Upgrade to htsjdk 3.0.0.

[cmnbroad]

The latest release of htsjdk changes the Allele class into an interface, and replaces it with a concrete implementation class SimpleAllele that has a different hashCode and Comparable implementation than before. One existing GenotypeConcordance test fails with the new implementation, fixed in this PR.

[gbggrant]

retest this please

[lbergelson]

@gbggrant We'd love to get this merged soon if someone could take a look at it.

[cmnbroad]

@gbggrant @kbergin I'm not sure who is responsible for picard-private these days, but the htsjdk update in this commit will likely result in the need for some (probably minor) source updates in picard-private. Is there someone else I should ping to give a heads up ?

[kbergin]

Thank you for letting us know @cmnbroad. I've made a ticket for pipelines team to address this in picard-private.