That's pretty weird. I'll look at it.
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Jim
You've probably got an invalid character (non-ascii) in one of your files, perhaps your session file. That shouldn't cause a memory issue however. I can't really help further without access to these files.
Are the files indexed with tabix?--
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How does this behavior compare with using the released version? The memory numbers you quote, BTW, are all very small and shouldn't cause any issues. How much memory are you allocating on startup (or, to rephrase, which distribution package are you using?)
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How does this behavior compare with using the released version? The memory numbers you quote, BTW, are all very small and shouldn't cause any issues. How much memory are you allocating on startup (or, to rephrase, which distribution package are you using?)
On 8/25/16 3:40 PM, Malcolm Cook wrote:
--It appears somewhat better.
I can now Control-F more times before IGV memory indicator begins to jump up and down and IGV becomes extremely sluggish. No errors or messages appear in console after initial session and track load.
Can I report more/better?
Thanks
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Those are both very small allocations, are you not running 64 bit
windows yet? You could try the packaged window app, which
bundles a 64 bit Java.
RE released version, it should handle and absolute path to a
fasta, or does that not work either?
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Yes, that is a valuable clue. The magic bin number "37450" was
causing problems in igv.js, I discovered it is not a real index
bin but a place to shove meta data. Could you share that tabix
file and its index (or is it one of the files in the session you
shared already)?
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Actually looking deeper this is strange. 37450 is beyond the range of allowed bins in a tabix indexed file. Its a little hard to see how you get this unless your contig length is > 2^29-1. Is that possible? If so it can't be indexed with tabix.
I'll need access to this file, then I can figure out what to
report to the htsjdk team.
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scaf_00001 27620446
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This happens even if I wait for the screen to repaint. I just happens faster if I hold the key down.
Jim,
Hi,
and quits.
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RE ctrl-f change, that's not by design, and are your sure you didn't have a few ctrl-Fs "in the queue" that were just catching up.
I would be interested in seeing where that concurent modifcation exception occured, it should be in the log.
On 8/26/16 9:23 PM, Cook, Malcolm wrote:
It is much much improved!
Is still managed to get a “Error loading features for interval: scaf_00005:8116714-8540335 java.util.ConcurrentModificationException” but this was after sitting on ctl-F for a few large scaffolds. And IGV recovered without freeze.
But, the behavior of contro-f now appears different. Instead of nav to next feature, it ppears to go forward to next currently not displayed feature. Is this by (re)design?
I sure can live with it, if so….
~m
On 8/26/16, 10:50 PM, "Jim Robinson" <igv-...@googlegroups.com on behalf of jrob...@broadinstitute.org> wrote:
Malcolm,
Can you try the snapshot build again? I made a change that improves it
greatly for me, but could you confirm? If you find it fixed it will
confirm I am on the right path, conversely I will look elsewhere.
Thanks
Jim
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OK. If you see the concurrent modification exception again
please open another ticket, and include the stack trace from the
log.
Jim