v0.11.0

• v0.11.0
  • 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 v0.10.0

Changes

• v0.10.0
  • unikmer: fix loading custom taxonomy files.
  • unikmer count:
    • new flag -d for only count duplicated 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.

unikmer v0.9.0

Changes

• v0.9.0
  • 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.

unikmer v0.8.0

Changelog

• 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.

unikmer v0.7.0

Changes

• v0.7.0
  • 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 duplicated 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.

unikmer v0.6.2

Changes

• unikmer encode: better output for bits presentation of encoded k-mers (-a/--all)

unikmer v0.6.1

Changes

• 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.

unikmer v0.6.0

Changes

• 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

unikmer v0.5.2

Changelog

• unikmer locate: fix bug
• unikmer: doc update

unikmer v0.5.1

Changelog

• v0.5.1
  • unikmer locate/uniqs: fix options checking
• v0.5.0
  • 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.