CHANGELOG.md

Changelog

• v0.21.0 - 2024-xx-xx
  • unikmer:
    • -i, --infile-list accepts stdin (-).
    • new global flag --skip-file-check.
    • change the global flag --nocheck-file to --skip-flag-check.
  • unikmer merge:
    • fix do not add the extension .unik if the value of flag -o/--out-prefix already has one.
• 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.
• 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 64.
• 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.
• v0.18.8 - 2021-09-17
  • use new version of nthash with better performance.
  • unikmer info: fix typoes.
• v0.18.7 - 2021-08-30
  • unikmer: better counting speed by upstream optimization of FASTA/Q parsing.
  • unikmer concat: fix parsing flag -n.
• v0.17.3 - 2021-05-16
  • unikmer: fix buiding for 386. #21
• v0.17.2 - 2021-02-05
  • 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 - 2021-01-18
  • unikmer rfilter: change handling of black list.
• v0.17.0 - 2021-01-15
  • syncmer value changed with different hash method.
  • unikmer count: syncmer value changed.
• v0.16.1 - 2020-12-28
  • change Header.Number from int64 to uint64
  • unikmer info: fix recounting problem for unsorted kmers but with Number.
• v0.16.0 - 2020-12-28
  • unikmer:
    • binary file format change: fix reading long description, and bump version to 5.0.
    • better binary file parsing performance.
• v0.15.0 - 2020-12-25
  • 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.
• v0.14.0 - 2020-11-25
  • 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.
• v0.13.0 - 2020-10-23
  • 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.
• v0.12.0 - 2020-09-24
  • 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
• v0.11.0 - 2020-07-06
  • new command: unikmer rfilter for filtering k-mers by taxonomic rank.
  • unikmer inter: new flag -m/--mix-taxid allowing part of files being whithout taxids.
  • unikmer dump: fix a nil pointer bug.
  • unikmer count:
    • fix checking taxid in sequence header.
    • fix setting global taxid.
  • unikmer count/diff/union: slightly reduce memory and speedup when sorting k-mers.
  • unikmer filter: change scoring.
  • unikmer count/locate/uniqs: remove flag --circular.
• v0.10.0 - 2020-05-21
  • unikmer: fix loading custom taxonomy files.
  • unikmer count:
    • new flag -d for only count duplicate k-mers, for removing singleton in FASTQ.
    • fix nil pointer bug of -t.
  • unikmer split: fix memery and last odd k-mer mising bug for given ONE sorted input file.
  • unikmer sort: skip loading taxonomy data when neither -u or -d given.
  • unikmer diff: 2X speedup, and requiring 1th file being sorted.
  • unikmer inter: 2-5X speedup, and requiring all files being sorted, sorted output by default.
• v0.9.0 - 2020-02-18
  • unikmer: new binary format supporting optional Taxids.
  • deleted command: unikmer subset.
  • new command: unikmer head for extracting the first N k-mers.
  • new command: unikmer tsplit for splitting k-mers according to taxid.
  • unikmer grep: support searching with taxids.
  • unikmer count: support parsing taxid from FASTA/Q header.
• v0.8.0 - 2019-02-09
  • unikmer:
    • new option -i/--infile-list, if given, files in the list file are appended to files from cli arguments.
    • improve performance of binary file reading and writing.
  • unikmer sort/split/merge: safer forcing deletion of existed outdir, and better log.
  • unikmer split: performance improvement for single sorted input file.
  • unikmer sort: performance improvement for using -m/--chunk-size.
  • unikmer grep: rewrite, support loading queries from .unik files.
  • unikmer dump: fix number information in output file.
  • unikmer concat: new flag -s/--sorted.
• v0.7.0 - 2019-09-29
  • new command unikmer filter: filter low-complexity k-mers.
  • new command unikmer split: split k-mers into sorted chunk files.
  • new command unikmer merge: merge from sorted chunk files.
  • unikmer view:
    • new option -N/--show-code-only for only showing encoded integers.
    • fix output error for -q/--fastq.
  • unikmer uniqs:
    • new option -x/--max-cont-non-uniq-kmers for limiting max continuous non-unique k-mers.
    • new option -X/--max-num-cont-non-uniq-kmers for limiting max number of continuous non-unique k-mers.
    • fix bug for -m/--min-len.
  • unikmer union:
    • new option -d/--repeated for only printing duplicate k-mers.
  • unikmer sort:
    • new option -u/--unique for removing duplicate k-mers.
    • new option -d/--repeated for only printing duplicate k-mers.
    • new option -m/--chunk-size for limiting maximum memory for sorting.
  • unikmer diff:
    • small speed improvements.
• v0.6.2 - 2019-01-21
  • unikmer encode: better output for bits presentation of encoded k-mers (-a/--all)
• v0.6.1 - 2019-01-21
  • unikmer dump:
    • new option -K/--canonical to keep the canonical k-mers.
    • new option -k/--canonical-only to only keep the canonical k-mers.
    • new option -s/--sorted to save sorted k-mers.
  • unikmer encode: add option -K/--canonical to keep the canonical k-mers.
• v0.6.0 - 2019-01-20
  • unikmer: check encoded integer overflow
  • new command unikmer encode: encode plain k-mer text to integer
  • new command unikmer decode: decode encoded integer to k-mer text
• v0.5.3 - 2018-11-28
  • unikmer count/dump: check file before handling them.
• v0.5.2 - 2018-11-28
  • unikmer locate: fix bug.
  • unikmer: doc update.
• v0.5.1 - 2018-11-07
  • unikmer locate/uniqs: fix options checking.
• v0.5.0 - 2018-11-07
  • unikmer diff: fix concurrency bug when cloning kmers from first file.
  • new command unikmer locate: locate Kmers in genome.
  • new command unikmer uniqs: mapping Kmers back to genome and find unique subsequences.
• v0.4.4 - 2018-10-27
  • unikmer: add global option -L/--compression-level.
  • unikmer diff: reduce memory occupation, speed not affected.
• v0.4.3 - 2018-10-13
  • unikmer diff: fix bug of hanging when the first file having no Kmers.
• v0.4.2 - 2018-10-13
  • unikmer stats/diff: more intuitional output
• v0.4.1 - 2018-10-10
  • Better performance of writing and reading binary files
• v0.4.0 - 2018-10-09
  • Binary serialization format changed.
  • new command unikmer sort: sort binary files
  • unikmer count/diff/union/inter: better performance, add option to sort Kmers which significantly reduces file size
  • unikmer dump: changed option
  • unikmer count: changed option
• v0.3.1 - 2018-09-25
  • Binary serialization format changed.
  • new command unikmer stats: statistics of binary files.
  • unikmer: adding global option -i/--infile-list for reading files listed in file.
  • unikmer diff: fixed a concurrency bug when no diff found.
• v0.2.1 - 2018-09-23
  • unikmer count: performance improvement and new option --canonical for only keeping canonical Kmers.
• v0.2 - 2018-09-09
  • new command unikmer sample: sample Kmers from binary files.
  • new global options:
    • -c, --compact: write more compact binary file with little loss of speed.
    • -C, --no-compress: do not compress binary file (not recommended).
  • some improvements.
• v0.1.0 - 2018-08-09
  • first release