pass reference to htsfile for better cram support

[ASLeonard]

Although cram files are supported, I believe it only works if you have internet connection to download or a local cache of the reference genome. Without these you get decode errors like these

[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/<your chromosome hash>": Connection refused

Since a reference is always required for variant calling, it is safe to always pass the reference to htslib when opening sam/bam/cram files. I tested this for a few different files with fairly default parameters and it worked fine, but I didn't test all possible modes.

[zhengzhenxian]

@ASLeonard Billion thanks for the PR! Will test then.

[aquaskyline]

Merged into v1.0.6.