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GMOD / JBrowseR

R interface to the JBrowse 2 Linear Genome View.
https://gmod.github.io/JBrowseR/
Apache License 2.0
35 stars 3 forks source link

fetchSizeLimit as a track_alignments function argument ? #23

Open PBMCHUGA opened 1 year ago

PBMCHUGA commented 1 year ago

Hi, Would it be possible to set up a "fetchSizeLimit": 1000 from R ? I tried to modify get_aligment_adapter function

... stringr::str_glue( '"adapter": {{ ', '"type": "BamAdapter", ', '"bamLocation": {{ ', '"uri": "{track_data}" ', "}}, ", '"index": {{ "location": {{ "uri": "{index}" }} }} ', ', "fetchSizeLimit" : 1000}}')) ...

without success, i might do something wrong...

Thanks a lot for your advice,

cmdcolin commented 1 year ago

were you seeing issues with fetchSizeLimit being hit? i anticipate releasing a new version where fetchSizeLimits were removed (this version of jbrowse https://jbrowse.org/jb2/blog/2023/06/08/v2.6.1-release/ removed these limits, but we have to release a new version of JBrowseR to CRAN)

PBMCHUGA commented 1 year ago

I may have not understood the parameter purpose. I wanted do decrease this limit to prevent web Browser to crash as my users have limited computing resources. So v2.6.1 will loose this “security” option ?

cmdcolin commented 1 year ago

can you describe the issue you are seeing that leads you to want to toggle this option? what are the characteristics of e.g. your bam file (deep sequencing, viewing it on large regions or small ones, etc)?

PBMCHUGA commented 1 year ago

Hi, It is limited to SNP or small indels (100X). So I want to prevent the user to load too much data at the same time, as it is not usefull and bring the computer to crash as RAM is limited.