Feat: Support for CRAM

[bcantarel]

For genomes with long chromosomes (like Marsupials) one cannot create BAM index files -- only CRAM with CSI files. For some commands like callpeak, these cram files can be converted into bed files, but for other commands like hmmratac, it seems like BAM is the only option.

[taoliu]

Good suggestion! We will implement it.

[taoliu]

It may take some time for us to add CRAM file support. But an easy solution is that we can try to enable BEDPE support for hmmratac. The BEDPE format file contains the genomic location information of each pair of reads in each row -- chromosome, start of the whole fragment, end of the whole fragment.

[bcantarel]

bedpe would be a great alternative!

[taoliu]

BEDPE support has been added #580

CRAM support will be added in the future. I need some planning on how to implement that. We didn't use any third-party libs to access BAM and BAI. Therefore I have to investigate how easy/hard to do the same for CRAM and whether we should use htslib.