Update the examples for recent bigrquery changes.

I recently made a change to the signature of the `query_exec` function in
`bigrquery` R package, which meant that all calls in the examples needed
updating. I've done that here, with a few notes/caveats:

 * The previous syntax *forced* you to use the `default_dataset` option, which
   isn't common in most BQ usage. In addition, it looks like all the examples
   have explicit `project:dataset.table` names, which is preferred anyway --
   so I've just dropped the extra arguments. If there's something more subtle
   going on that I didn't catch, let me know.

 * I also renamed `billing_project` to `project` everywhere -- this matches
   both the (updated) `bigrquery` docs and the BigQuery docs more closely.

 * I didn't update the `.md` files -- I did load up one and run it, but it
   looks like there were other changes unrelated to what I was up to that I
   was also picking up. I kept the output, and am happy to include it -- but I
   suspect it makes more sense to do them all at once.

 * My editor removed trailing whitespace in all the files I touched; I can
   revert those chunks if you're worried about `git blame` noise.
Update table names in sql.

(1) moved annotation tables to their own dataset

(2) updated 1,000 genomes table to one that has the schema emitted by varstore
Merge pull request #1 from craigcitro/bigrquery-update

Update Rmd files for the newest bigrquery updates.
Merge branch 'master' of github.com:deflaux/bigquery-examples
Update top level field name for calls.
Update literate programming story for new schema.

Also trying out the recent updates to knitr.
Removed pandoc header since it is getting displayed on github.
Removed pandoc header since it is getting displayed on github.
More SQL updates for the new schema.
More SQL updates per schema changes.
Get rid of trailing semi-colon in SQL.

Its not needed for BigQuery.
Update vcfstats story per schema changes.

Note that the queries that check whether any alleles correspond to the alternate_bases have become less efficient in this new schema.
Bug fix to allow query to run on entire dataset.
Re-render markdown for sample information data story.

Also tweaked a query to put an ORDER BY on the results.
Updated exploring-the-variant-data story per schema changes.

Note that QUAL is not in the table, so that query and plot is echo-ed but not evaluated for now.
Re-render markdown for understanding-alternate-alleles story.

Filter, id, and qual are currently missing from the schema; to be restored soon.

Also updated some of the related SQL to enforce an order so that the order of results do not change with each run.
Re-render markdown for reproducing-allelic-frequency story.

Also more fixes for the related SQL.
Re-render markdown for reproducing-hardy-weinberg-equilibrium story.

Also updated related SQL.
Re-render markdown for annotations-joins data story.

Also modified SQL with fixes and ORDER BY to maintain ordering across runs.
Updated non-data story queries.

There are a bunch of queries not used in any data stories.  They are all up to date now with the expection of any that reference quality, filter, or id fields (soon to be fixed).