DIAMOND v0.9.32

• 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.

DIAMOND v0.9.31

• 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).

DIAMOND v0.9.30

• 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.

DIAMOND v0.9.29

• 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.

DIAMOND v0.9.28

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

DIAMOND v0.9.27

• 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.

DIAMOND v0.9.26

• 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.

DIAMOND v0.9.25

• 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.

DIAMOND v0.9.24

• 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).

DIAMOND v0.9.23

• 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.