Fix `pysam.index()` calls which now use samtools 1.16 where
`samtools index input output` doesn't work any more if `output` is the path
of an already existing file, but `samtools index -o output input` works
fine.
Also:
- Pre-create the (empty) index file for mock test datasets as a unit test
reproducer of the above issue.
- Fix `test_cram` unit test that wasn't checking the return value of
`CRAM.set_index_file()`, which was in fact returning False because
`test-data/2.cram` was not sorted (updated now).
Nicola Soranzo
a850a47419