egateam/jrange

`jrange` operates ranges and links of ranges on chromosomes

• NAME
• SYNOPSIS
• DESCRIPTION
• REQUIREMENTS
• INSTALLATION
• EXAMPLES
• COMPARISON
  • BENCHMARK
• AUTHOR
• COPYRIGHT AND LICENSE

NAME

jrange operates ranges and links of ranges on chromosomes.

SYNOPSIS

$ jrange --help
Usage: <main class> [options] [command] [command options]
  Options:
    --help, -h
       Print this help and quit
       Default: false
  Commands:
    path      Replace ranges within links, incorporate hit strands and remove nested links
      Usage: path [options]
        Options:
          --file
             output filename instead of full path
             Default: false

    sort      Replace ranges within links, incorporate hit strands and remove nested links
      Usage: sort [options] <infiles>
        Options:
          --outfile, -o
             Output filename. [stdout] for screen.

    merge      Merge overlapped ranges via overlapping graph
      Usage: merge [options] <infiles>
        Options:
          --coverage, -c
             When larger than this ratio, merge ranges.
             Default: 0.95
          --outfile, -o
             Output filename. [stdout] for screen.
          --verbose, -v
             Verbose mode.
             Default: false

    clean      Replace ranges within links, incorporate hit strands and remove nested links
      Usage: clean [options] <infiles>
        Options:
          --bundle, -b
             Bundle overlapped links. This value is the overlapping size.
             Suggested value is [500].
             Default: 0
          --outfile, -o
             Output filename. [stdout] for screen.
          --replace, -r
             Two-column tsv file, normally produced by command merge.
          --verbose, -v
             Verbose mode.
             Default: false

    connect      (Unfinished) Connect range links in paralog graph
      Usage: connect [options] <infiles>
        Options:
          --outfile, -o
             Output filename. [stdout] for screen.

    covered      Covered regions from .ovlp.tsv files
      Usage: covered [options] <infiles>
        Options:
          --basecov
             coverage per base location
             Default: false
          --coverage, -c
             minimal coverage
             Default: 3
          --idt, -i
             minimal length of overlaps
             Default: 0.0
          --len, -l
             minimal length of overlaps
             Default: 1000
          --longest
             only keep the longest span
             Default: false
          --meancov
             mean coverage per base location
             Default: false
          --outfile, -o
             Output filename. [stdout] for screen.
          --paf
             input format as PAF
             Default: false

DESCRIPTION

This Java package is ported from the Perl package App::Rangeops.

REQUIREMENTS

Oracle/Open JDK 1.7 or higher.

INSTALLATION

• By Homebrew (Linuxbrew)

  brew install wang-q/tap/jrange

• By maven

  git clone https://github.com/egateam/jrange
  cd jrange
  
  mvn clean verify

EXAMPLES

# mvn clean verify
# java -jar target/jrange-*-jar-with-dependencies.jar sort src/test/resources/II.links.tsv -o stdout

jrange path
jrange path --file

jrange sort src/test/resources/II.links.tsv -o stdout

jrange merge src/test/resources/II.links.tsv -o stdout

cat src/test/resources/I.links.tsv |
    jrange merge stdin -o stdout

jrange clean src/test/resources/II.sort.tsv -o stdout

jrange clean src/test/resources/II.sort.tsv --bundle 500 -o stdout 

jrange clean src/test/resources/II.sort.tsv -r src/test/resources/II.merge.tsv -o stdout

