Releases: bbuchfink/diamond
Releases · bbuchfink/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.
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
, andsphylums
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
andsseq_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.