Merge pull request #22 from jkbonfield/master

CRAM specification
changed file cram specs file name
Make images non-executable
Build CRAMv2.1.pdf; add git version info and PDF bookmarks

Add repository URL and version information to the title page.
Use PDF bookmarks for the Table of Contents rather than using a page
or more for \tableofcontents.
Add CRAMv2.1.tex to README.md
Make READ1/READ2 flags correspond to the example

Hat tip @arlin, fixes #26.
Reinstate line breaks (trailing whitespace)
Update Padded SAM example to match Introduction's example

Fix r001's flags (hat tip @arlin, further fixes #26), r003's flags,
and the header VN.  Add r001/2's sequence mismatch as introduced
in 80bc68f7619da60eaa4f43a16878c4675e930570 and c8c0a443c0ebfea4deb8484fb77f9cb428e65476.
Tidy up footnotes

Swap MD and CT footnote texts so they are notes for the right items
(hat tip @lajoiem, fixes #25), use autoincrementing counter, place the
footnote marker *after* punctuation, disable hyperfootnotes as they
don't work from within tables.
Add links to mailing lists

(As suggested in passing in #28)
Add links to CSI specification and UCSC binning paper

Note that the 2^29-1 limitation is specific to the BAI format,
and add links to the generalised binning scheme in CSI.  Fixes #35.

Add footnote referencing Kent et al.  Fixes #29.
Fix typo in bin number for last 48kb bin