CramComplianceTest: four tests from htslib fail due to SAMRecord mismatch

[jmthibault79]

Subject of the issue

#1185 adds 4 test cases from htslib which only pass under Partial Verification: ce#1000, xx#repeated, xx#tlen, and xx#tlen2. Under Full Verification these fail with errors from SAMRecord equality comparisons which are not apparent from their default toString() representations:

java.lang.AssertionError: expected [x3 2/2 5b aligned to xx:7-11.] but found [x3 2/2 5b aligned to xx:7-11.]
Expected :x3 2/2 5b aligned to xx:7-11.
Actual   :x3 2/2 5b aligned to xx:7-11.

Investigate these issues and move to the Full Verification test.

Your environment

• version of htsjdk: PR Add 4 CRAM compliance tests from htslib #1185
  (942da36)
• version of java: Java 1.8.0_171 / IntelliJ CE 2018.1.6
• which OS: Mac OS X High Sierra 10.13.6