Added a secondary constructor to IntervalList that takes a dict.

[tfenne]

Description

I find myself writing these three lines of code again and again and again to initialize an IntervalList since it requires a SAMFileHeader with a useful SAMSequenceDictionary and there's no way to create a header from a dictionary as an expression.

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 decreased (-0.01%) to 68.908% when pulling aad6c66 on tf_interval_list_from_sd into c3d5a88 on master.

[magicDGS]

Why a private method in IntervalList and not a public static in IntervalUtil. It may be useful not only for construct an interval list...

[tfenne]

@magicDGS I wanted the secondary constructor there. It's ~3 lines of simple code - I don't think it warrants extracting to a separate utility class.

[tfenne]

Also, yay, SRA tests are failing.

[droazen]

I've found myself sometimes having to go from SAMSequenceDictionary -> SAMFileHeader as well in other contexts -- perhaps you could add a new constructor to SAMFileHeader that takes a SAMSequenceDictionary, and call into that constructor from your new IntervalList constructor?

Also, add a simple unit test so we have test coverage on the new constructor(s).

[droazen]

Review complete, back to @tfenne

[tfenne]

Sure @droazen I can do that instead. I wasn't sure there were other uses for it. I'll swap that around then merge.

[coveralls]

Coverage decreased (-0.009%) to 68.984% when pulling 8fb8a7a on tf_interval_list_from_sd into 21d8865 on master.