Changes

v0.9.4 - 2023-09-18

• kmcp merge:
  • trim tailing tab in merged result, down-stream results are not affected. #38
• kmcp profile:
  • fix log of "xx% (yy/zz) reads matched", the numerator should be the number of matched reads instead of reads belonging to references.
  • early quit when no target detected.
  • slightly speedup.

Links

OS	Arch	File, 中国镜像	Download Count
Linux	64-bit	kmcp_linux_amd64.tar.gz, 中国镜像
Linux	arm64	kmcp_linux_arm64.tar.gz, 中国镜像
macOS	64-bit	kmcp_darwin_amd64.tar.gz, 中国镜像
macOS	arm64	kmcp_darwin_arm64.tar.gz, 中国镜像
Windows	64-bit	kmcp_windows_amd64.exe.tar.gz, 中国镜像

Notes:

• please open an issue to request binaries for other platforms or compile from the source.
• run kmcp version to check update !!!
• run kmcp autocompletion to update shell autocompletion script !!!

Changes

v0.9.3 - 2023-07-16

• kmcp compute/split-genomes:

  • fix a bug in chunk computation when splitting circular genomes (--circular).

• kmcp search/merge:

  • append simple stats to the search result as comment lines, including the number of input and matched queries. e.g.,

      # input queries: 930254
      # matched queries: 923820
      # matched percentage: 99.3084%
    

• kmcp profile:

  • fix metaphlan out format. #34

  • show stats of the number of input and matched queries in log. It would be helpful to show whether the reference genomes cover all microorganisms in the sample.

      20:00:55.295 [INFO] 99.3084% (923820/930254) reads matched
      20:00:55.295 [INFO] 100.0000% (923820/923820) matched reads belong to the 2 references in the profile
    

• new tutorials:

  • Detecting specific pathogens
  • Detecting contaminated sequences

v0.9.2 - 2023-05-16

• kmcp profile/cos2simi/filter/index-info/merge-regions/query-fpr:
  • rename/unify the long flag --out-prefix to --out-file.
• kmcp profile:
  • fix the number of reads belonging to references in the profile when no matches are found, which should be 0 instead of 1.
• new command:
  • kmcp utils index-density: plotting the element density of bloom filters for an index file.
    An audience was concerned about it, but the results showed the elements (1s) are uniformly distributed in all BFs.

v0.9.1 - 2022-12-26

• kmcp search
  • faster speed for ARM architectures.
  • fix compilation for ARM architectures.

Changes

v0.9.0 - 2022-09-28

• compute:
  • smaller output files and faster speed.
  • more even genome splitting.
• index:
  • faster speed due to smaller input files.
• search:
  • more accurate and smaller query FPR following Theorem 2 in SBT paper, instead of the Chernoff bound.
  • change the default value of -f/--max-fpr from 0.05 to 0.01.
  • 10-20% speedup.
• profile:
  • more accurate abundance estimation using EM algorithm.
  • change the default value of -f/--max-fpr from 0.05 to 0.01.
  • mode 0: change the default value of -H/--min-hic-ureads-qcov from 0.55 to 0.7.
  • increase float width of reference coverage in KMCP profile format from 2 to 6.
• util query-fpr:
  • compute query FPR following Theorem 2 in SBT paper, instead of the Chernoff bound.
• new commands:
  • utils split-genomes for splitting genomes into chunks.
  • utils ref-info for printing information of reference (chunks), including the number of k-mers
    and the actual false-positive rate.

Changes

v0.8.3 - 2022-08-15

• kmcp: fix compiling from source for ARM architectures. #17
• search:
  • fix searching with paired-end reads where the read2 is shorter than the value of --min-query-len. #10
  • fix the log. #8
  • a new flag -f/--max-fpr: maximal false positive rate of a query (default 0.05). It reduces the unnecessary output when searching with a low minimal query coverage (-t/--min-query-cov).
• profile:
  • recommend using the flag --no-amb-corr to disable ambiguous reads correction when >= 1000 candidates are detected.
  • fix logging when using --level strain and no taxonomy given.

v0.8.3-alpha

• search:
  • fix panic for paired-end reads with read2 shorter than the value of --min-query-len. #10
  • fix log. #8
• profile:
  • recommend to use the flag --no-amb-corr to disable ambiguous reads correction when >= 1000 candidates are detected.

Changes

• v0.8.2 - 2022-03-26
  • search:
    • flag -g/--query-whole-file:
      • fix panic for invalid input.
      • add gaps of k-1 bp before concatatenating seqs.
    • add warning for invalid input.
  • profile:
    • allow modifying parts of parameters in preset profiling modes. #5
    • decrease thresholds of minimal reads and unique reads in preset profiling modes 1 and 2 for low coverage sequence data.
      the profiling results generated with mode 3 in the manuscript are not affected.

Changelog

• v0.8.1 - 2022-03-07
  • update help message, show common usages, add examples, add notes to important options.

v0.8.0 - 2022-02-24

• commands:
  • new command utils cov2simi: Convert k-mer coverage to sequence similarity.
  • new command utils query-fpr: Compute the maximal false positive rate of a query.
• compute:
  • update doc.
  • add flags compatibility check.
• search:
  • output the false positive rate of each match, rather than the FPR upper bound of the query.
    this could save some short queries with high similarity.
  • change default values of reads filter, because clinical data contain many short reads.
    • -c/--min-uniq-reads: 30 -> 10.
    • -m/--min-query-len: 70 -> 30.
  • update doc.
• profile:
  • rename flags:
    • --keep-main-matches -> --keep-main-matches.
    • --keep-perfect-match -> --keep-perfect-matches.
  • change default values:
    • --max-qcov-gap: 0.2 -> 0.4.
  • mode 0 (pathogen detection):
    • switch on flag --keep-main-matches
    • use --max-qcov-gap 0.4
  • update doc.