unikmer v0.20.0

v0.20.0 - 2023-11-11

• unikmer:
  • update help messages
  • rename subcommand uniqs to map.
  • do not add the extension .unik if the value of flag -o/--out-prefix already has one.
• unikmer sort:
  • fix the bug of using both -d/--repeated and -m/--chunk-size, which seems to existed for 4 years.
• unikmer merge:
  • fix the bug of missing one record when taxid information is contained.
• unikmer num:
  • -f/--force also support sorted files.
• unikmer map:
  • fix a bug of missing some regions.
• unikmer locate:
  • fix seq ID error in output.
  • deduplicate output.

Links

OS	Arch	File, 中国镜像	Download Count
Linux	64-bit	unikmer_linux_amd64.tar.gz, 中国镜像
Linux	arm64	unikmer_linux_arm64.tar.gz, 中国镜像
macOS	64-bit	unikmer_darwin_amd64.tar.gz, 中国镜像
macOS	arm64	unikmer_darwin_arm64.tar.gz, 中国镜像
Windows	64-bit	unikmer_windows_amd64.exe.tar.gz, 中国镜像

Notes:

• please open an issue to request binaries for other platforms.
• run unikmer version to check update !!!
• run unikmer autocompletion to update shell autocompletion script !!!

unikmer v0.19.1

v0.19.1 - 2022-12-26

• unikmer: When environment variable UNIKMER_DB is set, explicitly setting --data-dir will overide the value of UNIKMER_DB.
• unikmer uniqs: skip sequences shorter than K.
• unikmer count/encode: limit the maximum k-mer size to 65.

unikmer v0.19.0

v0.19.0 - 2022-04-25

• rename command genautocomplete to autocompletion.
• remove command help.
• change default value of option -j from 2 to 4.
• unikmer count/uniqs/locate: new flag -B/--seq-name-filter for filtering out unwanted sequences like plasmids.
• unikmer count: add support of .xz and .zst files.

unikmer v0.18.7

Changelog

• v0.18.7
  • unikmer: better counting speed by upstream optimization of FASTA/Q parsing.
  • unikmer concat: fix parsing flag -n.
• v0.17.3
  • unikmer: fix buiding for 386. #21

unikmer v0.17.2

Changelog

• v0.17.2
  • unikmer: slightly speedup for computing LCA.
  • unikmer rfilter:
    • flag -E/--equal-to supports multiple values.
    • new flag -n/--save-predictable-norank: do not discard some special ranks without order when using -L, where rank of the closest higher node is still lower than rank cutoff.
• v0.17.1
  • unikmer rfilter: change handling of black list.
• v0.17.0
  • syncmer value changed with different hash method.
  • unikmer count: syncmer value changed.

unikmer v0.16.1

Changelog

• v0.16.1
  • change Header.Number from int64 to uint64
  • unikmer info: fix recounting problem for unsorted kmers but with Number.
• v0.16.0
  • unikmer:
    • binary file format change: fix reading long description, and bump version to 5.0.
    • better binary file parsing performance.

unikmer v0.15.0

• v0.15.0
  • unikmer:
    • binary file minor change: increase description maximal length from 128 B to 1KB.
    • separating k-mers (sketches) indexing and searching from unikmer, including unikmer db info/index/search.
  • unikmer count: fix syncmer.
  • unikmer dump: new flag --hashed.
  • rename unikmer stats to unikmer info, and add new column description.

unikmer v0.14.0

• v0.14.0
  • unikmer union: fix bug when flag -s not given.
  • unikmer count/uniqs/locate: performance improvement on generating k-mers.
  • unikmer count/db: support scaled/minizimer/syncmer sketch.
  • unikmer stats: change format.

unikmer v0.13.0

• v0.13.0
  • new command unikmer common: Finding k-mers shared by most of multiple binary files.
  • unikmer common/count/diff/grep/rfilter/sort/split/union: faster sorting.
  • unikmer uniqs: better result for flag --circular.
  • unikmer search: fix a bug when searching on database with more than one hash.

unikmer v0.12.0

• v0.12.0
  • unikmer:
    • support longer k (k>32) by saving ntHash.
    • new flag -nocheck-file for not checking binary file.
  • new commands:
    • unikmer db index: constructing index from binary files
    • unikmer db info: printing information of index file
    • unikmer db search: searching sequence from index database
  • unikmer rfilter: change format of rank order file.
  • unikmer inter/union: speedup for single input file.
  • unikmer concat:
    • new flag -t/--taxid for assigning global taxid, this can slightly reduce file size.
    • new flag -n/--number for setting number of k-mers.
  • unikmer num:
    • new flag -f/--force for counting k-mers.
  • unikmer locate: output in BED6.
  • unikmer locate/uniqs: support multiple genome files.
  • unikmer uniqs:
    • stricter multiple mapping limit.
    • new flag -W/--seqs-in-a-file-as-one-genome.
  • unikmer count:
    • new flag -u/--unique for output unique (single copy) kmers