split more template instantiations into a separate cuda module

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18888936]
moved more template instantiations to a separate cuda module

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18889005]
split tag and aligner type definitions into a separate header

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18889046]
removed redundant include

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18889061]
removed spurious pragmas

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18889066]
removed useless includes

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18889082]
split more template instantiations to a separate module

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18889463]
removed include

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18889469]
removed more includes

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18889478]
implemented randomized hit selection with deterministic seeding based on the read names

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18891562]
checking for positive device counts

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18891566]
fixed read selection

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18891634]
reverted to correct per-read initialization of the seeds

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18891691]
removed superfluous include

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18892582]
removed unnecessary includes

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18895516]
split score.cu in multiple files to accelerate parallel builds

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18895542]
added a transform string set

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18899271]
fixed typenames, added comments

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18899279]
fixed doxygen comments

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18899281]
added transpose() method for HammingDistanceAligner

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18911039]