Call vcfreader.query in in parallel having strange unpredicted behaviors.

[wavefancy]

Hi Developers,

It seems vcfreader.query cannot be used in parallel. Below two ways will cause strange unpredicted behaviors. Any ideas on how to fix it in a parallel calling.

 vcfreader.query(chr, min_pos, max_pos).stream()
           .parallel()
           .forEach()

OR

.parallel()
.forEach(group->{
     vcfreader.query(chr, min_pos, max_pos).stream()
           .parallel()
           .forEach();
});

Best regards Wallace

[cmnbroad]

@wavefancy The iterators returned from VCF queries are backed by an underlying input stream, and generally maintain state that precludes being able to split them for use in parallel.