Releases: refresh-bio/kmer-db
Releases · refresh-bio/kmer-db
v2.0.4: Update in `all2all-sp` mode: `above` and `below` options supported.
v2.0.3: Bugfix release
Bugfix for wrong input (non-DNA).
v2.0.2: Second version
- 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
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
, anddistance
modes (-sparse
switch) with optional filtering (-above
/-below
), - Extended help information.
v1.9.4
v1.9.2
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
- 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).
v1.7.5
v1.7.3
Added:
- For performance reasons upper triangle (with diagonal) of distance matrix in all2all mode is no longer saved.
- Possibility to specify low threshold of k-mer minhash filter (-f-start parameter).
- When loading genome files, exact filenames are examined first. If this fails, an attempt to add predefined extensions is made.
- Added new distance measure
-mash-query
which is a mash distance calculated w.r.t. a query length (use if the query is much shorter than database sequences). - C++11 compatibility (compiles with G++ 4.8.5).
Fixed:
- Rare bug in hashtable when k-mer containing only T bases was treated as an empty entry. Now an empty item is indicated by a special value instead of a special key.
v1.6.2: After data structure update - stable
Note: Starting from this release version numbering conforms to major.minor.patch scheme.
Added:
- Switch
-phylip-out
indistance
mode which allows storing distance/similarity matrices in Phylip format.
Fixed several bugs from 1.51 release:
- Incorrect support of k-mer lengths < 16.
- Very long processing of long k-mers (k >= 26).
- Segmentation fault when storing minhashed k-mers on a disk (
minhash
mode).