Ensure sequences in analysis files are read in order.

For various reasons, we serialize sequences as:

0 -> foo
1 -> bar
...

Until now we were implicitly relying on the sequences being in order.
However external code may end up (due to bugs or otherwise) messing
with the ordering:

1 -> bar
0 -> foo
...

This change ensures that we don't get confused by that. Although
it's best if external code doesn't mess up the ordering, it's still
a good idea to be defensive about this.

Note that the sequences we serialize are short, so the extra sort
is not a performance concern.
Merge pull request #1346 from benjyw/sort_analysis_seqs

Ensure sequences in analysis files are read in order.