Current release: 0.2.0
cargo install intspan
```bash
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
```
```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
```
```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
```
```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
```
```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
```
```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
```
```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
```
```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
```
```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
```
```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
```
```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
```