added an extended cuda::load_pointer accepting various load modifiers

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17915149]
updated to latest version of CUB (1.1.1)

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17915161]
added 32-bit keys / 64-bit values

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17916169]
added bit ranges

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17929701]
Started adding support for a text-blocking algorithm, which uses substantially less temporary storage for the matrix columns at the expense of not
allowing early exits. At the moment it is only supported for scoring, and only for Gotoh - will be extended soon to SW and ED.

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17974789]
preliminary version of the Smith-Waterman benchmark

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17974930]
re-established internal headers

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17974985]
several fixes and optimizations

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17977942]
added SSW comparison

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17980468]
fixed GCUPS calculation for variable length reads

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17984537]
- added support for TextBlockingTag alignment to SW and ED
- added Edit Distance benchmark
- added OpenMP compilation

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17986286]
fixed windows build

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17986369]
added conditional compilation of SSWLIB

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17986530]
documented the SSWLIB option

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17986542]
fixed paths

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17987505]
added cpu benchmarks

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17987694]
added OpenMP parallelization

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17987786]
resizing batches based on available memory

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17990468]
fixed previous checkin - resize MD and CIGAR buffers according to the batch size

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17992787]
started fixing stats

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 17997334]