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Update to xg with graph PBWT support #229
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Was this fixed via your other PR? |
No, the other PR just loads paths into the vg graphs. This is pulling the new xg stuff from Japan. |
Gotcha. So this needs to be pulled in to get level with xg.
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The build failure suggests something wrong with the dynamic dependency or include path. |
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Yeah, it needs to copy the DYNAMIC headers to include. I should have finally put up the correct Makefile now. |
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The build works, but tests fail now because there are some very weird errors with find. I think I can figure out what's up. I need to get level with the new XG because I've got some modifications I need to apply there to change the way that path names are stored. I need to escape the block here: https://github.com/vgteam/xg/blob/master/src/xg.cpp#L1488 to ensure that it isn't causing contention when doing banded mapping. |
We should move DYNAMIC into vg rather than xg. We can download it to do an xg-only build, but otherwise let's put it in vg/deps. |
I'm getting segfaults in when vg tries to deallocate xg indexes. There may be other problems. |
Hmm. I was hoping I could do this without actually doing any work, but alas that I will move the dependency and figure out what is wrong with the -Adam On Fri, Mar 11, 2016 at 7:38 AM, Erik Garrison notifications@github.com
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I found the problem but don't understand it. Will post my stack trace in 15 I have an updated merge for xg as well, changing the build.
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Here we go:
I'm going to try to reproduce in xg itself. |
In xg's test directory:
Backtrace:
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It's not clear to me how it's getting a bad value (0x971) for child1_. It Is some kind of out-of-bounds access happening to corrupt things? On Fri, Mar 11, 2016 at 11:33 AM, Erik Garrison notifications@github.com
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Looks like the problem was soluble by forcing the dynamic wavelet tree to be allocated on the heap. |
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