering hits for identity or range cover not to function correctly when using the tabular format without traceback being enabled.
• Added warning messages to recommend block size parameters based on system RAM.

• Added the sensitivity modes --very-sensitive and --ultra-sensitive. Both modes are designed for finding distant hits of <40% identity with a sensitivity similar to BLAST, with the ultra-sensitive mode being the slightly more sensitive mode.
• The --block-size/-b parameter is set to 0.4 and the --index-chunks/-c parameter is set to 1 by default
  in the new sensitivity modes.
• Improved performance.
• Added the option --ext with possible values banded-fast and banded-slow to adjust band setup for Smith
  Waterman extensions (new default is banded-fast for the default and sensitive mode, and banded-slow otherwise).
• Added automatic disabling of alignment traceback if not required by the user-defined output fields in tabular
  output format.
• Changed the default value of the --max-hsps parameter (the maximum number of HSPs per target sequence to report for each query) to 1.
• Changed the default value of the --freq-sd parameter from 10 to 20 for the sensitive mode.
• Fixed a compiler error on FreeBSD.

• Fixed a bug that could cause makedb to produce invalid database files when using taxonomy features.
• Fixed a bug that could cause a crash when running in query-indexed mode.

WARNING: This version contains a serious bug that can cause incomplete results in blastx mode. Using it is not recommended.

• Fixed a bug in diamond view that would cause high memory usage and erroneous output.
• Reduced the use of temporary disk space.
• Fixed a database compatibility issue with big endian architectures.
• Fixed a bug that would cause a crash for query sequences shorter than 5 letters in blastx mode.
• Fixed a bug that would cause a crash when using a FASTA file as database parameter in blastx mode.
• Added support for the following new ranks in the NCBI taxonomy: biotype, clade, forma specialis, genotype, isolate, morph, pathogroup, serogroup, serotype, strain, subvariety.

WARNING: This version contains a serious bug that can cause incomplete results in blastx mode. Using it is not recommended.

• Fixed a compiler error for native builds.
• Fixed a compiler error for GCC 4.8.
• Fixed a compiler error when support for SSSE3 was enabled without support for SSE4.1.
• Implemented asynchronous loading of seed hits.

WARNING: This version contains a serious bug that can cause incomplete results in blastx mode. Using it is not recommended.

• Improved performance and sensitivity.
• Increased use of temporary disk space.
• Implemented support for the AVX2 instruction set.
• Fixed a bug on big-endian architectures.
• Fixed bugs for compilers with unsigned char.
• Fixed compiler errors for generic builds.
• Added compatibility of database files between little and big endian architectures.
• Fixed various issues related to Illegal instruction errors on macOS.
• Added option --file-buffer-size to set the size of the I/O buffers and set the default value to 64 MB.

Edit: fixed portability issue in the attached Linux binary.

WARNING: This version contains a serious bug that can cause incomplete results in blastx mode. Using it is not recommended.

• Fixed a bug that would generate an incorrect count of positive scoring letters in all output formats.
• Fixed a compiler error on macOS.
• Fixed an illegal instruction error on macOS.

• Improved performance.
• Composition based statistics use integer scoring. (This slightly changes all alignment scores.)
• Option --quiet will suppress startup message.
• Added output field scovhsp to print the subject coverage per HSP to the tabular format.
• Added option --culling-overlap to set the minimum overlap with a higher scoring hit for a hit to be deleted and changed the default value from 90% to 50%.
• Added command diamond test to run a series of regression tests.
• Fixed an off-by-one error of the query end position in the XML output format.

(Update 2020/06/08) Due to a bug, since this version DAA files are not backward compatible with previous versions when using frameshift alignment (option -F).

• Added support for output field cigar to the tabular format.
• Changed the maximum repeat period to 50 for tantan masking.
• Changed the tantan masking to ungapped mode.
• Improved the performance of repeat masking.
• Added output fields sskingdoms, skingdoms, and sphylums to print subject super kingdoms, subject kingdoms, and subject phylums.

• Fixed a bug that could cause taxonomy features to function incorrectly for databases created by versions 0.9.27 and 0.9.28. Please rebuild databases built with those versions if the --taxonmap option was used.

• Fixed a bug that could cause alignment score overflows for scores > 65535 in frameshift alignment mode.
• Fixed a clang compiler error.

• Improved performance of the seed matching stage.
• Seed frequency counts are computed based on hit seeds. (this slightly reduces performance while improving sensitivity)
• Added option --taxon-exclude to exclude list of taxon ids from search.
• Compiling from source will no longer perform a native build. Instead, a portable binary that contains code paths for multiple architectures will be produced, with dispatch logic that is invoked at runtime.

• Fixed a bug that could cause undefined behaviour when using a database file of format version < 2.
• Fixed a compiler error when compiled as generic C++.
• Program will no longer terminate with an error if unlink system call fails.
• Added option --tantan-minMaskProb to set minimum repeat probability for tantan masking and changed the default value to 0.9.
• Added option --tantan-maxRepeatOffset to set maximum tandem repeat period to consider and changed the default value to 15.
• Added option --tantan-ungapped to use tantan in ungapped mode and changed the default to gapped mode.
• Changed score matrix lambda calculation for tantan masking.
• Reference masking is recomputed during alignment runs.

• Added support for the sscinames output field to print subject scientific names to the tabular output format.
• Fixed a compiler error for GCC 8.2.
• Added option --stop-match-score to set the match score of stop codons.
• Fixed a bug that caused the qqual output field to not be correctly clipped to the aligned part of the query.
• Added output fields qseq_gapped and sseq_gapped to the tabular format.
• Raised compiler requirement to GCC 4.8.
• Fixed a bug that caused the final sequence positions to not be printed in the pairwise format.
• Allow using --min-score instead of --top for the LCA computation of the taxonomy output format.
• Reduced the number of temporary files.
• Added output field qstrand to the tabular format.
• Database format version changed to 3.
• Fixed a bug in the --range-culling mode that could cause undefined behaviour.

• Fixed a compiler error on macOS.
• Added --header option to output header for tabular output format.
• The quality string output in tabular format (qqual field) is clipped to the aligned part of the query.
• Print * as quality string if quality values are not available in tabular output format.
• Added field full_qqual to print unclipped query quality values to the tabular format.
• Added field full_qseq to print unclipped query sequence to the tabular format.
• Added support for using the hyphen character - to denote the standard input for input file parameters.
• Status messages are written to stderr.
• Fixed a bug that could incorrectly report queries as unaligned in the output of the --un option.
• Added option --al to write aligned queries to file.
• Added options --alfmt and --unfmt to set the format of the aligned/unaligned query file (supported values: fasta, fastq).

• Added shortcut --long-reads to set suitable parameters for long read alignment: --range-culling (query range-based hit culling), --top 10 (locally report hits within 10% of the best alignment score) and -F 15 (use frameshift alignment mode).
• Fixed a performance issue for very long query sequences. The "longs reads" mode can now efficiently align query sequences that are several megabases in length.
• Added support for using a FASTA file instead of a Diamond database as the --db parameter in alignment workflows. Note that this incurs substantial overhead and should not be used for large databases.
• Fixed an issue that could cause too high memory usage.
• Added output field qqual to print query FASTQ quality values to the tabular format.
• Changed license to GPL.
• Raised compiler requirement to GCC 4.6.
• Added option to use the DAA output format for diamond view.
• Added CL (command line) and VN (version) fields to the @PG SAM format header line.