removed vector_wrapper in favor of the new vector_view class

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18434147]
fixed vector_view signature

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18434275]
- added string prefetchers, useful to perform local-memory caching of known string objects
- used the above to speedup the implementation of the high-level batched alignment API

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18434378]
better coverage of common string types, now including infixes

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18434427]
doc updates

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18434497]
doc updates

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18434499]
doc fix

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18434519]
more doc fixes

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18434524]
one more doc fix

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18434529]
simplified infix interfaces

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18434978]
forgotten file from previous checkin

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18435081]
- simplified fmmap code
- added a tutorial covering it

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18438665]
added assignment operator

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18438724]
fixed indentation

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18438751]
one more indentation fix

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18438774]
Fix compilation without OpenMP

Change-Id: I4fc939803c9e2aec70245bd345afd363195848b8

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18439223]
Add a simple parser for Variant Call Format 4.2

Adds a fairly limited parser for VCF 4.2. Does not parse or validate the
INFO fields or any of the header metadata.

Change-Id: I1a521b386886e5c09dfb1cd2540f8423566afe6d

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18439224]
Parse reference sequences in the SAM header

Change-Id: I69759daa6bba756f3df2761b07bb798bb92d98e5

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18439227]
typos

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18440278]
added specific bounds on memory consumption as requested by Johannes Koester

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18441812]