jigv settings for targeted deep sequencing about jigv HOT 4 CLOSED

Hi Wendy, I don't think jigv is the cause. It's been a while since I've looked at this code but I just went through it and don't see any subsampling in the JS or the nim.
I also don't see any mention about 1500 in the igv.js code (not sure if you mention that as an exact number or just approximate).

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Thanks, Brent! Yes, it's not because of jigv (1500 is just approx). I think it has to do with the default subsamling of reads in igv.js (e.g. igvteam/igv.js#249). I am wondering if there's a way to pass some parameters to igv.js to turn off subsampling or set samplingDepth to a higher number?

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ah. I understand now. There's not a good way to do this. That's the major limitation of the current jigv the I never fixed--it's hard to allow the user to specify simple javascript to do things like set sampleDepth.

If you want to modify jigv, you can use this diff:

diff --git a/track.nim b/track.nim
index 94b8296..e9242f7 100644
--- a/track.nim
+++ b/track.nim
@@ -136,6 +136,7 @@ proc `%`*(T:Track): JsonNode =
     fields["coverageTrackHeight"] = % 24
     fields["showSoftClips"] = % true
     fields["viewAsPairs"] = % true
+    fields["samplingDepth"] = % 2000
   return JsonNode(kind: JObject, fields: fields)
 
 proc `$`*(T:Track): string =

and re-build. I'll have a look at making this easier with user-specified javascript from the command-line, but I don't see a simple way right now.

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Great! That's exactly what I was looking for! I will give it a try, thank you so much!

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