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GMOD / cram-js

Read CRAM v3 and v2 in node or in the browser
MIT License
18 stars 9 forks source link

Not loading cram #135

Open taniagmangolini opened 3 months ago

taniagmangolini commented 3 months ago

Recently I have opened an issue on IGV repository: https://github.com/igvteam/igv.js/issues/1805 about a problem loading cram files. Initially, the problem was on the IGV tool side because there was a harded-coded limit related to the fetch size limit. They removed the limit, but now the cram file does not load. IGV developers recommended openning an issue here to report the problem. It seems that cram-js cannot load deep coverage cram files. I can send you the files I am trying to load, if necessary.

cmdcolin commented 3 months ago

yes if you can send the cram files and reference genome fasta that would be great, you can send to colin.diesh@gmail.com

If there are any error messages that go with it let me know as well. Sometimes there are just memory and performance challenges with e.g. the deep coverage filesbut we try to handle as best we can :)

taniagmangolini commented 3 months ago

The IGV tries to load and after some time it shows the following error:

error
cmdcolin commented 3 months ago

thanks for the email. i found it loaded in the jbrowse 2, though it did have high memory consumption (which can put a page on the verge of the ah nao! type errors). i would have to do some memory profiling to see if there are any areas of memory usage that could be improved