Releases | Open Source Science

diamond - DIAMOND v2.1.13

Fixed an invalid error message for the cluster, deepclust and linclust workflows.
Added the option --oid-output to output ordinal IDs instead of accessions for the clustering workflows, reducing their memory use.
Added support for using the --multiprocessing feature on Windows.
Using --multiprocessing requires explicitly setting --parallel-tmpdir.
Fixed a bug that could cause a crash when the --target-indexed option was used.
As of now, a macOS binary is available for the GitHub release, supporting both x86 and Apple silicon CPUs. Using BLAST databases is also supported.
Added compatibility with later CMake versions (tested up to v4.0.3).
Added CMake option -DCROSS_COMPILE to disable auto-detection of host architecture.
Added compilation script to produce macOS fat binary.

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Published by bbuchfink 10 months ago

diamond - DIAMOND v2.1.12

Added support for the new NCBI taxonomic ranks "cellular root", "acellular root", "domain" and "realm".
Added support for using BLAST databases to the Bioconda release (thanks @mencian).
Fixed compiler errors for Clang 20.
Enabled transitive closure computation in earlier clustering rounds and for bi-directional coverage clustering.
Fixed an issue that could cause hits to be partially lost in frameshift alignment mode when they occured in both query strands for the same target.
Fixed an error parsing FASTQ files when quality value lines started with the @ character.
Fixed a compiler error on macOS.

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Published by bbuchfink 12 months ago

diamond - DIAMOND v2.1.11

Improved the performance and sensitivity of the cluster, deepclust and linclust workflows.
The --faster mode will by default use a minimizer sketch of fixed size per sequence instead of window-based minimizers.
Added the option --sketch-size to enable seeding using a minimizer sketch of the given size per sequence.
Cascaded clustering and iterated search will by default use the --fast mode with linearization in the second round.
The --round-coverage parameter is now also applied to uni-directional coverage clustering.
Cluster output files will correctly contain carriage returns on Windows.
Fixed generation of the Docker container against the latest version of the NCBI toolkit.
Fixed a bug that caused target coordinates not to be reported correctly in the tabular format in frameshift alignment mode.
Added the options --ungapped-evalue and --ungapped-evalue-short to set e-value thresholds for the ungapped hit filter.
Linearization of search or clustering rounds is limited to seeds of weight >= 10.
Fixed an issue that could cause an array size overflow error when using very large .dmnd databases with taxonomic annotation.
Fixed a bug that caused query letters to be printed as ARND instead of ACGT in the view workflow.
Fixed a bug that caused using paired end input files to malfunction with an error message.
Fixed a bug that could produce clustering errors when clustering at sequence identities >= 50% and processing the database in multiple super blocks.
Fixed a bug that could cause a crash in global ranking mode.
Accession parsing rules applied to database sequence accessions for the purpose of matching them to accessions in the taxonomy mapping file are now by default also applied to the accessions in the mapping file (disable using --no-parse-seqids).
Fixed an issue that could cause increased memory use in the hash join stage.
Added support for FASTA headers containing multiple sequence IDs separated by blank spaces (so far only the \1 character was supported as a separator).
Fixed an issue that could cause hanging or crashes in the Computing alignments stage.
--linsearch can now be used in conjunction with --iterate.
Fixed a compiler error for GCC 4.8.5.
Fixed a compiler error on Solaris.
Fixed compiler errors on systems that do not support the sysinfo function.
Fixed Bus error occuring on Sparc systems.
Compilation on Sparc systems can be performed without setting -DX86=OFF.
Fixed two issues that could cause increased memory use in the computing alignments stage.
Fixed a bug that caused superfluous quote characters in the JSON output format.
Linear search modes will by default use full-matrix extension.
Fixed an issue that could cause reduced performance in the masking sequences stage.
Fixed a bug that could cause a crash when using mutual coverage thresholds in blastx mode.
Fixed a bug that could cause a crash when the --include-lineage option was used.
When reading protein sequences that unexpectedly only contain DNA letters, an error message is only produced if the first 10 sequences in the input file all exhibit the problem.
Fixed a bug that caused setting --top 100 not to function correctly.
Fixed a bug that caused target coordinates not to be reported correctly in the output of the realign workflow.
Fixed a bug that did not permit using the --memory-limit/-M option for the realign workflow.
Fixed an issue that could cause non-deterministic output in frameshift alignment mode.
Fixed a bug that could cause a crash when using the XML output format in the view workflow.
Fixed an issue that could cause non-deterministic output for identically-scoring HSPs in the same target.
Disabled the default use of increased coverage and identity cutoffs in earlier clustering rounds.
Optimized the performance of the extension stage when coverage or approximate identity filters are used.
Optimized the performance of the extension stage when not using output fields that require alignment traceback.
Fixed an issue that could cause an incorrect order of cascaded clustering rounds.

