a versatile toolkit for k-mers with taxonomic information
unikmer: fix loading custom taxonomy files.unikmer count:
-d for only count duplicated k-mers, for removing singleton in FASTQ.-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: new binary format supporting optional Taxids.unikmer subset.unikmer head for extracting the first N k-mers.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:
-i/--infile-list, if given, files in the list file are appended to files from cli arguments.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 filter: filter low-complexity k-mers.unikmer split: split k-mers into sorted chunk files.unikmer merge: merge from sorted chunk files.unikmer view:
-N/--show-code-only for only showing encoded integers.-q/--fastq.unikmer uniqs:
-x/--max-cont-non-uniq-kmers for limiting max continuous non-unique k-mers.-X/--max-num-cont-non-uniq-kmers for limiting max number of continuous non-unique k-mers.-m/--min-len.unikmer union:
-d/--repeated for only printing duplicate k-mers.unikmer sort:
-u/--unique for removing duplicated k-mers.-d/--repeated for only printing duplicate k-mers.-m/--chunk-size for limiting maximum memory for sorting.unikmer diff: