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@bbuchfink bbuchfink released this Feb 2, 2020 · 17 commits to master since this release

  • 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.
Assets 4

@bbuchfink bbuchfink released this Nov 19, 2019 · 83 commits to master since this release

  • 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.
Assets 4

@bbuchfink bbuchfink released this Nov 6, 2019 · 94 commits to master since this release

  • Fixed a bug that could cause alignment score overflows for scores > 65535 in frameshift alignment mode.
  • Fixed a clang compiler error.
Assets 4

@bbuchfink bbuchfink released this Nov 1, 2019 · 99 commits to master since this release

  • 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.
Assets 4

@bbuchfink bbuchfink released this Sep 17, 2019 · 133 commits to master since this release

  • 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.
Assets 4

@bbuchfink bbuchfink released this Jul 23, 2019 · 147 commits to master since this release

  • 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.
Assets 4

@bbuchfink bbuchfink released this Dec 27, 2018 · 204 commits to master since this release

  • 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).
Assets 4

@bbuchfink bbuchfink released this Dec 2, 2018 · 219 commits to master since this release

  • 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.
Assets 4
  • v0.9.22
  • a5ef80e
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@bbuchfink bbuchfink released this May 11, 2018 · 318 commits to master since this release

  • 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.
Assets 4
  • v0.9.21
  • 131bd4d
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  • v0.9.21
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@bbuchfink bbuchfink released this Apr 20, 2018 · 342 commits to master since this release

  • Fixed compiler errors on some systems.
Assets 4
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