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Current bufferSize too small causing out of array bounds access error
When using vdb
with the newest MSA from GISAID I got illegal hardware instruction
error. After turning off the -O
flag during the compilation I identified that this was an Swift/ContiguousArrayBuffer.swift:575: Fatal error: Index out of range
error. Some quick bug hunt led me to the issue which occurred on this line:
https://github.com/variant-database/vdb/blob/ab73f5ee8f161ce998fa83825326db133e80ee59/vdbCreate.swift#L379
The bufferSize
is set to 50,000 (thus limiting the size of refBuffer
array), while the refBufferPosition
gets the value >57,000.
I fixed this in my local repo by changing the following line: https://github.com/variant-database/vdb/blob/ab73f5ee8f161ce998fa83825326db133e80ee59/vdbCreate.swift#L209
and setting the bufferSize
to 100,000.
Please let me know if you would like me to create a PR to fix this or whether this will be addressed in the future version.