# intspan
[](https://travis-ci.org/wang-q/intspan)
[](https://ci.appveyor.com/project/wang-q/intspan)
[](https://codecov.io/github/wang-q/intspan?branch=master)
[](https://crates.io/crates/intspan)
## Install
Current release: 0.2.0
`cargo install intspan`
## EXAMPLES
```bash
# cargo install --path . --force
intspan genome tests/resources/S288c.chr.sizes
intspan genome tests/resources/S288c.chr.sizes |
intspan stat tests/resources/S288c.chr.sizes stdin --all
intspan some tests/resources/Atha.yml tests/resources/Atha.list
intspan merge tests/resources/I.yml tests/resources/II.yml
intspan cover tests/resources/S288c.ranges
intspan cover tests/resources/S288c.ranges -c 2
intspan cover tests/resources/dazzname.ranges
intspan gff tests/resources/NC_007942.gff --tag tRNA
intspan range --op overlap tests/resources/intergenic.yml tests/resources/S288c.ranges
intspan span --op cover tests/resources/brca2.yml
intspan combine tests/resources/Atha.yml
jrunlist combine -o stdout tests/resources/Atha.yml
intspan compare \
--op intersect \
tests/resources/intergenic.yml \
tests/resources/repeat.yml
intspan split tests/resources/I.II.yml
intspan stat tests/resources/S288c.chr.sizes tests/resources/intergenic.yml
intspan stat tests/resources/S288c.chr.sizes tests/resources/I.II.yml
diff <(intspan stat tests/resources/Atha.chr.sizes tests/resources/Atha.yml) \
<(jrunlist stat -o stdout tests/resources/Atha.chr.sizes tests/resources/Atha.yml)
intspan statop \
--op intersect \
tests/resources/S288c.chr.sizes \
tests/resources/intergenic.yml \
tests/resources/repeat.yml
diff <(intspan statop \
--op intersect --all\
tests/resources/Atha.chr.sizes \
tests/resources/Atha.yml \
tests/resources/paralog.yml ) \
<(jrunlist statop \
-o stdout \
--op intersect --all \
tests/resources/Atha.chr.sizes \
tests/resources/Atha.yml \
tests/resources/paralog.yml )
intspan convert tests/resources/repeat.yml tests/resources/intergenic.yml |
intspan cover stdin |
intspan stat tests/resources/S288c.chr.sizes stdin --all
intspan merge tests/resources/repeat.yml tests/resources/intergenic.yml |
intspan combine stdin |
intspan stat tests/resources/S288c.chr.sizes stdin --all
```
## Benchmark 1
* Rust
```text
$ cd ~/Scripts/rust/intspan
$ cargo build --release --examples
$ command time -l target/release/examples/benchmark
["target/release/examples/benchmark"]
step 2
duration: 0.04019228699999999 s
step 3
duration: 0.048044463 s
step 4
duration: 0.101135046 s
step 5
duration: 0.378076464 s
step 6
duration: 0.6468764170000001 s
1.21 real 1.21 user 0.00 sys
1024000 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
259 page reclaims
0 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
304 involuntary context switches
```
* Java
```text
$ cd ~/Scripts/java/jintspan
$ mvn clean verify
$ command time -l java -jar target/jintspan-*-jar-with-dependencies.jar benchmark
step 2
duration 0.023358
step 3
duration 0.035295
step 4
duration 0.053588
step 5
duration 0.316216
step 6
duration 0.561500
1.12 real 1.38 user 0.07 sys
110718976 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
30334 page reclaims
4 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
1 signals received
4 voluntary context switches
926 involuntary context switches
```
* C
```text
$ cd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark
$ make
$ command time -l ./test_c benchmark
step 2
duration 0.022875
step 3
duration 0.032172
step 4
duration 0.057164
step 5
duration 0.294729
step 6
duration 0.525069
0.93 real 0.93 user 0.00 sys
1085440 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
274 page reclaims
0 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
176 involuntary context switches
```
* Perl
```text
$ cd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark
$ command time -l perl test_ai.pl benchmark
step 2
duration 2.506869
step 3
duration 2.831008
step 4
duration 2.969270
step 5
duration 46.395918
step 6
duration 96.724945
151.45 real 151.25 user 0.10 sys
6377472 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
1566 page reclaims
0 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
14911 involuntary context switches
```
* Perl XS
```text
$ cd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark
$ command time -l perl test_ai.pl benchmark xs
step 2
duration 0.273726
step 3
duration 0.296036
step 4
duration 0.344481
step 5
duration 2.072225
step 6
duration 9.789098
12.80 real 12.76 user 0.02 sys
6475776 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
1590 page reclaims
0 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
3016 involuntary context switches
```
## Benchmark 2
* Rust
```text
$ cd ~/Scripts/rust/intspan
$ cargo build --release --examples
$ command time -l target/release/examples/file
["target/release/examples/file"]
step 1 create
duration: 0.022158192 s
step 2 intersect
duration: 0.846951539 s
step 3 intersect runlist
duration: 0.9379064089999999 s
1.81 real 1.80 user 0.00 sys
2555904 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
633 page reclaims
0 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
383 involuntary context switches
```
* Java
```text
$ cd ~/Scripts/java/jintspan
$ mvn clean verify
$ command time -l java -jar target/jintspan-*-jar-with-dependencies.jar file
step 1 create
duration 0.071450
step 2 intersect
duration 0.499175
step 3 intersect runlist
duration 0.789997
1.52 real 1.69 user 0.14 sys
308686848 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
78554 page reclaims
2 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
1 signals received
3 voluntary context switches
2034 involuntary context switches
```
* C
```text
$ cd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark
$ make
$ command time -l ./test_c file
step 1 create
duration 0.118375
step 2 intersect
duration 2.174462
step 3 intersect runlist
duration 18.218233
20.51 real 20.42 user 0.05 sys
2121728 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
521 page reclaims
6 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
6360 involuntary context switches
```
* Perl
```text
$ cd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark
$ command time -l perl test_ai.pl file
==> test against large sets
step 1 create
duration 4.548069
step 2 intersect
duration 61.313397
step 3 intersect runlist
duration 61.335031
127.25 real 126.56 user 0.38 sys
11943936 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
2924 page reclaims
1 page faults
0 swaps
0 block input operations
0 block output operations
0 messages sent
0 messages received
0 signals received
6 voluntary context switches
45869 involuntary context switches
```
* Perl XS
```text
$ cd ~/Scripts/cpan/AlignDB-IntSpanXS/benchmark
$ command time -l perl test_ai.pl file xs
==> test against large sets
step 1 create
duration 0.116019
step 2 intersect
duration 8.530752
step 3 intersect runlist
duration 8.677303
17.37 real 17.26 user 0.05 sys
9822208 maximum resident set size
0 average shared memory size
0 average unshared data size
0 average unshared stack size
2407 page reclaims
0 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
7011 involuntary context switches
```