Releases: refresh-bio/kmer-db
Releases · refresh-bio/kmer-db
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-querywhich 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-outindistancemode 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 (
minhashmode).
v1.51
- Serious reduction of time and memory requirements of
buildmode caused by the changes of the data structures. E.g., when tested on full k-mer spectrum of 40715 pathogen genomes, time and memory footprint decreased by 1/3 (1h30 to 1h, 60 to 40GB). - Several new parameters added.
- Lots of bugs fixed.