CRAM files with CSI index do not work

[Bjoernsen]

Hi,

I just ran into an issue with picard (3.4.0) . I have a CRAM file for a large genome. This is why it does not have a CRAI index, but a CSI index.

Unfortunately, it dies with the message CRAM index must be a BAI or CRAI stream (see https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/samtools/CRAMFileReader.java#L208)

Would it be possible to enable/allow CRAMs with CSI indices, too?

Thank you!