Quickstart (CLI)#
First, install hictk with one of the methods listed in the Installation section.
Next, verify that hictk was installed correctly with:
user@dev:/tmp$ hictk --version
hictk-v0.0.12
Command line interface#
hictk CLI support performing common operations on .hic and .cool files directly from the shell.
Verifying file integrity#
hictk validate interactions.cool --validate-index
hictk validate interactions.hic
For more detailed examples refer to File validation
Reading interactions#
hictk supports reading interactions from .hic and .cool files through the hictk dump
command:
user@dev:/tmp$ hictk dump interactions.cool
0 0 1745
0 1 2844
0 2 409
...
user@dev:/tmp$ hictk dump interactions.cool --join
chr2L 0 10000 chr2L 0 10000 1745
chr2L 0 10000 chr2L 10000 20000 2844
chr2L 0 10000 chr2L 20000 30000 409
...
For more detailed examples refer to Reading interactions
Other operations#
API#
Refer to Quickstart (API).