Releases: bbuchfink/diamond
Releases · bbuchfink/diamond
DIAMOND v2.1.9
- Corrected the prefix of the query length field for the SAM format.
- Added the size modifiers 'T', 'M' and 'K' for the
--memory-limit
/-M
option. - Added the option
--mutual-cover
to cluster sequences by mutual coverage percentage of the cluster representative and member sequence. - Added the option
--symmetric
for computing greedy vertex cover with symmetric edges. - Fixed an issue that caused the
--approx-id
option and theapprox_pident
output field not to work correctly when using the--anchored-swipe
option. - Added the option
--no-reassign
to prevent reassignment to closest representative for the greedy vertex cover and clustering workflows. - Added the option
--connected-component-depth
to activate clustering of connected components at a given maximum depth for the greedy vertex cover and the clustering workflows. - Fixed a compiler error for Clang v17.
- Improved search performance when searching with mutual coverage threshold by filtering for sequence length ratio.
- Added the sensitivity mode
--shapes-30x10
with sensitivity approximately equivalent to--mid-sensitive
. - Added the options
--round-coverage
and--round-approx-id
to set per round cutoffs for cascaded clustering. - The CMake switch
-DKEEP_TARGET_ID
is now obsolete and the corresponding function is always available. - Added the option
--include-lineage
to the taxonomic classification format to include taxonomic lineage in the output. - Added native support for the ARM NEON instruction set (contributed by @althonos).
DIAMOND v2.1.8
- Fixed an issue that could cause reduced performance when running in query-indexed mode.
- Added support for the JSON output format (option
-f json-flat
). - Added the option
--sam-query-len
to output query length in SAM format.
DIAMOND v2.1.7
- Fixed a bug that caused taxonomy names not to be loaded correctly for the
makedb
workflow. - Fixed a bug that caused a crash when using the
--target-indexed
option. - Fixed an error when using the
--tmpdir
option for themakedb
workflow. - Added a warning message when sequence accessions are shortened due to parsing rules for the
makedb
workflow. - Added the option
--no-parse-seqids
to disable parsing of sequence accessions. - Changed the command line help to print options separated by command.
- Fixed an issue that the
--ignore-warnings
option could not be used for themakedb
workflow.
DIAMOND v2.1.6
- Fixed compatibility issues on older systems without support for AVX2.
- Fixed linker errors when compiled with
-DX86=OFF
. - Fixed a compiler error on macOS systems.
- Fixed a bug that could cause missing tags in the XML output format and unaligned queries not to be reported correctly.
- Fixed a bug that caused the PAF output format not to work correctly.
DIAMOND v2.1.5
- Disabled the use of frequency based seed masking when using the linear-time search feature with respect to the targets.
- Fixed a bug that caused a
Database file is not a BLAST database
error message for theprepdb
workflow. - Fixed a bug that caused a segmentation fault when using BLAST databases.
- Added line numbers for error messages when reading taxonomy mapping files.
- Fixed a bug that could cause a crash when using the
greedy-vertex-cover
workflow without the--out
and--centroid-out
options. - Fixed a bug that caused the
greedy-vertex-cover
workflow to only produce a trivial clustering. - Fixed a bug that caused the last codon of the -2 reading frame to be translated incorrectly.
- Reduced the memory use of the clustering workflow.
- Updated the bundled NCBI toolkit to the latest version.
DIAMOND v2.1.4
- Leading spaces are now trimmed and tabulator characters escaped as
\t
in sequence titles, and a warning message is produced. - Blank sequence titles are now replaced by
N/A
, and a warning message is produced. - Fixed a bug that could cause a
Traceback error
in certain cases. - Fixed a bug that caused the
qlen
andscore
output fields not to be reported correctly for therealign
workflow. - Added an error message when using unsupported output fields for the
realign
workflow. - Fixed an issue that could cause a
Missing fields in input line
error when clustering. - Optimized the performance of the
linclust
workflow. - Reduced the memory use of the clustering workflow.
- Fixed a bug that caused using standard input as the query not to work.
DIAMOND v2.1.3
- Fixed compiler errors for GCC 4.8.
- Fixed a GCC compiler error.
- Fixed a segfault issue occuring when compiled using GCC 12 on ARM64 systems.
- Fixed an issue that caused missing support for AVX2.
DIAMOND v2.1.2
- The iterated search mode (option
--iterate
) now uses a linear-time feature as the first search round. - Added the
linclust
command to cluster using only a single linear-time search round. - Fixed compiler errors on macOS.
