-
Notifications
You must be signed in to change notification settings - Fork 64
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
CircularView structural variant chord track slow when using VCF backend #994
Comments
Just adding as a note: 45M track crashes the circular view jbrowse-components/test_data/config_demo.json Lines 335 to 350 in 97f38e9
|
note that the 45MB gzip data inflates to 475MB ungzipped, so a lot of time is spent spinning on parsing the data. flamegraph looks like a lot of time spent doing parse line, checkline, etc sort of similar to #2681 if we want to handle such size files, part of it will be making parsing code faster |
random other note: the clinvar vcf file would probably currently not display anything in the circular view anyways because it does not have breakends and translocations |
probably a misguided issue |
This took 100 seconds to load for me. Profiling isn't immediately revealing but there is a lot of work in the VCF and tabix parsing
Note that our common use case is now driving from a Spreadsheet view but this may be of interest still, so this is low priority
http://localhost:3000/?config=test_data%2Fconfig_demo.json&session=eJylWsmO20YQ_RWDZ3nQ-6JbbMOxE8QxZpTxEhgCRbakjilSITmLPdC_p6iNY6Q4SIo3SWy-Lr7aXlH9kJTpJiTT5F24e3YVmiZW5TPBBHvOzHPmZ9xOlZ5KfcGM-ZxMkk1ar2KZTNkkyev0LtQfYt6uk6l0apLcxnDXJNM_H5KYA2T8HJu_5Hr2O9zXftt2u7yMdXZTpPU1rIRfq-WyCe1lmse0hBuf8wttmfVGCmO9ct6YSbLYvg_1-_tkqrwXXtkLIZQSjHcbtnWafX20Y_NTw3_-uv3l137Hq7a-ydqbOi2u0xq2aV-uqzqfdTfCoqwql3EFV1t4bli9qEPatPMsLbNQz9cr7udZt76BtYvwPYa6M_amuexuABYu-O7LJFnHPFyHuo1ZWlyGJn4Pb9IyL2D7ZVo04bBgv-VVKELWVvWLm7btNjxeL6rsa8hfx3ZWfYhlXt0lUzAbLuSxSRdFeLvZVnX7uqo3PWSIq3ULrDBwxSaWcXOzOdjWcSX0JGm2aRbLVfeVw5ptmufHr46dtnzf_8iPQNexibDl0a_mDP6iu-P4q2B707ZF-i3kl2EF5B28UIflu0M8cWCsadO63cdKKME9QnmhmRF8AutuQ92E_Pw4adOEzaL4dry7Yz7ZTR4DCgxQcu-llSRA-W9A7h2D8JKMBKgwQM61EtaQADUC6JjnWhiahQYBtBxMZMaSAC0CqD2XzhiaUxwCqIw0CvxCAvQYIBdcQuyQADlDEKXWUllFI5EjuQKIjBnNaYHDkWThUjrNndc0RCxbONjnnXU0RCxdmJXKa0WLbo7lCxNaculpwcORhPFMamU1Lbw5kjCOc68FJz4zkjDWMWuFIroFSRjIaOG8oz2yQPLFSHCLFrRHFki6KMeFp8a2QLJFc8mUNrT0-4hVRS0s08S6_QnzCfQ9qoFm3jRtNV-nWyQeoUs7TewHZr7Jlh0ukorKSSk9LSrNPKvuO1zEVcp6LS2tmIO9aVl2wEg1UsaBEKVFvZmn27zDxYLVCCE8sYPP_14UHS5SmZSBStLJYhJuvlh0uEidB1wmPbET2XnWrvQAE9w45gQtJFQH7AeAtWdKEC2erwrGGPdiXoOKrzYIOrR6Ih9_lAd4IZAMESDFiGJWnaxWg1aDFlXGj0OXw-jOW0dD90dKGHsC3ULbHck4JoqccYZWOs64qNgCXE2La3viWj_BBrTjsfGHCToHPW8sy5isg5He0-K6ZxkT8tZzYkPh9hR0T9BslXY0-N5sTJNaodVImjFlCrjC08p_j4tNdFZwNSq1YUofZrkbIcZajfYWQ5VHPS6WJEYJSWOjTxJshjSQfrQxpbcXG59BFVAH03NlfsJ9MBwQu0pPB-Y-mKg9zeyeDqwWSWv5yKQWGM0ChiSaputxseQTThLT46xk-LD3mFGSOMqeg8MNwnthxmkCKO_D4Iw54suMc_EfVkuOS-JIfnanxLS09mqk3pDYzKYdcWLrYZGapKTxI61V2MQmtRgpBxTGrZRjuVXYuAZNfGRdlti0Bmp6ZNtTmMsAlvpu6pQVZjArFIecHMkFFhDMjKYYG-CZpr7k5ScuhqdAxWAsHmk00kik92PlhUK4kN2_ZyNhUWuto4ksd6rww9EmHYysI21Gxgbp9FihpZCElo5rYqM-Z97wfA0igDjqnIm2T4BzO3IgUcigI0GCjy3ISLOToMCJfwadeB5WRNJw4pvzPqsxKpQaO-RILJSlEzRYcapwfPiti7DGjS3L2P_AVhJrRq-UsbcB3nNaPf4Nm5o08ZVybyM2omsQrcQ_ek6xO5zGSpj_7K4vcHdWV0XxcX__4fOn_ef28UmF2eEYxTqGOq2zdXfEYX_z-fTHKrRNMn34YcUPZx26i_vTGcMrzqc13gwtefVou_25jaJIt_uHfNhNkmUs2lDPwj2QkSSHgyjJ4wMoO1iUZm28Da_-h91PXNvtz46U8CVW5dsSHFFmocPb7f4BQCsIgA
The text was updated successfully, but these errors were encountered: