Clean up Iterators / Iterables

[mattsooknah]

1. See the comment on SecondaryOrSupplementarySkippingIterator - it combines a peekable iterator with an implicit filter, but it would be cleaner if these were implemented separately and then composed.
2. Should we get rid of, or rename, NotPrimarySkippingIterator (currently unused)? The problem is that it only filters out secondary (but not supplementary) alignments, but someone new to the code might well assume that "not primary" means neither secondary not supplementary.
3. Where possible, we should make Iterators also implement Iterable so that for-each syntax can be used.

[lbergelson]

That's a crazily specific class to begin with. Definitely agree that it should be a composite of filtering iterator wrapped around a peeking iterator or something like that.

[nh13]

For (2) the intention is that it is either primary or secondary (see the Multi-mapping section in the SAM spec). Supplementary is something different.