Adding further documentation for the alignment/CIGAR fields.
Reads metadata changes
Merge remote-tracking branch 'upstream/master' into metadata

necessary,
Tidy up the reference fields and comments
Fix doc link
Add optional id field to read alignment
Merge pull request #101 from cassiedoll/metadata

Read and Variant metadata changes
Merge pull request #100 from fnothaft/update-alignment-docs

Update alignment docs
Merge pull request #91 from cassiedoll/read.id

Add an id field to read alignment
clarify secondary/supplementary comments
more comment clarification
Nest several metadata fields under GAExperiment
Merge pull request #106 from dglazer/master

comment cleanup for loose ends from #100
Merge pull request #105 from cassiedoll/reference-cleanups

Tidy up the reference fields and comments
Merge pull request #107 from cassiedoll/metadata-experiment

Nest several metadata fields under GAExperiment
Remove readCount field

We haven't found this field to be too useful - and it will be non-trivial to implement, so I'm proposing removing it for v0.5