CRAM 2.1

The CRAM specification has been updated to version 2.1 to allow for "end of file" marker. The change is expected to be compatible with existing tools.

Please see the specification for more details:
https://github.com/enasequence/cramtools/blob/master/CRAMFIleFormat2.1.pdf?raw=true.

The java implementation has been updated accordingly: https://github.com/enasequence/cramtools.

A freshly build jar file can be downloaded here:https://github.com/enasequence/cramtools/blob/master/cramtools-2.1.jar?raw=true.

Please note that for files with pre-2.1 versions there may be a warning about missing EOF marker. For files with version 2.1 or later a missing EOF marker should cause an error. Please report any issues on github issue tracker (https://github.com/enasequence/cramtools/issues?state=open) or to cram-dev@ebi.ac.uk mailing list.