2.7.0

Small release with bug fixes and new functions. CRAM users probably want to upgrade due a change which will make use of CRAM indexes in some cases they were not being used before.

There are minor incompatible API changes in this update. Some old deprecated code was removed. There are some new deprecations where API improvements have made old code unnecessary. The upgrade path should be clear for anyone making use of newly deprecated code.

add tag aware merge samdictionary #689
fixed an issue with NM case sensitivity #728
0808588 Add a mergeDictionary utility to SAMSequenceDictionary to be used by picard in MergeBamAlignment
6f0512b Fix for Issue 574: CRAM index (#716)
Add option to deep copy attributes in ReverseComplement #717
b497630 preventing non-deterministic test failure in RelativeIso8601DateTest #578 (#710)
7ab2531 deleting SAMFileReader and SAMTruncatedFileReader (#699)
88b6719 IndexingVariantContextWriter cleanup (#706)
224cfc1 adding Hamming Distance functions to StringUtil (#690)
b5fd3c0 fixed the text codec to enable empty strings TA:Z:"" as per latest hts-spec
fbba536 adding additional write method to Index, fixes #430 (#683)
0e6edc7 Added support for an empty NM tag in SA tag fields using '*' character (#693)
255e41a annotating deprecated methods with @Deprecated (#698)
7886768 Added a secondary constructor to IntervalList that takes a dict. (#703)
21d8865 Fix JexlMap and GenotypeJEXLContext NullPtrException (#668)
fb1ba06 Fix BEDCodec.canDecode() to handle block-compressed extensions (#704)