Let me start with general comments:

Amusingly, it currently says that the file sizes are off by one: it sees one fewer bytes than Files.size() reports.

This is not true. This error comes from the way you loop and compute total size:

long total = 0;
int readCalls = 0;
for (int read = 1; read > 0; ) {
  readCalls ++;
  read = chan.read(buf);
  buf.flip();
  total += read; // On the last call you read -1 and sum it to total size, thus the mismatch
}

In general the for loop seems a bit strange to me, I would have used something like (not tested):

while (chan.read(buf) > 0) {
  readCalls++;
  total += buf.position();
  buf.flip();
}
readCalls++; // We must count the last call

This is also noticeably slower than gsutil (perhaps because it's single-threaded?).

What does this mean? Is it slower at reading the size metadata or at downloading the file? Can you share some numbers?

Amusingly, it currently says that the file sizes are off by one: it sees one fewer bytes than Files.size() reports.
This is not true. This error comes from the way you loop and compute total size:

Thank you! Indeed it's obvious now.

This is also noticeably slower than gsutil (perhaps because it's single-threaded?).
What does this mean? Is it slower at reading the size metadata or at downloading the file? Can you share some numbers?

Downloading the file. Here's what I see:

$ time gsutil cp gs://<redacted>/dbsnp_138.b37.256m.vcf /tmp/
Copying gs://<redacted>/dbsnp_138.b37.256m.vcf...
Downloading file:///tmp/dbsnp_138.b37.256m.vcf:                  214.89 MiB/214.89 MiB    
Downloading file:///tmp/dbsnp_138.b37.256m.vcf:                  214.89 MiB/214.89 MiB    
Downloading file:///tmp/dbsnp_138.b37.256m.vcf:                  214.89 MiB/214.89 MiB    
Downloading file:///tmp/dbsnp_138.b37.256m.vcf:                  214.89 MiB/214.89 MiB    

real    0m11.984s
user    0m7.618s
sys 0m4.513s
$ target/appassembler/bin/CountBytes gs://<redacted>dbsnp_138.b37.256m.vcf
gs://<redacted>/dbsnp_138.b37.256m.vcf: 901305932 bytes.
Reading the whole file...
Read all 901305931 bytes in 42s. (19 calls to chan.read)

We can see that gsutil takes 1/4th of the time. The way it prints it suggests that it did 4 parallel downloads (each of 1/4th the size).

Are we OK to merge?

@jean-philippe-martin just merged. As usual: thanks!

You are welcome!