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Releases: shenwei356/unikmer

unikmer v0.20.0

08 Jun 10:03
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v0.20.0 - 2023-11-11 Github Releases (by Release)

  • 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
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Linux arm64 unikmer_linux_arm64.tar.gz,
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macOS 64-bit unikmer_darwin_amd64.tar.gz,
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macOS arm64 unikmer_darwin_arm64.tar.gz,
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Windows 64-bit unikmer_windows_amd64.exe.tar.gz,
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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

26 Dec 01:57
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v0.19.1 - 2022-12-26 Github Releases (by Release)

  • 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

25 Apr 12:46
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v0.19.0 - 2022-04-25 Github Releases (by Release)

  • 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

30 Aug 02:51
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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

05 Feb 02:00
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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

28 Dec 09:24
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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

25 Dec 02:29
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  • 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

25 Nov 07:04
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  • 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

23 Oct 12:21
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  • 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

24 Sep 07:36
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  • 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