There are also some noteworthy changes here:
  - We do always respect the sort-order specified in the header
  - If the sort order is not mentioned in the header or no header
    exists we coordinate-sort the file.
  - We do not use indexing to determine if a file is coordinate sorted,
    because this does not work reliably with samtools/pysam > 1.X,
    since arbitrarily sorted files can be indexed now.

This also fixes advanced metadata setting (sort_order, bam_version and more),
which appears to have been broken. This probably went by unnoticed because of the catch-all
try-except-pass.
The downside to fixing this is that I had to (temporarilly, hopefully)
comment out the reference_names, reference_lengths, bam_header and readgroups attributes,
because they led to the following error:

```
galaxy.model.metadata DEBUG 2017-11-19 14:47:30,540 loading metadata from file for: HistoryDatasetAssociation 582
galaxy.jobs.runners.local ERROR 2017-11-19 14:47:30,636 Job wrapper finish method failed
Traceback (most recent call last):
  File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/local.py", line 130, in queue_job
    job_wrapper.finish(stdout, stderr, exit_code)
  File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/__init__.py", line 1357, in finish
    self.sa_session.flush()
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 157, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2019, in flush
    self._flush(objects)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2137, in _flush
    transaction.rollback(_capture_exception=True)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
    compat.reraise(exc_type, exc_value, exc_tb)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2101, in _flush
    flush_context.execute()
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 373, in execute
    rec.execute(self)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 532, in execute
    uow
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 170, in save_obj
    mapper, table, update)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 706, in _emit_update_statements
    execute(statement, multiparams)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 914, in execute
    return meth(self, multiparams, params)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement
    compiled_sql, distilled_params
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context
    context)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1341, in _handle_dbapi_exception
    exc_info
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=cause)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context
    context)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute
    cursor.execute(statement, parameters)
OperationalError: (psycopg2.OperationalError) index row size 7208 exceeds maximum 2712 for index "ix_history_dataset_association_metadata"
HINT:  Values larger than 1/3 of a buffer page cannot be indexed.
Consider a function index of an MD5 hash of the value, or use full text indexing.
 [SQL: 'UPDATE history_dataset_association SET update_time=%(update_time)s, blurb=%(blurb)s, peek=%(peek)s, metadata=%(_metadata)s WHERE history_dataset_association.id = %(history_dataset_association_id)s'] [parameters: {'_metadata': <psycopg2.extensions.Binary object at 0x119ed8990>, 'update_time': datetime.datetime(2017, 11, 19, 13, 47, 30, 598058), 'history_dataset_association_id': 582, 'blurb': '3.5 KB', 'peek': 'Binary bam alignments file'}]
```

Checking if pysam.index succeeds tests whether a file is coordinate sorted.
If pysam.index fails to index htslib writes to stderr and this fails set meta
tool. To prevent this we run this in a subprocess and discard stderr.

We only need samtools for the dataproviders, which shouldn't
be used by these tools.

…e', and 'force' is now required since we precreate the destination location.

…ts in the object store

Before pysam-developers/pysam#586 is merged and a new release is out
we create a symlink to the tbi file, which is required for creating TabixFile
instances. Since we want to cleanup the symlinks I turned `get_data_file` into a contextmanager.
Along the way I also changed many open()/close() calls to `with` statements.

This renames some variables to make it clearer what files they reflect.
Also adds a very basic test that this works as intended.