- Fixed a bug that caused invalid alignment traceback output for the DAA
view
workflow. - Added the
merge-daa
workflow to merge DAA files. - Fixed an error when using the
--max-target-seqs/-k
option for the DAAview
workflow. - Removed AVX2 support from the Windows release binary to ensure compatibility with older systems.
- Permitted the
--ignore-warnings
option for thecluster
anddeepclust
workflows. - Use unlinked temporary files for database blocks in clustering workflows.
- Fixed a bug that could cause invalid results when using a clustering step with linearization as the final round in combination with database processing in multiple super blocks.
- The
--lin-stage1
option can now be used without compilation using the-DEXTRA=ON
cmake option. - Added the option to specify the
_lin
suffix for sensitivity keywords for the--iterate
option to activate linear-time feature. - Added the option
--linsearch
to activate linear-time feature for the search workflows. - Fixed a bug that caused the
ppos
andpositive
output fields not to work for therealign
workflow. - Fixed an issue that caused motif masking not to work when compiled with link time optimization.
DIAMOND v2.1.1
- Fixed compilation errors on non-x86 systems and for the clang compiler.
- Fixed an error message when running the
recluster
workflow. - Fixed a bug that could cause an
invalid varint encoding
error when using the DAA format. - Fixed a bug that could cause corrupted DAA output.
- Fixed a bug that caused an error in the
view
workflow. - Adjusted the hit culling heuristic of the frameshift alignment mode to be less aggressive.
DIAMOND v2.1.0
- Added the
cluster
workflow to cluster protein sequences. - Added the
realign
workflow to generate clustering output. - Added the
recluster
workflow to correct errors in clusterings. - Added the
reassign
workflow to reassign cluster members to their closest centroid. - Added the option
-M/--memory-limit
to set a memory limit for clustering workflows. - Added the
--approx-id
option to filter alignments by approximate sequence identity and to set an approximate sequence identity threshold for clustering. - Added the
--member-cover
option to set the coverage threshold of the cluster member sequence. - Added the
--cluster-steps
option to set steps for cascaded clustering. - Added the
--clusters
option to specify clustering input file. - The
blastx
mode will now mask any open reading frame below the minimum required length as specified by--min-orf
. - The
blastx
mode will only count unmasked letters towards the block size. - Fixed a bug that caused an error when using the global ranking mode.
- Added the fast mode as the first round in iterative searches.
- Fixed a bug that caused the program not to function on systems without support for SSE4.1.
- Improved multi-threaded load balancing of gapped extension computations.
- Improved performance of seed extension stage when HSP filter settings are used.
- Added the option
--soft-masking
with possible values0
andtantan
to permit soft-masking using the tantan algorithm. - Fixed a bug that could cause an
inflate error
in multiprocessing mode. - Added the option
--swipe
to compute full Smith Waterman alignments of all queries against all targets. - Added the sensitivity mode
--faster
. - Added the output fields
approx_pident
andcorrected_bitscore
to the tabular format. - Added the
--lin-stage1
option to linearize comparisons in the seeding stage by only considering hits against the longest query sequence for identical seeds (only supported when compiled with-DEXTRA=ON
). - Added the
--kmer-ranking
option to rank sequences when--lin-stage1
is used (only supported when compiled with-DKEEP_TARGET_ID=ON
). - Added the option
--no-block-size-limit
to deactivate upper limits for the block size when the--memory-limit
option is used. - Added the
greedy-vertex-cover
workflow to compute clustering based on alignments. - Added the
--edge-format
option to set edge format for greedy vertex cover. - Added the
--edges
option to set input file for greedy vertex cover. - Added the
--centroid-out
option to output centroid sequences for greedy vertex cover. - Added the
--unaligned-targets
option to generate an output file of unaligned targets. - Fixed an issue that failed compilation using the Intel Compiler.
- Fixed an issue that could cause a segmentation fault in rare cases.
- The
--header
option can now be used with the parametersimple
to enable simple headers for the tabular format, or without a parameter to enable headers for the clustering format. - Added the option
--mp-self
to optimize self-alignment in multiprocessing mode. - Added the option
--query-or-subject-cover
to report alignments if the query or the subject cover (or both) are above the given threshold. - Removed support for the
--comp-based-stats 2
option (now equivalent to--comp-based-stats 3
). - Removed hit culling in case of overlapping target ranges in frameshift alignment mode.
- Added the option
--anchored-swipe
to activate anchored SWIPE extension.