diamond

• Fixed a compiler error.
• Improved performance for very small query files.

• Fixed a performance issue.

• improved performance
• improved support for alignments with long gaps
• removed SEG masking
• added low complexity masking using tantan
• changed license to AGPL

Note that this release requires database rebuilding.

• Fixed unclear std::exception error messages.
• Fixed sequence titles in XML format to be compatible with blast2go.
• XML and pairwise format contain full length titles by default.

• Added support for the staxids field to the tabular format, allowing to generate a list of NCBI taxonomy IDs associated with the aligned subject sequence. A description of how to use the option is contained in the manual.
• Fixed a bug that would cause an error message for empty DAA files.
• All scoring matrices use the respective default gap penalties from BLAST.
• Added check for SSSE3 instruction set.
• Added diamond-sse2 to the binary package.

Fixed a compiler error.

Fixed a compiler error on 32 bit systems.

Fixed a compiler error.

• modified option --no-self-hits to also require matching sequence titles for filtering of a self hit
• fixed a bug that could cause a crash in the joining output blocks stage

• improved speed and sensitivity
• fixed an issue that could cause too high memory usage in certain cases

• Added compositional score adjustments (option --comp-based-stats (0,1)). This is a useful feature for filtering false positive hits and is enabled by default.
• Removed --single-domain option and replaced by --max-hsps, to set the maximum number of Hsps per query/subject pair, to be consistent with BLAST. This option is set to 1 by default as getting more than 1 Hsp per subject seems to be confusing users.
• Added option --no-self-hits to filter identical self-hits.

• slightly improved sensitivity
• added option to report unaligned queries: --unal (0=no, 1=yes)
• pairwise, XML and SAM format will report unaligned queries by default
• added option to filter alignments by subject cover (--subject-cover)

• fixed an issue that could cause a crash when using view on incomplete DAA files

• slightly improved sensitivity
• added support for the BLAST pairwise format (option -f 0)

Added support for gzip compressed files containing multiple gzip streams.

• The program now compiles as generic C++ code and thus can be used on hardware platforms other than the Intel/AMD x86-64.
• Added option to write unaligned queries to file (--un).

• fixed a bug with the qseq field in the blast tabular format
• added qtitle and btop fields to the blast tabular format
• fixed a bug that could cause a crash when passing a nonexistant input file
• fixed an issue that could cause unexpectedly long runtimes in certain cases

Added output of line numbers for errors that occur while reading the input file.

Added option to change the genetic code used for translation of query in blastx mode (option --query-gencode, see here for a list of possible values: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).

Fixed the XML format to fill in the Hit_id and Hit_accession fields.