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Published by bbuchfink over 1 year ago

diamond - DIAMOND v2.1.10

Fixed a bug that could cause a crash when using a bi-directional coverage cutoff in query-indexed mode.
Fixed a bug that caused the --include-lineage option to malfunction for targets with no taxonomic assignment available.

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Published by bbuchfink over 1 year ago

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 the approx_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).

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Published by bbuchfink over 2 years ago

diamond - 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.

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Published by bbuchfink almost 3 years ago

diamond - 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 the makedb 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 the makedb workflow.

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Published by bbuchfink about 3 years ago

diamond - 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.

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Published by bbuchfink about 3 years ago

diamond - 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 the prepdb 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.

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Published by bbuchfink about 3 years ago

diamond - 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 and score output fields not to be reported correctly for the realign 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.

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Published by bbuchfink over 3 years ago

diamond - 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.

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Published by bbuchfink over 3 years ago

diamond - 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 DAA view workflow.
Removed AVX2 support from the Windows release binary to ensure compatibility with older systems.
Permitted the --ignore-warnings option for the cluster and deepclust 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 and positive output fields not to work for the realign workflow.
Fixed an issue that caused motif masking not to work when compiled with link time optimization.

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Published by bbuchfink over 3 years ago

diamond - 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.

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Published by bbuchfink over 3 years ago

diamond - 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 values 0 and tantan 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 and corrected_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 parameter simple 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.

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Published by bbuchfink over 3 years ago

diamond - DIAMOND v2.0.15

Fixed a bug (present since v2.0.12) that caused the diamond view workflow to report a zero bit score for all alignments.

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Published by bbuchfink about 4 years ago

diamond - DIAMOND v2.0.14

Fixed a compiler error on Linux systems that do not define _SC_LEVEL3_CACHE_SIZE.
Fixed an error when using --unal 1 with the cigar output field.
Fixed an illegal instruction error on systems that did not support AVX2.
Fixed a bug (present since v2.0.12) that could cause an error or suboptimal alignments when HSP filter settings were used.

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Published by bbuchfink over 4 years ago

diamond - DIAMOND v2.0.13

Fixed a bug that caused invalid bit scores in frameshift alignment mode.

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Published by bbuchfink over 4 years ago

diamond - DIAMOND v2.0.12

Fixed an error when using HSP filter settings together with a BLAST database.
Optimized the performance of alignment traceback.
A non-default setting of --max-hsps will now recompute a full-matrix Smith Waterman alignment with the ranges of the known HSPs masked in the target.
A non-default setting for --max-hsps can now be used together with --ext full.
The sensitivity levels used for iterated searches can now be manually set by using a space-separated list after the --iterate option.
Seeds are masked based on complexity instead of frequency by default.
Added the option --seed-cut to set a complexity cutoff for indexed seeds.
Added the option --freq-masking to enable masking seeds based on frequency.
The fast, default, mid-sensitive and sensitive modes will by default softmask a fixed set of highly abundant sequence motifs.
Added the option --motif-masking (0,1) to enable or disable motif masking.
Added the option --masking seg to enable SEG masking of target sequences (BLAST default) instead of tantan masking.
Fixed a bug that caused the full_sseq output field to contain invalid information or to produce an error when using a BLAST database.
Changed composition based statistics to use BLOSUM62 background frequencies.
Fixed the zstd dependency in the Dockerfile.
Added support for gap letters in BLAST databases.
Fixed a bug that caused the --custom-matrix option not to function correctly.
Changed the overlap for merging adjoining bands to >0.0.
Use more moderate filtering of HSPs in the chaining stage.

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Published by bbuchfink over 4 years ago

diamond - DIAMOND v2.0.11

Fixed a bug that could cause invalid output when using --masking 0 combined with the global ranking mode.
Enabled lazy repeat masking in the query-indexed and contiguous seed modes when using global ranking.
Added detection of cache size to auto-enable query-indexed mode.