jrange covered src/test/resources/1_4.pac.paf.ovlp.tsv -o stdout
    
jrange covered src/test/resources/1_4.pac.paf.ovlp.tsv --basecov -o stdout
    
jrange covered src/test/resources/1_4.pac.paf.ovlp.tsv --meancov -o stdout

jrange covered src/test/resources/11_2.long.paf --paf -o stdout

# (Unfinished)
#jrange connect src/test/resources/II.clean.tsv -o stdout
#jarnge reduce

COMPARISON

BENCHMARK

bash benchmark/run.sh

• OSX 10.14 i7-8700k oracleJDK8

==> merge <==
==> jrange merge lastz blast
        4.10 real         4.37 user         0.64 sys
2230620160  maximum resident set size
         0  average shared memory size
         0  average unshared data size
         0  average unshared stack size
    544047  page reclaims
      2264  page faults
         0  swaps
         0  block input operations
         0  block output operations
         0  messages sent
         0  messages received
         1  signals received
       267  voluntary context switches
      4859  involuntary context switches
==> linkr merge lastz blast
        7.93 real         7.90 user         0.01 sys
  10047488  maximum resident set size
         0  average shared memory size
         0  average unshared data size
         0  average unshared stack size
      2163  page reclaims
       299  page faults
         0  swaps
         0  block input operations
         0  block output operations
         0  messages sent
         0  messages received
         0  signals received
         1  voluntary context switches
      1528  involuntary context switches
==> rangeops merge lastz blast
      107.08 real       296.72 user         0.69 sys
  81563648  maximum resident set size
         0  average shared memory size
         0  average unshared data size
         0  average unshared stack size
    197561  page reclaims
       115  page faults
         0  swaps
         0  block input operations
         0  block output operations
       140  messages sent
       131  messages received
         0  signals received
       379  voluntary context switches
    100948  involuntary context switches

==> clean <==
==> jrange clean sort.clean
        2.33 real         3.46 user         0.34 sys
1150685184  maximum resident set size
         0  average shared memory size
         0  average unshared data size
         0  average unshared stack size
    282645  page reclaims
        14  page faults
         0  swaps
         0  block input operations
         0  block output operations
         0  messages sent
         0  messages received
         1  signals received
        30  voluntary context switches
      4889  involuntary context switches
==> linkr clean sort.clean
        2.54 real         2.52 user         0.00 sys
  17698816  maximum resident set size
         0  average shared memory size
         0  average unshared data size
         0  average unshared stack size
      4314  page reclaims
        16  page faults
         0  swaps
         0  block input operations
         0  block output operations
         0  messages sent
         0  messages received
         0  signals received
         0  voluntary context switches
       881  involuntary context switches
==> rangeops clean sort.clean
       50.40 real        50.29 user         0.06 sys
  84758528  maximum resident set size
         0  average shared memory size
         0  average unshared data size
         0  average unshared stack size
     25062  page reclaims
         0  page faults
         0  swaps
         0  block input operations
         0  block output operations
         0  messages sent
         0  messages received
         0  signals received
         4  voluntary context switches
      5001  involuntary context switches

==> clean bundle <==
==> jrange clean bundle sort.clean
        4.34 real         6.10 user         0.36 sys
1164464128  maximum resident set size
         0  average shared memory size
         0  average unshared data size
         0  average unshared stack size
    286390  page reclaims
         0  page faults
         0  swaps
         0  block input operations
         0  block output operations
         0  messages sent
         0  messages received
         3  signals received
         0  voluntary context switches
      4843  involuntary context switches
==> linkr clean bundle sort.clean
        4.94 real         4.93 user         0.00 sys
  22179840  maximum resident set size
         0  average shared memory size
         0  average unshared data size
         0  average unshared stack size
      5422  page reclaims
         2  page faults
         0  swaps
         0  block input operations
         0  block output operations
         0  messages sent
         0  messages received
         0  signals received
         0  voluntary context switches
       269  involuntary context switches
==> rangeops clean bundle sort.clean
       81.84 real        81.47 user         0.19 sys
  90705920  maximum resident set size
         0  average shared memory size
         0  average unshared data size
         0  average unshared stack size
     26608  page reclaims
         0  page faults
         0  swaps
         0  block input operations
         0  block output operations
         0  messages sent
         0  messages received
         0  signals received
         4  voluntary context switches
     29956  involuntary context switches

AUTHOR

Qiang Wang <[email protected]>

COPYRIGHT AND LICENSE

This software is copyright (c) 2016 by Qiang Wang.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.