Yf fix test removed deprecated methods relating to nm

[yfarjoun]

Description

Bug in SequenceUtil.calculateMdAndNmTags() whereby bases with different case (upper/lower) in reference or read are considered different despite the sam-spec saying that regarding SEQ: "No assumptions can be made on the letter cases." This has caused validatino problems for files that had their NM values set via SequenceUtil.calculateMdAndNmTags() (which takes case into account) and validated via SequenceUtil.calculateSamNmTag() (which, correctly, ignores case)

This PR fixes calculateMdAndNmTags by the same mechanism as used by calculateSamNmTag, adds a test to both functions (also testing MD at the same time) and gives variables in calculateMdAndNmTags more meaningful names.

Also, while I'm there I removed several deprecated functions that are not used.

I would like to nominate @jacarey for review as he seems to be the original author of calculateSamNmTag.

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)

[coveralls]

Coverage increased (+0.2%) to 69.264% when pulling 1c5354e on yf_fix_test_removed_deprecated_methods_relating_to_NM into 88b6719 on master.

[jacarey]

May as well update the javadoc while we are in here.

[jacarey]

👍

[yfarjoun]

waiting for tests to pass, then merging.

[coveralls]

Coverage increased (+0.2%) to 69.258% when pulling 4f1ca66 on yf_fix_test_removed_deprecated_methods_relating_to_NM into 88b6719 on master.