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Published by bbuchfink almost 5 years ago

diamond - DIAMOND v2.0.10

Using BLAST databases now requires a preprocessing step using the command prepdb. The command line is: diamond prepdb -d /path/to/database. This call runs quickly and will write some small auxiliary files into the database directory.
Improved performance of searching small query files.
Added the "iterative" search mode (option --iterate) to search the query dataset with increasing sensitivity, only searching queries at the target sensitivity that do not produce a significant alignment at a lower sensitivity search. For example, using --sensitive --iterate will first search the query file at default sensitivity, and search all query sequences again in --sensitive mode that fail to align in the first round.
Added the "global ranking" mode (option -g) to set a limit on the number of Smith Waterman extensions per query, with the target sequences ranked by their ungapped extension scores.
Added the --fast sensitivity mode that is faster and less sensitive than the default mode.
Reduced the time for loading target sequences from BLAST databases.
Added the contiguous-seed mode (option --algo ctg) to improve performance for small query files.
Added support for using --comp-based-stats (3,4) in combination with --ext full.
Fixed a bug that could cause a Traceback error when using --comp-based-stats (3,4) in rare cases.
Changed the full_sseq output field to always contain unmasked sequences.
Fixed an issue that could cause target output order to be nondeterministic in case of identically scoring hits.
Added support for reading zstd-compressed input files (auto-detected) and writing zstd-compressed output files (option --compress zstd) (requires compilation using cmake -DWITH_ZSTD=ON).
Compilation with BLAST database support requires the zstd library.
Added error message when reading protein sequences from FASTA files that only contain DNA letters (can be disabled using --ignore-warnings).

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Published by bbuchfink almost 5 years ago

diamond - DIAMOND v2.0.9

Reduced the memory use of database building with taxonomy mapping.
Removed the limitation of sequence accession length.
Fixed a bug that could cause using a BLAST database not to function correctly.
Added support for using BLAST alias databases (created by blastdb_aliastool).
Reduced the memory use of the seed hit sorting stage.
Improved the consistency of results when running in query-indexed mode (--algo 1).
Added the option --skip-missing-seqids to ignore cases of missing sequences in the database when using the --seqidlist option.
The --min-orf parameter now defaults to 1 in frameshift alignment mode.
Added support for using BLAST databases to the Docker container.

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Published by bbuchfink about 5 years ago

diamond - DIAMOND v2.0.8

Added support for directly using BLAST database files instead of the Diamond-formatted .dmnd database files. This feature is not yet available through all release channels. It can currently be accessed by downloading the GitHub release version or by compiling from source. Taxonomy features are not yet supported for BLAST databases.
Added the option --seqidlist to filter the database by sequence accession (only supported for BLAST databases).
Fixed a bug that caused the --dbsize option not to function correctly.
Added the command makeidx and the option --target-indexed that provide an optimisation specialized for small databases (<10 Mb). (see: https://github.com/bbuchfink/diamond/wiki/5.-Advanced-topics#small-database-optimization)
Added the option --mp-recover to recover aborted runs in multiprocessing mode.

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Published by bbuchfink about 5 years ago

diamond - DIAMOND v2.0.7

Added support for computing full-matrix instead of banded Smith Waterman extensions (command line option --ext full).
Added support for the new prot.accession2taxid.FULL.gz taxonomy mapping file from NCBI.
Added the option --gapped-filter-evalue to set the e-value threshold of the gapped filter heuristic.
Added setting the scores of the mask letter according to BLAST rules when a compositionally adjusted matrix is used.
Changed formatting of e-values to print two decimals instead of one.
Added the output field qseq_translated to print the translation of the aligned part of the query sequence.
Added support for providing two input files to --query/-q when running alignment in blastx mode.
Added the output field full_qseq_mate to print the sequence of the query's mate (enabled when using two query files in blastx mode).
Fixed a bug that could cause a crash in blastx mode for very long queries.

