When creating a CRAM file, the SAM header from the input is propagated to the output, but I don't think there is any checking to validate that the reference being used matches the sequence dictionary in the header. At a minimum we should issue a warning when this happens.
When creating a CRAM file, the SAM header from the input is propagated to the output, but I don't think there is any checking to validate that the reference being used matches the sequence dictionary in the header. At a minimum we should issue a warning when this happens.
Somewhat related to https://github.com/samtools/htsjdk/issues/506.