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Releases: refresh-bio/kmer-db

v2.2.3: Added `-version` switch

22 Oct 09:00
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v2.2.2: Added unified filtering and sampling

04 Oct 10:43
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  • Added rows sampling (-sample-rows option) in all2all-sp and all2all-parts modes.
  • Added unified filtering based on any specified measure (parameters -above, -above_eq, -below, and -below_eq replaced with -min and -max options).
  • Changed interface in distance mode: only one measure allowed, output file has to be specified.

NOTE: In this release an Kmer-db interface has changed slightly: -above/-above_eq/-below/-below_eq options have been replaced with -min/ -max and distance mode requires additional argument. Please update your pipelines accordingly.

v2.0.5: Updates in tests and automatic building scripts

12 Sep 22:24
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Updates in tests and automatic building scripts

v2.0.4: Update in `all2all-sp` mode: `above` and `below` options supported.

29 Aug 20:31
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v2.0.3: Bugfix release

28 Jun 19:39
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Bugfix for wrong input (non-DNA).

v2.0.2: Second version

26 Jun 20:51
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  • Added new modes: all2all_sparse, all2all_parts,
  • Serious time and memory optimizations,
  • Support of MacOS (Apple M and x86 CPUs) and ARM platforms.

v1.11.1

07 Mar 22:48
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Changes from the previous release:

  • Removed deadlock in -multisample-fasta mode,
  • Added support of sparse inputs in distance mode,
  • Added support of sparse outputs in all2all, new2all, and distance modes (-sparse switch) with optional filtering (-above/-below),
  • Extended help information.

v1.9.4

28 May 15:40
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GitHub Actions badge fixed

v1.9.2

17 Aug 19:29
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Changes from the last release:

  • Output matrices can be stored in sparse format (-sparse switch).
  • Better workload balancing.
  • Improved parallelization scheme in new2all mode (few-fold speed improvement).
  • Reduced memory footprint of -multisample-fasta mode.
  • More than one input FASTA files supported in -multisample-fasta mode.
  • Added -extend switch which allows extending existing kmer database.
  • Serialization/deserialization works much faster now.
  • Fixed serious bug in -multisample-fasta mode which caused incorrect kmers counting.

v1.7.6

18 Nov 11:57
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  • Sources compile under macOS.
  • Basic tests have been added.
  • Fixed bug in distance mode when sequence id contained spaces.
  • Makefile update (automatic detection of support of AVX2, different handling of CFLAGS and LDFLAGS).