Naive locking around build_requested for race condition (AUE-382)

Lock around build requested to avoid a scenario where builds that are requested
are not made.
cleanup
compensating for test names causes more problems than it solves, so skip it
+ clean up FASTQs in /tmp after bwamem finishes aligning

  - This is one of several immediate tasks that will help reclaim some
    of /tmp disk space that is being used with HiSeq X Ten data.  See
    BIO-1229 for more details.
+ simplify directory existence tests

  - right now there is no need to do additional checks delegated to a
    function.
+ remove accidental debug message used in testing
Fix case of Genome::SoftwareResult->get(id => 'xxxx')
Revert "Avoid using SR->get with args other than ID"

This reverts commit 01258c6d5376e4e0645654942419cfda908951e4.
It should no longer be necessary with the SR fix.
+ clean up FASTQs in /tmp -- take two

  - this is a second refactor attempt after a discussion in [github
    genome pull request 301][1] and further offline discussion with @tabbott.

  - this is midway refactor.  @tabbott's original lambda suggestion is
    probably the best way to do things long-term, but the desired
    refactor may get unwieldy and out of scope for immediate needs.

    The basic goal is to place the temporary file deletion logic in the
    base class, rather than in the subclass.  This is because the input
    files supplied to the aligners get generated in the base class.

  - The Bwamem test:

       lib/perl/Genome/InstrumentData/AlignmentResult/Bwamem.t

    as been reset back to the original version before this feature
    branch started.

[1]: https://github.com/genome/genome/pull/301/
Always define the boolean expression.
+ remove DB::single in AlignmentResult.t test

  - oops!
+ initial the default temp_input_files queue array in class definition

  - this is more idiomatic in Genome
+ place temp fastq files in queue closer to their creation

  - this is @tmooney's recommend idea.  See commentary at:

    https://github.com/indraniel/genome/commit/dddbd5920c8ccd49b2a261395807f71631097957
+ make the add items to the temporary queue public

  - this is @brummett's first suggestion in github's genome pull request
    301.

    https://github.com/genome/genome/pull/301
+ make an explicit debug message when the temp queue is empty
+ remove needless pass statement in test
+ refactor for loop in show_temporary_input_files_queue

  - this is @brummett's second suggestion in github's genome pull request 301

    https://github.com/genome/genome/pull/301
factor timing code out of _faster_get
remove trailing whitespace
Fix vaf calculations

For per-library vaf: Instead of dividing by the total depth (across all libraries) we need to
divide by the depth in just that one library.

For total vaf: Instead of summing up per-library vaf we need to
calculate the coverage and depth directly.