{"action":"created","issue":{"url":"https://api.github.com/repos/dozmorovlab/HiCcompare/issues/7","repository_url":"https://api.github.com/repos/dozmorovlab/HiCcompare","labels_url":"https://api.github.com/repos/dozmorovlab/HiCcompare/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/dozmorovlab/HiCcompare/issues/7/comments","events_url":"https://api.github.com/repos/dozmorovlab/HiCcompare/issues/7/events","html_url":"https://github.com/dozmorovlab/HiCcompare/issues/7","id":359014503,"node_id":"MDU6SXNzdWUzNTkwMTQ1MDM=","number":7,"title":"Working with cooler files","user":{"login":"Phlya","id":2895034,"node_id":"MDQ6VXNlcjI4OTUwMzQ=","avatar_url":"https://avatars3.githubusercontent.com/u/2895034?v=4","gravatar_id":"","url":"https://api.github.com/users/Phlya","html_url":"https://github.com/Phlya","followers_url":"https://api.github.com/users/Phlya/followers","following_url":"https://api.github.com/users/Phlya/following{/other_user}","gists_url":"https://api.github.com/users/Phlya/gists{/gist_id}","starred_url":"https://api.github.com/users/Phlya/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Phlya/subscriptions","organizations_url":"https://api.github.com/users/Phlya/orgs","repos_url":"https://api.github.com/users/Phlya/repos","events_url":"https://api.github.com/users/Phlya/events{/privacy}","received_events_url":"https://api.github.com/users/Phlya/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-09-11T12:01:06Z","updated_at":"2018-09-13T23:02:49Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nI am trying to use HiCCompare with cooler files. Is it right that you are suggesting to dump the pixels from the cooler (basically, a 7-column bedpe file), but then read all of them into memory to convert into an R sparse matrix? The problem is that this is very slow for high resolutions (e.g. 10 kb), and also takes up a lot of memory... Is it impossible to just read the data directly from the cooler file, which is just an hdf5 container, for each chromosome while running normalization and calling of differential interactions, so that the whole genome is never stored in memory?\r\n\r\nThanks,\r\nIlya"},"comment":{"url":"https://api.github.com/repos/dozmorovlab/HiCcompare/issues/comments/421179311","html_url":"https://github.com/dozmorovlab/HiCcompare/issues/7#issuecomment-421179311","issue_url":"https://api.github.com/repos/dozmorovlab/HiCcompare/issues/7","id":421179311,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMTE3OTMxMQ==","user":{"login":"mdozmorov","id":864945,"node_id":"MDQ6VXNlcjg2NDk0NQ==","avatar_url":"https://avatars2.githubusercontent.com/u/864945?v=4","gravatar_id":"","url":"https://api.github.com/users/mdozmorov","html_url":"https://github.com/mdozmorov","followers_url":"https://api.github.com/users/mdozmorov/followers","following_url":"https://api.github.com/users/mdozmorov/following{/other_user}","gists_url":"https://api.github.com/users/mdozmorov/gists{/gist_id}","starred_url":"https://api.github.com/users/mdozmorov/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mdozmorov/subscriptions","organizations_url":"https://api.github.com/users/mdozmorov/orgs","repos_url":"https://api.github.com/users/mdozmorov/repos","events_url":"https://api.github.com/users/mdozmorov/events{/privacy}","received_events_url":"https://api.github.com/users/mdozmorov/received_events","type":"User","site_admin":false},"created_at":"2018-09-13T23:02:49Z","updated_at":"2018-09-13T23:02:49Z","author_association":"CONTRIBUTOR","body":"That is fantastic, thanks, @Phlya! We will incorporate you code in the documentation. "}}
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