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Published by bbuchfink over 5 years ago

diamond - DIAMOND v2.0.6

Changed the computation of expected values to use the method described in Park, Y., Sheetlin, S., Ma, N. et al. New finite-size correction for local alignment score distributions. BMC Res Notes 5, 286 (2012).
Enabled the use of a custom scoring matrix without having to specify the statistical parameters (option --custom-matrix).
Added support for compositional matrix adjust as described in Yi-Kuo Yu, Stephen F. Altschul, The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions, Bioinformatics, Volume 21, Issue 7, 1 April 2005, Pages 902–911. Three additional modes have been added that can be enabled by setting --comp-based-stats (2,3,4) (the feature is not enabled by default and does not support translated searches at the moment).
Fixed a bug that could cause incorrect alignment coordinates, gaps counts and sequence identities being reported by diamond view.
Targets are sorted by bit score instead of e-value in the alignment output when the --top parameter is used.
Disabled support of custom scoring matrices for the DAA format.
Fixed a bug that caused the use of a custom scoring matrix not to function correctly.
Fixed an issue that caused the portable binary not to function on systems that did not support AVX.
Added the option --no-unlink to prevent unlinking of temporary files.

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Published by bbuchfink over 5 years ago

diamond - DIAMOND v2.0.5

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

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Published by bbuchfink over 5 years ago

diamond - DIAMOND v2.0.4

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.

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Published by bbuchfink almost 6 years ago

diamond - DIAMOND v2.0.3

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.

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Published by bbuchfink almost 6 years ago

diamond - DIAMOND v2.0.2

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.

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Published by bbuchfink almost 6 years ago

diamond - DIAMOND v2.0.1

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.

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Published by bbuchfink almost 6 years ago

diamond - DIAMOND v2.0.0

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.

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Published by bbuchfink almost 6 years ago

diamond - DIAMOND v0.9.36

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.

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Published by bbuchfink almost 6 years ago

diamond - DIAMOND v0.9.35

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.

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Published by bbuchfink almost 6 years ago

diamond - DIAMOND v0.9.34

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.

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Published by bbuchfink almost 6 years ago

diamond - DIAMOND v0.9.33

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.

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Published by bbuchfink about 6 years ago

diamond - 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.

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Published by bbuchfink about 6 years ago

diamond - 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).

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Published by bbuchfink about 6 years ago

diamond - 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.

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Published by bbuchfink over 6 years ago

diamond - 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.

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Published by bbuchfink over 6 years ago

diamond - 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.

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Published by bbuchfink over 6 years ago

diamond - 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.

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Published by bbuchfink over 6 years ago

diamond - 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.

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Published by bbuchfink over 6 years ago

diamond - 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.

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Published by bbuchfink almost 7 years ago

diamond - 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).

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Published by bbuchfink over 7 years ago

diamond - 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.

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Published by bbuchfink over 7 years ago

diamond - DIAMOND v0.9.22

Added output field full_sseq to 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.

- C++
Published by bbuchfink about 8 years ago

diamond - DIAMOND v0.9.21

Fixed compiler errors on some systems.

- C++
Published by bbuchfink about 8 years ago

diamond - DIAMOND v0.9.20

Added Bioconda installation instructions to the manual.
Added official docker release: https://hub.docker.com/r/buchfink/diamond/
Fixed a bug that could cause corrupted output if compression was activated.
Fixed an issue that could cause high memory usage by automatic use of the query-indexed algorithm.

- C++
Published by bbuchfink about 8 years ago

This release provides the option to conduct filtered searches by taxonomy. Using --taxonlist followed by a comma-separated list of NCBI taxonomy IDs will search only against matching reference sequences. Any taxonomic rank can be used. For example, use --taxonlist 562 to search against all E. coli sequences; use --taxonlist 2 to search against all bacterial sequences.

This feature requires taxonomy data to be built directly into the database. The --taxonmap and --taxonnodes options now need to be provided exclusively to the makedb command if taxonomy features are to be used.

This release changes the database format and requires database rebuilding. To rebuild the database from an existing one, a Unix pipe can be used like this: /path/to/old/diamond getseq -d dbfile | /path/to/new/diamond makedb -d newdb

- C++
Published by bbuchfink about 8 years ago

diamond - DIAMOND v0.9.18

Optimized output writing performance.
Fixed a bug in the XML output format.

- C++
Published by bbuchfink over 8 years ago

diamond - DIAMOND v0.9.17

Added option --range-culling to restrict hit culling to overlapping query ranges. This feature is designed for long query DNA sequences that may span several genes. In these cases, the default of reporting the 25 best overall hits could cause hits to a lower scoring gene to be overshadowed. But just increasing the number of alignments reported will bloat the output size and reduce performance. Using this feature along with -k 25 (default), a hit will only be deleted if at least 50% of its query range is spanned by at least 25 higher or equal scoring hits. Using this feature along with --top 10, a hit will only be deleted if its score is more than 10% lower than that of a higher scoring hit over at least 50% of its query range. The percentage is configurable using --range-cover. Note that this feature is currently only available in frameshift alignment mode.
Fixed a compiler error on FreeBSD.
Fixed escape sequences in XML output.

