v1.2.0

This is a major release with some larger and many smaller changes. These notes emphasize the large changes. See commit history for details

• Code related to read parsing was completely rewritten to improve
  scalability to many threads. In short, the critical section is
  simpler and parses input reads in batches rather than one at a time.
  The improvement applies to all read formats.
• --reads-per-batch command line parameter added to specify the number
  of reads to read from input file at once
• TBB is now the default threading library. We consistently found TBB to give
  superior thread scaling. It is widely available and widely installed.
  That said, we are also preserving a "legacy" version of Bowtie that,
  like previous releases, does not use TBB. To compile Bowtie source
  in legacy mode use NO_TBB (TODO: insert actual flag here). To
  use legacy binaries, download the appropriate binary archive with
  "legacy" in the name.
• Bowtie now uses a queue-based lock rather
  than a spin or heavyweight lock. We find this gives superior thread
  scaling; we saw an order-of-magnitude throughput improvements at
  120 threads in one experiment, for example.
• Unnecessary thread synchronization removed
• Fixed colorspace parsing when primer base is present
• Fixed bugs related to --skip command line option