- Added support for output field
cigarto 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, andsphylumsto print subject super kingdoms, subject kingdoms, and subject phylums.
Assets
4
- 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
--taxonmapoption was used.
Assets
4
- Fixed a bug that could cause alignment score overflows for scores > 65535 in frameshift alignment mode.
- Fixed a clang compiler error.
Assets
4
- 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-excludeto 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.
Assets
4
- 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-minMaskProbto set minimum repeat probability for tantan masking and changed the default value to 0.9. - Added option
--tantan-maxRepeatOffsetto set maximum tandem repeat period to consider and changed the default value to 15. - Added option
--tantan-ungappedto 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.
Assets
4
- Added support for the
sscinamesoutput field to print subject scientific names to the tabular output format. - Fixed a compiler error for GCC 8.2.
- Added option
--stop-match-scoreto set the match score of stop codons. - Fixed a bug that caused the
qqualoutput field to not be correctly clipped to the aligned part of the query. - Added output fields
qseq_gappedandsseq_gappedto 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-scoreinstead of--topfor the LCA computation of the taxonomy output format. - Reduced the number of temporary files.
- Added output field
qstrandto the tabular format. - Database format version changed to 3.
- Fixed a bug in the
--range-cullingmode that could cause undefined behaviour.
Assets
4
- Fixed a compiler error on macOS.
- Added
--headeroption to output header for tabular output format. - The quality string output in tabular format (
qqualfield) 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_qqualto print unclipped query quality values to the tabular format. - Added field
full_qseqto 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
--unoption. - Added option
--alto write aligned queries to file. - Added options
--alfmtand--unfmtto set the format of the aligned/unaligned query file (supported values:fasta,fastq).
Assets
4
- Added shortcut
--long-readsto 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
--dbparameter 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
qqualto 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.
Assets
4
- Added output field
full_sseqto tabular output format. - Database sequences that exceed the maximum accession length will no longer cause an error.
- Added support for PAF output format.
- Optimized performance of database taxonomy filtering.
Assets
4
- Fixed compiler errors on some systems.