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I had to turn off multithreaded GAM read because this would break on Mac:
vg construct -r test/1mb1kgp/z.fa -v test/1mb1kgp/z.vcf.gz > z.vg
vg sim -n 10000 -s 23 -a -x z.vg > sim.gam
# This fails
vg stats -a sim.gam
# This works
vg view -aj sim.gam | wc -l
Especially with --threads 1
to vg stats
, I would get a signal 11 inside the wrapper code that makes a C++ input stream an hFILE
implementation that htslib can read, if I enabled multithreading on the BGZF.
I probably need to make a small test C program or a test case in libvgio
to make sure bgzf_mt
isn't somehow broken on Mac, and gradually add more stuff to it until I can figure out what is going on.
I turned off multithreading in libvgio commit cb4a54c.
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