- C++
Published by bbuchfink over 8 years ago

diamond - DIAMOND v0.9.16

Fixed a bug that caused an error for non-SSSE3 builds.

- C++
Published by bbuchfink over 8 years ago

diamond - DIAMOND v0.9.15

Highly improved performance of frameshift alignment mode.

- C++
Published by bbuchfink over 8 years ago

diamond - DIAMOND v0.9.14

Added support for frameshift alignments (option -F to set the frameshift penalty). For example: diamond blastx -F 15 ...

Enabling this feature will have the aligner tolerate missing bases in DNA sequences and is most recommended for long, error-prone sequences like MinION reads.

In the pairwise output format, frameshifts will be indicated by \ and / for a shift by +1 and -1 nucleotide in the direction of translation respectively.

Note that this feature is disabled by default. This release changes the DAA format. DAA files created by this version are not backward compatible with previous versions.

- C++
Published by bbuchfink over 8 years ago

diamond - DIAMOND v0.9.13

Fixed query positions in pairwise format for translated searches.
Changed default behaviour of --max-hsps option to report an unlimited number of HSPs for a single query/subject pair. Previously, only the single best HSP for a query/subject pair was reported. Since several HSPs are not uncommon for multidomain proteins and may contain valuable information, the default behaviour has been changed to report any HSP if its query and subject ranges are not enveloped by a higher scoring HSP.

- C++
Published by bbuchfink over 8 years ago

diamond - DIAMOND v0.9.12

Fixed dbinfo command to be able to read older database formats.
Adjusted XML format for better compatibility with Blast2Go.
Fixed a potential error when running multiple instances of Diamond.

- C++
Published by bbuchfink over 8 years ago

diamond - DIAMOND v0.9.11

Added option --xml-blord-format for alternative-style XML format.
Fixed a bug that could cause a crash when writing compressed output files.

- C++
Published by bbuchfink over 8 years ago

diamond - DIAMOND v0.9.10

Added --strand option to choose query strand for translated searches.
Added dbinfo command to show information about a database file.

- C++
Published by bbuchfink almost 9 years ago

diamond - DIAMOND v0.9.9

Added taxonomic classification format.
Fixed a bug in getseq printing masked residues.
Fixed parsing of UniRef100_ sequence id prefixes.
Added support for using the staxids output field in diamond view.

The taxonomic classification format is a new output format that does not print alignments, but only a taxonomic classification for each read using the LCA algorithm.

- C++
Published by bbuchfink almost 9 years ago

diamond - DIAMOND v0.9.8

Fixed a compiler error.

- C++
Published by bbuchfink almost 9 years ago

diamond - DIAMOND v0.9.7

Fixed compiler errors.
Changed XML format for better compatibility with Blast2Go.

- C++
Published by bbuchfink almost 9 years ago

diamond - DIAMOND v0.9.6

Fixed compiler errors.

- C++
Published by bbuchfink almost 9 years ago

diamond - DIAMOND v0.9.5

Added support for named pipes.
Added support for reading input files from stdin.
Added more elaborate file I/O error messages.

- C++
Published by bbuchfink almost 9 years ago

diamond - DIAMOND v0.9.4

Improved performance.
Fixed a bug in the query-indexed algorithm.
Empty sequences are ignored instead of generating an error.

- C++
Published by bbuchfink almost 9 years ago

diamond - DIAMOND v0.9.3

Fixed a bug that could cause hanging.
Fixed a bug that could cause an error when using the staxids output field and the --unal option.

- C++
Published by bbuchfink about 9 years ago

diamond - DIAMOND v0.9.2

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

- C++
Published by bbuchfink about 9 years ago

diamond - DIAMOND v0.9.1

Fixed a performance issue.

- C++
Published by bbuchfink about 9 years ago

diamond - DIAMOND v0.9.0

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.

- C++
Published by bbuchfink about 9 years ago

diamond - DIAMOND v0.8.38

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.

- C++
Published by bbuchfink about 9 years ago

diamond - DIAMOND v0.8.37

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.

- C++
Published by bbuchfink about 9 years ago