Add 4 CRAM compliance tests from htslib

[jmthibault79]

Description

Looking at htslib CRAM round trip, I noticed 6 that were missing from CramComplianceTest. These 4 pass with Partial Verification but need further investigation. Two others c2#pad and md#1 are not included here because they do not pass Partial Verification.

CRAM files generated using samtools view

Checklist

• Code compiles correctly
• New tests covering changes and new functionality
• All tests passing
• Extended the README / documentation, if necessary
• Is not backward compatible (breaks binary or source compatibility)

[codecov-io]

Codecov Report

Merging #1185 into master will increase coverage by 0.009%.
The diff coverage is n/a.

@@              Coverage Diff               @@
##             master     #1185       +/-   ##
==============================================
+ Coverage      68.4%   68.409%   +0.009%     
- Complexity     8014      8030       +16     
==============================================
  Files           541       542        +1     
  Lines         32690     32769       +79     
  Branches       5529      5537        +8     
==============================================
+ Hits          22360     22417       +57     
- Misses         8126      8147       +21     
- Partials       2204      2205        +1

Impacted Files	Coverage Δ	Complexity Δ
...va/htsjdk/samtools/sra/SRAIndexedSequenceFile.java	62.162% <0%> (-2.703%)	6% <0%> (-1%)
.../htsjdk/samtools/util/ProgressLoggerInterface.java	0% <0%> (ø)	0% <0%> (?)
...rc/main/java/htsjdk/samtools/util/BinaryCodec.java	69.686% <0%> (+0.42%)	70% <0%> (+15%)	⬆️
src/main/java/htsjdk/samtools/SAMFileHeader.java	68.263% <0%> (+1.198%)	45% <0%> (+1%)	⬆️
...a/htsjdk/samtools/util/AbstractProgressLogger.java	45.902% <0%> (+5.517%)	7% <0%> (+1%)	⬆️

[cmnbroad]

@jmthibault79 Adding these test seems like a good idea. Since all of the existing tests in the partialVerification provider have corresponding tickets and a comment that explains the why they fail full verification, can we do that for the new ones ? Otherwise I feel like we're just adding more mystery. Especially if any of them fail 2.1 round tripping but succeed for 3.0. I'd lobby to not spend time on 2.1 round tripping failures, and just focus on 3.0.

As for c2#pad and md#1, I'd say the same thing (add them as tests, completely commented out since they fail even partial verification, and add a ticket the failure). Otherwise lets just delete them iif they're unreferenced.

[jmthibault79]

c2#pad passes fully with regenerated CRAM files, so I added it here.

Added links to issues to the 5 new failing tests, including md#1

[cmnbroad]

Thanks for adding those @jmthibault79. @lbergelson this LGTM for merging once the tests pass.

[lbergelson]

Looks good to me. 👍