fixed docs

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18728865]
fixed indexing type

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18732272]
fixed iterator interfaces

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18747416]
fixed operator++

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18747423]
removed const qualifiers

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18747427]
fixed calls to thrust::reduce() and strided iterator interfaces

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18749401]
- added lower/upper_bound_index
- fixed packed-stream assign() to deterministically take the modulo of input symbols

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18749948]
fixed Prefix and Suffix implementations, previously inverted

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18753654]
replaced sample size estimation by an actual computation

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18764915]
minor version bump

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18764921]
added -msse4.2 (considerably speeding up popcount)

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18766658]
fixed mgpu context creation to use the current device

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18766887]
added a scoped timer

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18767158]
added empty constructors

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18767198]
Allow picking a GPU architecture when running CMake

Adding -DGPU_ARCHITECTURE:STRING=sm_20 to the cmake command line will
now build nvbio for Fermi chips.

Default is sm_35 if no architecture is specified on the command line
(matches existing behavior).

Change-Id: I3da014214393016e0b12d37ec74d7fd0b70c2380

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18775458]
Add symbol constants to the DNA alphabets

The purpose of this is to allow comparing symbols across different
alphabets.

Change-Id: I5862c27a9784db8a4c750988892a42abcfe65d52

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18775459]
added a utility function to compare string-set suffixes

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18776822]
minor fixes

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18776828]
fixed comment

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18776831]
generalized ChunkLoader interface

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18777895]