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Due to (unfortunate) multiple ways to indicate that read is unmapped allowed by SAM format
specification, one may need this convenience shortcut. Checks both 'read unmapped' flag and
alignment reference index/start.
Our life would be so much easier if all sam files followed the specs. In reality,
sam files (including those generated by maq or bwa) miss headers altogether. When
reading such a SAM file, reference name is set, but since there is no sequence dictionary,
null is always returned for referenceIndex. Let's be paranoid here, and make sure that
we do not call the read "unmapped" when it has only reference name set with ref. index missing
or vice versa.