I try on Linux and It seems that you are right.
For information I use the package biogo/hts and the "problem" happens when
I use the function NewChunkReader who takes file position and retrieve data
from the big file (bgzipped).
Thank you for your answer.
Le mardi 21 janvier 2020 14:40:33 UTC+
Could it be that the files from disk are "hot" in cache on the second run?
Try emptying the cache before the second run. Linux:
sync; echo 3 > /proc/sys/vm/drop_caches
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