Germline allele should be listed for clonal consensus germlines

[Jason Vander Heiden]

The --cloned flag of CreateGermlines should add additional columns defining which allele was used for germline assignment for each clone, as it's currently possible for the V_CALL, D_CALL or J_CALL column for a sequence to be out of sync with the germline sequence in clonal groups with ambiguous allele calls.

[ssnn]

@javh and @lc664 See commit 5f2b374. It needs testing. I used a dummy file, it would be good if you could test it with your data.

[Jason Vander Heiden]

Looks okay to me.