Improve implementation of CRAM support

[scwatts]

• the initial mechanism to support CRAM input has been to simply handle under the internal BAM filetype
• support for CRAM should be more explicit and be given an internal CRAM filetype instead
• more generally, inputs of a specific filetype should have some restrictions around file extension

[luan-n-nguyen]

See commits:

• f17c17c: Add CRAM/CRAM_REDUX/CRAI filetypes. Internally, these are treated the same as BAM/BAM_REDUX/BAI files
• 2f928e7: Update docs regarding starting from CRAM, and add warning regarding performance issues with reading small CRAMs

[scwatts]

I appreciate the start you've made on this, I'll make some adjustments to generalise the implementation further prior to the 2.2.0 release as planned