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Nicola Soranzo
a850a47419
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).
