- NAME
- SYNOPSIS
- DESCRIPTION
- REQUIREMENTS
- INSTALLATION
- EXAMPLES
- COMPARISON
- AUTHOR
- COPYRIGHT AND LICENSE
jrange
operates ranges and links of ranges on chromosomes.
$ 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
This Java package is ported from the Perl package App::Rangeops
.
Oracle/Open JDK 1.7 or higher.
-
By Homebrew (Linuxbrew)
brew install wang-q/tap/jrange
-
By maven
git clone https://github.com/egateam/jrange cd jrange mvn clean verify
# 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
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
Qiang Wang <[email protected]>
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.